From 069908c8700142bb48a51a2036b8b233fd301a46 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 5 Jun 2023 10:11:30 -0400 Subject: [PATCH 001/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index ca205b58f..075f040ea 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.0": - version "1.0.31" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.31.tgz#82cb842ef6aa573b9323d524734678ce17dddffb" - integrity sha512-CzKDdeaSx0vq5CNnKD8HtfRR8VeFoRm28nJsgs3C7044babMgddqKS+JeWF48BZ0VkenoT3EaV85Xm8g8VUXiA== + version "1.0.33" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.33.tgz#f3d64b83f62800be2e0155bf5231fef52a68cdfa" + integrity sha512-3piF1ZUe7SeWAkabzICerFWHC/+L/1BGfTxpSYhKPu/5wqfSYXio16oaak+5elT8QogrboMEJ9vBc9bae5i+Ag== From a983e2a8b49602c94f6317b977d7b189981e433e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 5 Jun 2023 10:48:07 -0400 Subject: [PATCH 002/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 075f040ea..d70c6621c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.0": - version "1.0.33" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.33.tgz#f3d64b83f62800be2e0155bf5231fef52a68cdfa" - integrity sha512-3piF1ZUe7SeWAkabzICerFWHC/+L/1BGfTxpSYhKPu/5wqfSYXio16oaak+5elT8QogrboMEJ9vBc9bae5i+Ag== + version "1.0.34" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.34.tgz#218f9166e13391e35ab35c175fabe71584264703" + integrity sha512-4STV/1uVRhrvu+KJCDiLeWWhO4w8/6UwoyXtCbloImHPIx9X7eF0aHw+KbmV506VhtVgOSNM3RC5tyf/ENlUsw== From 81bc4627c4b4c7172ff5468a79a7679289c7ede2 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 7 Jun 2023 00:14:45 -0400 Subject: [PATCH 003/204] upgrade client code --- Site/yarn.lock | 6 +++--- build.xml | 8 +++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index d70c6621c..f453e36a4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.0": - version "1.0.34" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.34.tgz#218f9166e13391e35ab35c175fabe71584264703" - integrity sha512-4STV/1uVRhrvu+KJCDiLeWWhO4w8/6UwoyXtCbloImHPIx9X7eF0aHw+KbmV506VhtVgOSNM3RC5tyf/ENlUsw== + version "1.0.35" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.35.tgz#d522b959ce3892e259d94e5fa2fbe4581c84eba9" + integrity sha512-Rsd/OTaVL9XwozWa3biWmli1zgGNx+ZGUotPbcsdprdGqHM/+/t7jGUj4ju/+aUE+kL6EU1nNDnzj78Y+T/knA== diff --git a/build.xml b/build.xml index 80e251696..6d85c830c 100644 --- a/build.xml +++ b/build.xml @@ -116,9 +116,11 @@ - - - + + + + + From 262eed0316efaf1785a3e7561ac0d71559384bc5 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 9 Jun 2023 09:33:48 -0400 Subject: [PATCH 004/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f453e36a4..f8ec0786e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.0": - version "1.0.35" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.35.tgz#d522b959ce3892e259d94e5fa2fbe4581c84eba9" - integrity sha512-Rsd/OTaVL9XwozWa3biWmli1zgGNx+ZGUotPbcsdprdGqHM/+/t7jGUj4ju/+aUE+kL6EU1nNDnzj78Y+T/knA== + version "1.0.36" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.36.tgz#4ccd3712070f0b9d024ba3a87164e2c15fca0a4b" + integrity sha512-vj+RV161yhf7J2//3hnExAhmPho8Hl+FLOtIZT1vtLd63B0DoXmkAPhJmsB52a6hG3bIbPXGNVgGfRsW6jnk9g== From fe22ec08a29af1cbec04c151b2cac535ddc3824d Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 9 Jun 2023 12:37:47 -0400 Subject: [PATCH 005/204] Add automation for upgrading npm-managed web assets There are three components to this PR: 1. Change package.json to use the `latest` tag. This makes it so that upgrading to the latest production release does not change the package.json file, while "patch" versions would. (Note, this is not the same a semver-patch.) 2. Configure dependabot to create a pull request when it detects new versions of @veupathdb packages. It will only do so for versions that only change the lockfile. With 1 above, this effectively only allows upgrading to the `latest` tag version. 3. Add a workflow to automatically merge dependabot PRs for @veupathdb packages. --- .github/dependabot.yml | 16 +++++++++++ .github/workflows/auto-merge-dependabot.yml | 32 +++++++++++++++++++++ Site/package.json | 2 +- Site/yarn.lock | 2 +- 4 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/auto-merge-dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..76befdc23 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,16 @@ +# Configure dependabot to create a pull request when it finds a new version of +# @veupathdb npm packages. + +version: 2 +updates: + - package-ecosystem: "npm" + directory: "/Site" + schedule: + interval: "daily" + time: "23:00" + timezone: "America/New_York" + allow: + - dependency-name: "@veupathdb/*" + commit-message: + prefix: "npm" + versioning-strategy: "lockfile-only" diff --git a/.github/workflows/auto-merge-dependabot.yml b/.github/workflows/auto-merge-dependabot.yml new file mode 100644 index 000000000..6bbfe2873 --- /dev/null +++ b/.github/workflows/auto-merge-dependabot.yml @@ -0,0 +1,32 @@ +# Automatically merge dependabot PRs for @veupathdb packages + +name: Dependendabot auto-approve +on: pull_request_target + +permissions: + contents: write + pull-requests: write + +jobs: + dependabot: + runs-on: ubuntu-latest + if: ${{ github.actor == 'dependabot[bot]' }} + steps: + - name: Dependabot metadata + id: metadata + uses: dependabot/fetch-metadata@v1.5.1 + with: + github-token: "${{ secrets.GITHUB_TOKEN }}" + - name: Enable auto-merge for Dependabot PRs + if: > + ${{ + contains(steps.metadata.outputs.dependency-names, '@veupathdb') && + ( + steps.metadata.outputs.update-type == 'version-update:semver-patch' || + steps.metadata.outputs.update-type == 'version-update:semver-minor' + ) + }} + run: gh pr merge --auto --merge "$PR_URL" + env: + PR_URL: ${{github.event.pull_request.html_url}} + GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} diff --git a/Site/package.json b/Site/package.json index 6ef34e33c..3b169e36e 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "^1.0.0" + "@veupathdb/genomics-site": "latest" } } diff --git a/Site/yarn.lock b/Site/yarn.lock index f8ec0786e..04934c997 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@^1.0.0": +"@veupathdb/genomics-site@latest": version "1.0.36" resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.36.tgz#4ccd3712070f0b9d024ba3a87164e2c15fca0a4b" integrity sha512-vj+RV161yhf7J2//3hnExAhmPho8Hl+FLOtIZT1vtLd63B0DoXmkAPhJmsB52a6hG3bIbPXGNVgGfRsW6jnk9g== From 365577d75bb3daf767f2669e1bed71630d48d9c6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 10 Jun 2023 03:56:24 +0000 Subject: [PATCH 006/204] npm: bump @veupathdb/genomics-site from 1.0.36 to 1.0.37 in /Site Bumps @veupathdb/genomics-site from 1.0.36 to 1.0.37. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 04934c997..623c1114c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@latest": - version "1.0.36" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.36.tgz#4ccd3712070f0b9d024ba3a87164e2c15fca0a4b" - integrity sha512-vj+RV161yhf7J2//3hnExAhmPho8Hl+FLOtIZT1vtLd63B0DoXmkAPhJmsB52a6hG3bIbPXGNVgGfRsW6jnk9g== + version "1.0.37" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.37.tgz#e06e2eb42c440c1ba681ed979534427214878366" + integrity sha512-uI3ObA50rxJuz0XN/zBnS48J39zhk7VRRfGlyb9t9UmFTmONHBOLmhmvm/RSwDpV1gPf1HLls8m0ECaYWuke3A== From 7905c5376c42188a7e486cc2c909b77e4c102781 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 21 Jun 2023 03:56:25 +0000 Subject: [PATCH 007/204] npm: bump @veupathdb/genomics-site from 1.0.37 to 1.0.38 in /Site Bumps @veupathdb/genomics-site from 1.0.37 to 1.0.38. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 623c1114c..4ec7263b7 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@latest": - version "1.0.37" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.37.tgz#e06e2eb42c440c1ba681ed979534427214878366" - integrity sha512-uI3ObA50rxJuz0XN/zBnS48J39zhk7VRRfGlyb9t9UmFTmONHBOLmhmvm/RSwDpV1gPf1HLls8m0ECaYWuke3A== + version "1.0.38" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.38.tgz#603e08e2c597f34e9f1ee090c5534c8406cda2c7" + integrity sha512-TkTi0XSl2DNakMpIJiirxB4mp4P/PCklnvaVD/8BXYY0w8xq6tMuv/u7Wybi4Vh347Fr/MkYz6MPLuPQ+zQNhA== From ae8aa4f09a47f17a7ed1a05724661aecb05bf89b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 27 Jun 2023 03:56:25 +0000 Subject: [PATCH 008/204] npm: bump @veupathdb/genomics-site from 1.0.38 to 1.0.39 in /Site Bumps @veupathdb/genomics-site from 1.0.38 to 1.0.39. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4ec7263b7..9460f4a3d 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@latest": - version "1.0.38" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.38.tgz#603e08e2c597f34e9f1ee090c5534c8406cda2c7" - integrity sha512-TkTi0XSl2DNakMpIJiirxB4mp4P/PCklnvaVD/8BXYY0w8xq6tMuv/u7Wybi4Vh347Fr/MkYz6MPLuPQ+zQNhA== + version "1.0.39" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.39.tgz#869452e758c550ebd570bcd51a6456beb2efb5b9" + integrity sha512-9A/fZBLxYKDmUuVOAGu047W3HGVO6iw+hRxbRqcUsGkrLN3DPhaqvHluHRLRMGPB8kf8zKxvn2kCZj8+HS+qRA== From 3ab4ef6253d472698e3ab0142e9dbc285fb7fb70 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 28 Jun 2023 13:27:46 -0400 Subject: [PATCH 009/204] upgrade client code --- Site/package.json | 2 +- Site/yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Site/package.json b/Site/package.json index 3b169e36e..11c1ba7cb 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "latest" + "@veupathdb/genomics-site": "^1.0.40" } } diff --git a/Site/yarn.lock b/Site/yarn.lock index 9460f4a3d..d345182e5 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@latest": - version "1.0.39" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.39.tgz#869452e758c550ebd570bcd51a6456beb2efb5b9" - integrity sha512-9A/fZBLxYKDmUuVOAGu047W3HGVO6iw+hRxbRqcUsGkrLN3DPhaqvHluHRLRMGPB8kf8zKxvn2kCZj8+HS+qRA== +"@veupathdb/genomics-site@^1.0.40": + version "1.0.40" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.40.tgz#c3161f96d50a9064f37e044b1d3bcf8068edcf62" + integrity sha512-RvnqjZ2tR/ue/Hiq6YzSCZzMenLGaKr71kwTBQw3spHQD+iwo/yGTbiV/rP5Kvk+u7inra5sv4EkWWTqkFym2A== From 655e89d4e3b343d2f69a18764d89aba4a45a59e4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:15:47 +0000 Subject: [PATCH 010/204] npm: bump @veupathdb/genomics-site from 1.0.40 to 1.0.42 in /Site Bumps @veupathdb/genomics-site from 1.0.40 to 1.0.42. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index d345182e5..784a7ccfa 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.40" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.40.tgz#c3161f96d50a9064f37e044b1d3bcf8068edcf62" - integrity sha512-RvnqjZ2tR/ue/Hiq6YzSCZzMenLGaKr71kwTBQw3spHQD+iwo/yGTbiV/rP5Kvk+u7inra5sv4EkWWTqkFym2A== + version "1.0.42" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.42.tgz#e86512a4183b293c2fb5fd2d6b07476d5405b992" + integrity sha512-Zi1NhIU5g/Qpa5lUJEVKow0RpDqaMddzGvsxIEF1iJLVvhCTnVSGN8C1CCqbcOo8IavrAlgvo4y5UuvxJIV+Rw== From 75d76f63c21ce97cdb7277f594d31c166a633a96 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Wed, 5 Jul 2023 11:30:24 -0400 Subject: [PATCH 011/204] script and module to get submit to big-PI Predictor in Fungi -refs #51412 --- Site/cgi-bin/fungalGPI.pl | 15 +++++++ View/lib/perl/CgiApp/FungalGPI.pm | 66 +++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 Site/cgi-bin/fungalGPI.pl create mode 100644 View/lib/perl/CgiApp/FungalGPI.pm diff --git a/Site/cgi-bin/fungalGPI.pl b/Site/cgi-bin/fungalGPI.pl new file mode 100644 index 000000000..f0a21c933 --- /dev/null +++ b/Site/cgi-bin/fungalGPI.pl @@ -0,0 +1,15 @@ +#!/usr/bin/perl + +use strict; + +use lib "@targetDir@/lib/perl"; +$ENV{GUS_HOME} = '@targetDir@'; + + +use ApiCommonWebsite::View::CgiApp::FungalGPI; + +my $app = + ApiCommonWebsite::View::CgiApp::FungalGPI->new(); + +$app->go(); + diff --git a/View/lib/perl/CgiApp/FungalGPI.pm b/View/lib/perl/CgiApp/FungalGPI.pm new file mode 100644 index 000000000..5641087bd --- /dev/null +++ b/View/lib/perl/CgiApp/FungalGPI.pm @@ -0,0 +1,66 @@ +# returns Fungal GPI Modification Site Prediction and reports if running in cgi or Apache::Registry environment + +package ApiCommonWebsite::View::CgiApp::FungalGPI; +@ISA = qw( EbrcWebsiteCommon::View::CgiApp ); + +use strict; +use URI::Escape; +use LWP::UserAgent; +use HTTP::Request::Common qw(POST); +use EbrcWebsiteCommon::View::CgiApp; + +use Data::Dumper; + + +sub run { + + my ($self,$cgi) = @_; + + my $project_id = $cgi->param('project_id'); + my $LSet = $cgi->param('LSet'); + my $source_ID = $cgi->param('source_ID'); + my $id_type = 'protein'; + + my $qh = $self->getQueryHandle($cgi); + my $sql; + + if($id_type eq 'protein'){ + $sql = "SELECT sequence FROM apidbtuning.proteinsequence WHERE source_id = '" . $source_ID . "' AND project_id = '" . $project_id . "'"; + }else{ + die "cannot find the protein sequence from database based on entered source_ID and project_id" ; + } + + + my $sh = $qh->prepare($sql); + $sh->execute(); + my $seq = $sh->fetchrow_array(); + $sh->finish(); + + my $ua = LWP::UserAgent->new; + my $args = "CMD=Put&LSet=$LSet&Sequence=" . $seq; + my $req = new HTTP::Request POST => 'https://mendel.imp.ac.at/gpi/cgi-bin/gpi_pred_fungi.cgi'; + + $req->content_type('application/x-www-form-urlencoded'); + $req->content($args); + my $response = $ua->request($req); + + print $cgi->header("text/html"); + my $html = " + + + + "; + + print $html; + + + print $response -> {_content}; + + +} + + + +1; + + From 6faa814e6c7b710717c04f892718b587a03e0791 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 5 Jul 2023 12:07:22 -0400 Subject: [PATCH 012/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 784a7ccfa..6d6b7326e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.42" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.42.tgz#e86512a4183b293c2fb5fd2d6b07476d5405b992" - integrity sha512-Zi1NhIU5g/Qpa5lUJEVKow0RpDqaMddzGvsxIEF1iJLVvhCTnVSGN8C1CCqbcOo8IavrAlgvo4y5UuvxJIV+Rw== + version "1.0.43" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.43.tgz#0e36b128e9dfe3f1fd4849a9be9cc053a342ea28" + integrity sha512-Tnk8pfSx2xKTNeLVlU9j6U678XadLV52ydlYYS/9pKlU6Pz6Ic7EcUxzHihXHnF5GGGyPmmvjqPmhSCtWT4sTg== From c249180c9f514dd13847e5ef6e4aea8bcb8264cc Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Wed, 5 Jul 2023 12:13:28 -0400 Subject: [PATCH 013/204] until we release so qa can be tested --- .../roles/conifer/vars/ApiCommon/production/VectorBase.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml index be7b1d7c8..ee0763771 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml @@ -2,5 +2,5 @@ --- eda: # enable for feature and beta sites - enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.', 'q2.')) else 'false' }}" - + # enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.', 'q2.')) else 'false' }}" + enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.')) else 'false' }}" From fc0854eb7c2b6863748d00298880b448f11eed32 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 5 Jul 2023 23:08:53 -0400 Subject: [PATCH 014/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6d6b7326e..a50b20882 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.43" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.43.tgz#0e36b128e9dfe3f1fd4849a9be9cc053a342ea28" - integrity sha512-Tnk8pfSx2xKTNeLVlU9j6U678XadLV52ydlYYS/9pKlU6Pz6Ic7EcUxzHihXHnF5GGGyPmmvjqPmhSCtWT4sTg== + version "1.0.44" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.44.tgz#4d41147e8e48100330f5c835f5bb41d0f27217df" + integrity sha512-k63WtlWjnrNOxGAXmw7c75a/3+PQT027kyZA/n/B6r77kcbu+iQmyAFABUKFMnISMdouTg0G9R3Ec2S+V7x8+A== From 2978fe4066d6bd395f3f85c5d834105f726ff41f Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 6 Jul 2023 11:28:36 -0400 Subject: [PATCH 015/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a50b20882..6c2785aba 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.44" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.44.tgz#4d41147e8e48100330f5c835f5bb41d0f27217df" - integrity sha512-k63WtlWjnrNOxGAXmw7c75a/3+PQT027kyZA/n/B6r77kcbu+iQmyAFABUKFMnISMdouTg0G9R3Ec2S+V7x8+A== + version "1.0.45" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.45.tgz#716874ff653c239a588ecb17ff754c425d35e601" + integrity sha512-65AcrwJ8zrABZ61ziYnyZKJw5RKIZ00tokJsznEjL0FucxaAMBtSEfQKo+sLUjBOI9H4Fydj/7Vwfi2/Mpk29A== From 94b42ef97e3057d687eb3f3e98ce72f06d60cf33 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 7 Jul 2023 03:18:29 +0000 Subject: [PATCH 016/204] npm: bump @veupathdb/genomics-site from 1.0.45 to 1.0.46 in /Site Bumps @veupathdb/genomics-site from 1.0.45 to 1.0.46. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6c2785aba..abe65327b 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.45" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.45.tgz#716874ff653c239a588ecb17ff754c425d35e601" - integrity sha512-65AcrwJ8zrABZ61ziYnyZKJw5RKIZ00tokJsznEjL0FucxaAMBtSEfQKo+sLUjBOI9H4Fydj/7Vwfi2/Mpk29A== + version "1.0.46" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.46.tgz#4832e617f812355c9887b328453a8bb342450f30" + integrity sha512-HIPF1o9f65yW5wXD1qokLmI5TW77kAKy4SjLn1HHV87Zk8yU/2O0ehULZfhgtzB0piikmzId2rLzeIR39BalYQ== From 42692c74f2c718aaa1c18efbcc45b44793b03c43 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 7 Jul 2023 10:36:35 -0400 Subject: [PATCH 017/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index abe65327b..6b84595a2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.40": - version "1.0.46" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.46.tgz#4832e617f812355c9887b328453a8bb342450f30" - integrity sha512-HIPF1o9f65yW5wXD1qokLmI5TW77kAKy4SjLn1HHV87Zk8yU/2O0ehULZfhgtzB0piikmzId2rLzeIR39BalYQ== + version "1.0.47" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.47.tgz#e3194e3b290b96e6aa93d8a95a1ed7b585fb0fa3" + integrity sha512-RRfGsybzyQMTTgytVO75VXTnW08a2x/urQt2dka8SOl2qOEXkT2IuyfpIgegdyC3uxlOuFaxk07ZWek+DMGEtw== From 9259c3d123b36bee4375676279abcaedbd3c68c0 Mon Sep 17 00:00:00 2001 From: Cristina Aurrecoechea Date: Sun, 9 Jul 2023 10:41:09 -0400 Subject: [PATCH 018/204] v1.0.48 banner vectorbase redmine 51701 --- Site/package.json | 2 +- Site/yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Site/package.json b/Site/package.json index 11c1ba7cb..0e157efa4 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "^1.0.40" + "@veupathdb/genomics-site": "^1.0.48" } } diff --git a/Site/yarn.lock b/Site/yarn.lock index 6b84595a2..eb637857d 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@^1.0.40": - version "1.0.47" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.47.tgz#e3194e3b290b96e6aa93d8a95a1ed7b585fb0fa3" - integrity sha512-RRfGsybzyQMTTgytVO75VXTnW08a2x/urQt2dka8SOl2qOEXkT2IuyfpIgegdyC3uxlOuFaxk07ZWek+DMGEtw== +"@veupathdb/genomics-site@^1.0.48": + version "1.0.48" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.48.tgz#8d3a87289b04cfce0c421f49af268637132123e9" + integrity sha512-LHKpeKNvP7ojW/l9DWLc/kD/fos10wqadBoRWiJnTe2r8buMFJ7pTOxn/HR9HZs+PcGufcKpHzZXuRJMXpxc0g== From 84da76f11ee934c136c094c19bb59f83734fa73b Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 11 Jul 2023 14:35:23 -0400 Subject: [PATCH 019/204] client: banners for VB, clinepi access self editing UI --- Site/package.json | 2 +- Site/yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Site/package.json b/Site/package.json index 0e157efa4..4c9119477 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "^1.0.48" + "@veupathdb/genomics-site": "^1.0.49" } } diff --git a/Site/yarn.lock b/Site/yarn.lock index eb637857d..462c41399 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@^1.0.48": - version "1.0.48" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.48.tgz#8d3a87289b04cfce0c421f49af268637132123e9" - integrity sha512-LHKpeKNvP7ojW/l9DWLc/kD/fos10wqadBoRWiJnTe2r8buMFJ7pTOxn/HR9HZs+PcGufcKpHzZXuRJMXpxc0g== +"@veupathdb/genomics-site@^1.0.49": + version "1.0.49" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.49.tgz#19c43ad3dada3eae7ada0fd9e2ee524e101187de" + integrity sha512-CbYxBEJH34GH3N2ppXxuF4x2226fhZY+pAyKmfsZ9NjGZHLHCIIXL0POu9EbaDW5ANbOIpgWfxhbg79azVT85Q== From 97f8049bba4f6379f2e5439614271b9eca4a56fa Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 11 Jul 2023 17:08:42 -0400 Subject: [PATCH 020/204] q2 eda enabled --- .../roles/conifer/vars/ApiCommon/production/VectorBase.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml index ee0763771..269fe13b0 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml @@ -2,5 +2,5 @@ --- eda: # enable for feature and beta sites - # enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.', 'q2.')) else 'false' }}" - enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.')) else 'false' }}" + enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.', 'q2.')) else 'false' }}" + #enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.')) else 'false' }}" From cdf7b30bdad90eae8892be66365c3c88f5089066 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 18 Jul 2023 15:31:16 -0400 Subject: [PATCH 021/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 462c41399..4d32334c5 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.49" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.49.tgz#19c43ad3dada3eae7ada0fd9e2ee524e101187de" - integrity sha512-CbYxBEJH34GH3N2ppXxuF4x2226fhZY+pAyKmfsZ9NjGZHLHCIIXL0POu9EbaDW5ANbOIpgWfxhbg79azVT85Q== + version "1.0.51" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.51.tgz#dc3a5713092727ffbaadfb07284e42dbf266a22b" + integrity sha512-2bl11W0qDztd01LAPTH1IsHDYWJ/AgFmOO0unuIiWF2KK8E2ctn/eA3PrAc9DedMKpoYSETbP9+6aGrkl13PQA== From 2619e954bc34fc5d742bc277b54a4069e3e20d8d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 22 Jul 2023 03:55:29 +0000 Subject: [PATCH 022/204] npm: bump @veupathdb/genomics-site from 1.0.51 to 1.0.52 in /Site Bumps @veupathdb/genomics-site from 1.0.51 to 1.0.52. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4d32334c5..b2207baae 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.51" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.51.tgz#dc3a5713092727ffbaadfb07284e42dbf266a22b" - integrity sha512-2bl11W0qDztd01LAPTH1IsHDYWJ/AgFmOO0unuIiWF2KK8E2ctn/eA3PrAc9DedMKpoYSETbP9+6aGrkl13PQA== + version "1.0.52" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.52.tgz#3868262d33fb8f7bbb28903f9d4cec33c9d39f5a" + integrity sha512-yNUW6tclL1FgbqanEpDfn6dGOGMfFpRdDRy47b9lZDlUm2Sy3vPH6tFZT2igqftUWJmgqx3EFLoPeemkPS8Pfw== From 84ab14f7da1b8de2c6117dea66986e4ae5e5b0f8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 26 Jul 2023 03:04:13 +0000 Subject: [PATCH 023/204] npm: bump @veupathdb/genomics-site from 1.0.52 to 1.0.53 in /Site Bumps @veupathdb/genomics-site from 1.0.52 to 1.0.53. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index b2207baae..55b8ad54d 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.52" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.52.tgz#3868262d33fb8f7bbb28903f9d4cec33c9d39f5a" - integrity sha512-yNUW6tclL1FgbqanEpDfn6dGOGMfFpRdDRy47b9lZDlUm2Sy3vPH6tFZT2igqftUWJmgqx3EFLoPeemkPS8Pfw== + version "1.0.53" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.53.tgz#11aab8e1fedddcf66cc118650a57104b6c9f4fe2" + integrity sha512-nY8/5MCJVa/gUzCub+QjJzXpP0/WhhZVHBkxTXZfIcoCWBI1L8CcleuGiVp0eCnbI1zuRy9dK8DzMeosy6uDxg== From e7e43b2efefa5fb0b378c10d6587b482445aed0c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 28 Jul 2023 03:51:25 +0000 Subject: [PATCH 024/204] npm: bump @veupathdb/genomics-site from 1.0.53 to 1.0.54 in /Site Bumps @veupathdb/genomics-site from 1.0.53 to 1.0.54. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 55b8ad54d..b95c6f18f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.53" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.53.tgz#11aab8e1fedddcf66cc118650a57104b6c9f4fe2" - integrity sha512-nY8/5MCJVa/gUzCub+QjJzXpP0/WhhZVHBkxTXZfIcoCWBI1L8CcleuGiVp0eCnbI1zuRy9dK8DzMeosy6uDxg== + version "1.0.54" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.54.tgz#c423fbd71fc1883a020445ad60633d3ca9b6d90b" + integrity sha512-nHMLPa1po2ImNTATTKaOvFOs6KTZf+NpjT+MBrXUeJnqL98rf659VBLOHNLwWsNH79YXSSd0bsdkahLxMCNb4w== From 298b3083225a6b26e343a4a37cd0d829f1314971 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 4 Aug 2023 03:42:42 +0000 Subject: [PATCH 025/204] npm: bump @veupathdb/genomics-site from 1.0.54 to 1.0.55 in /Site Bumps @veupathdb/genomics-site from 1.0.54 to 1.0.55. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index b95c6f18f..b0b00f3e2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.54" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.54.tgz#c423fbd71fc1883a020445ad60633d3ca9b6d90b" - integrity sha512-nHMLPa1po2ImNTATTKaOvFOs6KTZf+NpjT+MBrXUeJnqL98rf659VBLOHNLwWsNH79YXSSd0bsdkahLxMCNb4w== + version "1.0.55" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.55.tgz#59591c2f7686e0b1c002ca188ce2aa0236275e9e" + integrity sha512-kEmg8vjCP49bp0NMizkGatC9dYZnz0F6e4DYDuaA6r6XIiynCmUV+2MlcUsJP7Ou+IOtwbUbIcdhyw5GUFsGpQ== From f9ce3233cd3f16cb963040400e74e5dffe7547ca Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 8 Aug 2023 03:25:27 +0000 Subject: [PATCH 026/204] npm: bump @veupathdb/genomics-site from 1.0.55 to 1.0.56 in /Site Bumps @veupathdb/genomics-site from 1.0.55 to 1.0.56. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index b0b00f3e2..8b2a38a66 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.55" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.55.tgz#59591c2f7686e0b1c002ca188ce2aa0236275e9e" - integrity sha512-kEmg8vjCP49bp0NMizkGatC9dYZnz0F6e4DYDuaA6r6XIiynCmUV+2MlcUsJP7Ou+IOtwbUbIcdhyw5GUFsGpQ== + version "1.0.56" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.56.tgz#6fe41d45175c01c5f50581b614c38a772c55a4e9" + integrity sha512-zwwkSio/AYTOXa3hWmbgT/3mvlswbbxHbAvQO9Tl19kl+lmwKsCylelUW1einXZAWp8nAzlHr7PqQ3HP05vgUA== From c0a45c55e3b5454f3131945ddbd28c2ced3a9e78 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 10 Aug 2023 09:34:39 -0400 Subject: [PATCH 027/204] widen graph -refs #51998 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 203b8b79c..8829cf34c 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1766,6 +1766,13 @@ RADJUST 1; +# fungi - mory70-15_Ruiz_Mory_2020_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_9d559d0fae; + +sub getPlotWidth { return 1000; } + +1; + #-------------------------------------------------------------------------------- # TEMPLATE_ANCHOR rnaSeqGraph @@ -1788,3 +1795,4 @@ package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_b1ac1e329c; sub getPlotWidth { return 800; } 1; + From e59c2f2a24c3dbed2af02050e070de33ceff4e11 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 11 Aug 2023 03:39:26 +0000 Subject: [PATCH 028/204] npm: bump @veupathdb/genomics-site from 1.0.56 to 1.0.58 in /Site Bumps @veupathdb/genomics-site from 1.0.56 to 1.0.58. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 8b2a38a66..36c5e0127 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.56" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.56.tgz#6fe41d45175c01c5f50581b614c38a772c55a4e9" - integrity sha512-zwwkSio/AYTOXa3hWmbgT/3mvlswbbxHbAvQO9Tl19kl+lmwKsCylelUW1einXZAWp8nAzlHr7PqQ3HP05vgUA== + version "1.0.58" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.58.tgz#8dc69a94822e4d76ed9a43c4f09f79e301908e46" + integrity sha512-8HKYoPHkhQWtAtkfOTxXHCm782UYWkktAPSWTma1aOOz+ALceKjd4eK31r0oiYghuJ3EW+3i7p6ZA6DGZOjwfA== From f27342cbf407ed424932a41ef1203e48d2b82750 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 16 Aug 2023 03:01:28 +0000 Subject: [PATCH 029/204] npm: bump @veupathdb/genomics-site from 1.0.58 to 1.0.59 in /Site Bumps @veupathdb/genomics-site from 1.0.58 to 1.0.59. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 36c5e0127..f06f45286 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.58" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.58.tgz#8dc69a94822e4d76ed9a43c4f09f79e301908e46" - integrity sha512-8HKYoPHkhQWtAtkfOTxXHCm782UYWkktAPSWTma1aOOz+ALceKjd4eK31r0oiYghuJ3EW+3i7p6ZA6DGZOjwfA== + version "1.0.59" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.59.tgz#b31b74a0f39fe7d9be7ee08f7e1f9b5f74c48af3" + integrity sha512-ohC1nXgqbDtazbxXftO4aUYkbLA3e/c4PchhGerLjKucJIkVy2fs6W5i3MCxSQdCdIfKF/4CHTWXdMfiS+HVhg== From 1d099452c80be8e39675ca47800e96f4aeb662dc Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Wed, 16 Aug 2023 15:21:18 -0400 Subject: [PATCH 030/204] widen fungi Liu graph -ref #52028 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 8829cf34c..09ee69723 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1773,6 +1773,18 @@ sub getPlotWidth { return 1000; } 1; + + +# fungi - calbSC5314_Liu_calbSC5314_2015_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_d133a8e1d9; + +sub getPlotWidth { return 1200; } + +1; + + + + #-------------------------------------------------------------------------------- # TEMPLATE_ANCHOR rnaSeqGraph From a5ce38f90fb9452344dfc72e6a96a6e3b4a74948 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 17 Aug 2023 09:50:00 -0400 Subject: [PATCH 031/204] widen host Liu graph -ref #52028 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 09ee69723..591981b2e 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1783,6 +1783,13 @@ sub getPlotWidth { return 1200; } 1; +# host - hsapREF_Liu_calbSC5314_2015_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_5f2c5bb6f7; + +sub getPlotWidth { return 600; } + +1; + #-------------------------------------------------------------------------------- From 2fd287e459bea2ca92d54463f277c4d7c7d1d041 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 17 Aug 2023 10:03:40 -0400 Subject: [PATCH 032/204] widen vect Choi graph -ref #52031 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 591981b2e..3fb6ba321 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1790,6 +1790,13 @@ sub getPlotWidth { return 600; } 1; +# vect - aaegLVP_AGWG_SRP034735_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_f279b1d0f8; + +sub getPlotWidth { return 750; } + +1; + #-------------------------------------------------------------------------------- From 0f3eacbaf9db1f5ea1b7fbf3dc58536c4efead89 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 17 Aug 2023 11:09:30 -0400 Subject: [PATCH 033/204] better host Liu graph -ref #52028 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 3fb6ba321..094e70dfd 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1786,7 +1786,7 @@ sub getPlotWidth { return 1200; } # host - hsapREF_Liu_calbSC5314_2015_ebi_rnaSeq_RSRC package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_5f2c5bb6f7; -sub getPlotWidth { return 600; } +sub getPlotWidth { return 550; } 1; From 98059dbe2047e8b3bae0892b86d4c3f503678ea1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 19 Aug 2023 03:23:32 +0000 Subject: [PATCH 034/204] npm: bump @veupathdb/genomics-site from 1.0.59 to 1.0.61 in /Site Bumps @veupathdb/genomics-site from 1.0.59 to 1.0.61. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f06f45286..dcca2357a 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.59" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.59.tgz#b31b74a0f39fe7d9be7ee08f7e1f9b5f74c48af3" - integrity sha512-ohC1nXgqbDtazbxXftO4aUYkbLA3e/c4PchhGerLjKucJIkVy2fs6W5i3MCxSQdCdIfKF/4CHTWXdMfiS+HVhg== + version "1.0.61" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.61.tgz#14f39d707581c29c28b6e3e604a863e7a8ea385e" + integrity sha512-RpSdle3Kq9gFC3fHnR89PiI68mMreC+FshHZa3Llbc4B5Ojso1RWhSUXqGkFOWPZ+s6hKwyOlR2oncGVr/5qYQ== From 4f1cadea09c89524ea0029130c0e8f3cdeba82f9 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 23 Aug 2023 09:49:06 -0400 Subject: [PATCH 035/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index dcca2357a..a047a4ea9 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.61" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.61.tgz#14f39d707581c29c28b6e3e604a863e7a8ea385e" - integrity sha512-RpSdle3Kq9gFC3fHnR89PiI68mMreC+FshHZa3Llbc4B5Ojso1RWhSUXqGkFOWPZ+s6hKwyOlR2oncGVr/5qYQ== + version "1.0.62" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.62.tgz#2de68a4034774901193435ae29879bf92d21d622" + integrity sha512-z2EIUPBAip+nAkEFA7jeA23KRM0aVNLIhYR7v2SjO7aIgaS+hjAKCp+/qa3aWMdCd8+rKd29KAgEvTCEC86T/A== From d479cc550c9b4c6f7d6cf6112497065d45d77b5a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 25 Aug 2023 03:16:59 +0000 Subject: [PATCH 036/204] npm: bump @veupathdb/genomics-site from 1.0.62 to 1.0.63 in /Site Bumps @veupathdb/genomics-site from 1.0.62 to 1.0.63. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a047a4ea9..5e6f418ab 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.62" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.62.tgz#2de68a4034774901193435ae29879bf92d21d622" - integrity sha512-z2EIUPBAip+nAkEFA7jeA23KRM0aVNLIhYR7v2SjO7aIgaS+hjAKCp+/qa3aWMdCd8+rKd29KAgEvTCEC86T/A== + version "1.0.63" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.63.tgz#57fe088b9a4da2c4ec3f46cecd2aaa2bcc4a66e2" + integrity sha512-4vKQvAlq0XWPqW3Iqvua4FNE1qk2W9Bp0q58svtUtASMi05rWTEvt1crAQ09S3WcsJZXbZGZ1aPSUuuXof2P8A== From 751d989404542d5e6f6112bdfe1e1cf54b91ee25 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Fri, 25 Aug 2023 10:55:53 -0400 Subject: [PATCH 037/204] add webservice path to jbrowse org specific tracks --- .../apicommon/service/services/jbrowse/JBrowseService.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java index b90e5c31d..36db811e4 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java @@ -147,6 +147,8 @@ public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") St String gusHome = getWdkModel().getGusHome(); String projectId = getWdkModel().getProjectId(); String buildNumber = getWdkModel().getBuildNumber(); + String webservicesDir = getWdkModel().getProperties().get("WEBSERVICEMIRROR"); + List command = new ArrayList(); command.add(gusHome + "/bin/jbrowseOrganismSpecificTracks"); @@ -154,6 +156,7 @@ public Response getJbrowseOrganismSpecificTracks(@PathParam("organismAbbrev") St command.add(projectId); command.add(isApollo); command.add(buildNumber); + command.add(webservicesDir); return responseFromCommand(command); } From ceeb6015a881ae75277118d40e3e09ab352656db Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 26 Aug 2023 03:22:08 +0000 Subject: [PATCH 038/204] npm: bump @veupathdb/genomics-site from 1.0.63 to 1.0.64 in /Site Bumps @veupathdb/genomics-site from 1.0.63 to 1.0.64. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 5e6f418ab..f47862b91 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.63" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.63.tgz#57fe088b9a4da2c4ec3f46cecd2aaa2bcc4a66e2" - integrity sha512-4vKQvAlq0XWPqW3Iqvua4FNE1qk2W9Bp0q58svtUtASMi05rWTEvt1crAQ09S3WcsJZXbZGZ1aPSUuuXof2P8A== + version "1.0.64" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.64.tgz#cbde56b83065cc0dc9d9aad6778e8d703dfe3ba3" + integrity sha512-NN424wJQYa9nxanuXW9z5QvFn/Hpgha+vAKEdmK+dbGvb5/fvWHoE/eRM4zG6rKU0tuhsdR6fOwLIrQ72jPdSg== From 65bd6c4cd25b22261d2a307c40e63f285db97c81 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 30 Aug 2023 03:01:44 +0000 Subject: [PATCH 039/204] npm: bump @veupathdb/genomics-site from 1.0.64 to 1.0.65 in /Site Bumps @veupathdb/genomics-site from 1.0.64 to 1.0.65. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f47862b91..6f25a4c40 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.64" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.64.tgz#cbde56b83065cc0dc9d9aad6778e8d703dfe3ba3" - integrity sha512-NN424wJQYa9nxanuXW9z5QvFn/Hpgha+vAKEdmK+dbGvb5/fvWHoE/eRM4zG6rKU0tuhsdR6fOwLIrQ72jPdSg== + version "1.0.65" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.65.tgz#dd3201e87f84d65e611937d3462fc83ef6f06965" + integrity sha512-qJzxGxiUl6Ay9ceKCCBEWc6T8N+uO80ZT6lfw8qKVhBMM4x/slk6oAhiUIINW2Mga6wMREz1gey29MZgopOwDw== From 164f15e8afad8f2d6f90ea64c7aacc50def5564b Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Wed, 30 Aug 2023 09:40:45 -0400 Subject: [PATCH 040/204] widen graph for agamPEST_ERP113663 -refs #52095 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 094e70dfd..97c6935c5 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1798,6 +1798,14 @@ sub getPlotWidth { return 750; } 1; +# vect - agamPEST_ERP113663_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_df981c3f82; + +sub getPlotWidth { return 1000; } + +1; + + #-------------------------------------------------------------------------------- # TEMPLATE_ANCHOR rnaSeqGraph From e5da2b20c4e4f08aca914162e761d8a08bc2b1a4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 31 Aug 2023 03:43:39 +0000 Subject: [PATCH 041/204] npm: bump @veupathdb/genomics-site from 1.0.65 to 1.0.66 in /Site Bumps @veupathdb/genomics-site from 1.0.65 to 1.0.66. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6f25a4c40..78e8492c6 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.65" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.65.tgz#dd3201e87f84d65e611937d3462fc83ef6f06965" - integrity sha512-qJzxGxiUl6Ay9ceKCCBEWc6T8N+uO80ZT6lfw8qKVhBMM4x/slk6oAhiUIINW2Mga6wMREz1gey29MZgopOwDw== + version "1.0.66" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" + integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== From c8ebd8f1dc8823303c6ec3c69d4a6bdd74e76b90 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 2 Sep 2023 03:57:17 +0000 Subject: [PATCH 042/204] npm: bump @veupathdb/genomics-site from 1.0.66 to 1.0.67 in /Site Bumps @veupathdb/genomics-site from 1.0.66 to 1.0.67. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 78e8492c6..7dbf27082 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.66" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" - integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== + version "1.0.67" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.67.tgz#e922314adca24e04b0be558cee53956571ac98ca" + integrity sha512-On+NXaHZTKdySxVHNzcRhdiDZszB7WCo7FqeV6Qj/XrEELjgM4Sk6YxfviWzjl+IuZpMXXfW7oXYy8UEf4HA5g== From a2f3676fce8f16d8ceb8be1fa25a2443c334931f Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 5 Sep 2023 10:49:01 -0400 Subject: [PATCH 043/204] revert to web-monorepo 1.0.66 --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7dbf27082..78e8492c6 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.67" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.67.tgz#e922314adca24e04b0be558cee53956571ac98ca" - integrity sha512-On+NXaHZTKdySxVHNzcRhdiDZszB7WCo7FqeV6Qj/XrEELjgM4Sk6YxfviWzjl+IuZpMXXfW7oXYy8UEf4HA5g== + version "1.0.66" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" + integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== From 5931a9530a70cfd22fb02364dca2885911eb0769 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 6 Sep 2023 03:03:14 +0000 Subject: [PATCH 044/204] npm: bump @veupathdb/genomics-site from 1.0.66 to 1.0.67 in /Site Bumps @veupathdb/genomics-site from 1.0.66 to 1.0.67. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 78e8492c6..7dbf27082 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.66" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" - integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== + version "1.0.67" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.67.tgz#e922314adca24e04b0be558cee53956571ac98ca" + integrity sha512-On+NXaHZTKdySxVHNzcRhdiDZszB7WCo7FqeV6Qj/XrEELjgM4Sk6YxfviWzjl+IuZpMXXfW7oXYy8UEf4HA5g== From c0fcc382e2107bcd664b1250cb5d1845813e4d25 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Wed, 6 Sep 2023 09:27:07 -0400 Subject: [PATCH 045/204] revert to web-monorepo 1.0.66 --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7dbf27082..78e8492c6 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.67" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.67.tgz#e922314adca24e04b0be558cee53956571ac98ca" - integrity sha512-On+NXaHZTKdySxVHNzcRhdiDZszB7WCo7FqeV6Qj/XrEELjgM4Sk6YxfviWzjl+IuZpMXXfW7oXYy8UEf4HA5g== + version "1.0.66" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" + integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== From 5a6c9497aeb2fb6cfb59fd189cf6198c1abfead0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 7 Sep 2023 03:22:56 +0000 Subject: [PATCH 046/204] npm: bump @veupathdb/genomics-site from 1.0.66 to 1.0.68 in /Site Bumps @veupathdb/genomics-site from 1.0.66 to 1.0.68. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 78e8492c6..9d6c7fe03 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.66" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.66.tgz#ee0b4a4a00589fdf26c64c2b39e6b76fdb9f1ace" - integrity sha512-EOvAYgL7eo3JVlbheJWYh6n7vegSPtTx7bRYqeUv25ZXxfMKBBTE+NZAfkhnLEwTV0tdy2Lb2e1PxrKvxAni9A== + version "1.0.68" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.68.tgz#662c8221ab528432ea5f33721ce3c294fb50d379" + integrity sha512-AaDMh4QAP/ktcpeogGs4tpOQhI6xvXGgM6S2QOlUxyNh8sG3+kPBJEvizG8o2YSI497hd+tuEm2vsJlO3ZLkfg== From 988b51b6481d50fe8eb70daadd606f6cd734dd4f Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 8 Sep 2023 10:18:27 -0400 Subject: [PATCH 047/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 9d6c7fe03..af384635f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.68" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.68.tgz#662c8221ab528432ea5f33721ce3c294fb50d379" - integrity sha512-AaDMh4QAP/ktcpeogGs4tpOQhI6xvXGgM6S2QOlUxyNh8sG3+kPBJEvizG8o2YSI497hd+tuEm2vsJlO3ZLkfg== + version "1.0.70" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.70.tgz#c701108c19421a323b138d3630ef14b91c5aeb75" + integrity sha512-FuRmkx9eqlvxYYpNBaiyJ0b4Jegn/Z4J2Y82qPQFT9596ncTemhUcfa+t46fktMUEf1TfhWAYc9JX63EUuN7og== From 80dc68952fd8226df4744747e84d2ecc18de506a Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 11 Sep 2023 09:47:03 -0400 Subject: [PATCH 048/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index af384635f..2cd02ed16 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.70" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.70.tgz#c701108c19421a323b138d3630ef14b91c5aeb75" - integrity sha512-FuRmkx9eqlvxYYpNBaiyJ0b4Jegn/Z4J2Y82qPQFT9596ncTemhUcfa+t46fktMUEf1TfhWAYc9JX63EUuN7og== + version "1.0.73" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.73.tgz#d74ee796b08907cd5bdf9507b1758ffa16c56abd" + integrity sha512-fgRAPK9S3fQg4XwbKHgI4D/bpI6zQvUSgPVWkUV0hyXw9yzivmIMEwrHxAcu+KfENDfC5c1V6JbXwTcUbQE5zA== From a3663b5a7fc28c53f9f86585246bbf5ca98642bd Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 12 Sep 2023 07:23:03 -0400 Subject: [PATCH 049/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2cd02ed16..5b756ecb3 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.73" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.73.tgz#d74ee796b08907cd5bdf9507b1758ffa16c56abd" - integrity sha512-fgRAPK9S3fQg4XwbKHgI4D/bpI6zQvUSgPVWkUV0hyXw9yzivmIMEwrHxAcu+KfENDfC5c1V6JbXwTcUbQE5zA== + version "1.0.74" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.74.tgz#1c9de421555aff7ed9b38c0af4f9b451f63d3113" + integrity sha512-VcWUdefxKsfgicf4bdLob3TMX7qBUiON/ljnnYdcpXeVso3ZGYg4iS8dYdpDKwlEX2sCx/0XdhDc1g6D816mtg== From e7c7af143176b4271aefdf1fc5a84e1beeb9bc8e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 12 Sep 2023 12:51:03 -0400 Subject: [PATCH 050/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 5b756ecb3..6af1bbe18 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.74" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.74.tgz#1c9de421555aff7ed9b38c0af4f9b451f63d3113" - integrity sha512-VcWUdefxKsfgicf4bdLob3TMX7qBUiON/ljnnYdcpXeVso3ZGYg4iS8dYdpDKwlEX2sCx/0XdhDc1g6D816mtg== + version "1.0.75" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.75.tgz#4dbef0511438677309db08f0f374370d200e9c0c" + integrity sha512-5r6pxtk42zAgn7XcbsJs6CTeaR5BJ5UXZpaIuehfBkgM3hU5gL/efVx3ByUJ4j6YoWafReScElqsSXS3iVg5/Q== From cfb21fefb95b6b0c494d1515026bf6e342cd56dd Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 13 Sep 2023 22:22:03 -0400 Subject: [PATCH 051/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6af1bbe18..f10377673 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.75" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.75.tgz#4dbef0511438677309db08f0f374370d200e9c0c" - integrity sha512-5r6pxtk42zAgn7XcbsJs6CTeaR5BJ5UXZpaIuehfBkgM3hU5gL/efVx3ByUJ4j6YoWafReScElqsSXS3iVg5/Q== + version "1.0.77" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.77.tgz#ca65f5a2f473e51cf569a180fa08e87ada589ff9" + integrity sha512-Ou7+WTUS+S8nAUa8jO4n4PPelrzybnc8UYPsY0/tVdrPpGmlPVqyRdVZvRFPNAgCe39mCuDEn1Owjc7vXqe28g== From 671778985d8db07c9e7f7901e229c1808005269f Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 14 Sep 2023 11:30:21 -0400 Subject: [PATCH 052/204] Remove conifer file since all vectorbase sites should have eda_enabled --- .../roles/conifer/vars/ApiCommon/production/VectorBase.yml | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml deleted file mode 100644 index 269fe13b0..000000000 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/VectorBase.yml +++ /dev/null @@ -1,6 +0,0 @@ -# $SourceFileURL$ ---- -eda: - # enable for feature and beta sites - enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.', 'q2.')) else 'false' }}" - #enabled: "{{ 'true' if hostname.startswith(('feature.', 'b1.', 'b2.', 'q1.')) else 'false' }}" From 2832e92b141854373b4831ee69766a4476de6d91 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 16 Sep 2023 03:51:49 +0000 Subject: [PATCH 053/204] npm: bump @veupathdb/genomics-site from 1.0.77 to 1.0.78 in /Site Bumps @veupathdb/genomics-site from 1.0.77 to 1.0.78. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f10377673..6807b8e06 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.77" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.77.tgz#ca65f5a2f473e51cf569a180fa08e87ada589ff9" - integrity sha512-Ou7+WTUS+S8nAUa8jO4n4PPelrzybnc8UYPsY0/tVdrPpGmlPVqyRdVZvRFPNAgCe39mCuDEn1Owjc7vXqe28g== + version "1.0.78" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.78.tgz#a6acef867c9b42170c9e431ed3557d141bb90ff4" + integrity sha512-GjkmFP16zn1dU+Pzsb6vdE7TjK6wzJGdoRjPb5t64FFYIOYpPW3ADa23wL4F/nKNTdVy3Ru+58WnR+VjxEWk1g== From c0c5909ce82e6c31950a27d2b7b4eb72f736ef6e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Sep 2023 03:44:47 +0000 Subject: [PATCH 054/204] npm: bump @veupathdb/genomics-site from 1.0.78 to 1.0.79 in /Site Bumps @veupathdb/genomics-site from 1.0.78 to 1.0.79. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6807b8e06..118971afa 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.78" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.78.tgz#a6acef867c9b42170c9e431ed3557d141bb90ff4" - integrity sha512-GjkmFP16zn1dU+Pzsb6vdE7TjK6wzJGdoRjPb5t64FFYIOYpPW3ADa23wL4F/nKNTdVy3Ru+58WnR+VjxEWk1g== + version "1.0.79" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.79.tgz#bad9a40e8a7da17f2d9c9784e8f63b9308a832af" + integrity sha512-ZEn/0togdBLkUqD7srsSGgyypvfvMrahDaD8nCK27iO30ZDzrd4GLzQWtpPQwK1s8jBNuI2Or73E2puvylB0aQ== From 576f615ec391266dc56841a41275c2ce55513c9c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 29 Sep 2023 03:36:50 +0000 Subject: [PATCH 055/204] npm: bump @veupathdb/genomics-site from 1.0.79 to 1.0.80 in /Site Bumps @veupathdb/genomics-site from 1.0.79 to 1.0.80. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 118971afa..cd5ba91ed 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.79" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.79.tgz#bad9a40e8a7da17f2d9c9784e8f63b9308a832af" - integrity sha512-ZEn/0togdBLkUqD7srsSGgyypvfvMrahDaD8nCK27iO30ZDzrd4GLzQWtpPQwK1s8jBNuI2Or73E2puvylB0aQ== + version "1.0.80" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.80.tgz#0c684fa671857fbed7df1d7cfa76422aa74065a1" + integrity sha512-A6KyWObRkWji+I+R3fAzEGf5wbsgRh2rfFzgRmVtAwJdgSNkhi0rwmnlTT+4TyPKGUazaMbsXxoCDjdAy2syoA== From a1e82b085cd0b333982fd756d892bdc62d721a82 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 4 Oct 2023 03:15:41 +0000 Subject: [PATCH 056/204] npm: bump @veupathdb/genomics-site from 1.0.80 to 1.0.81 in /Site Bumps @veupathdb/genomics-site from 1.0.80 to 1.0.81. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index cd5ba91ed..03c6a4131 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.80" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.80.tgz#0c684fa671857fbed7df1d7cfa76422aa74065a1" - integrity sha512-A6KyWObRkWji+I+R3fAzEGf5wbsgRh2rfFzgRmVtAwJdgSNkhi0rwmnlTT+4TyPKGUazaMbsXxoCDjdAy2syoA== + version "1.0.81" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.81.tgz#9a6055e4b45b887eec2cb90101e08ac2b1e58eaa" + integrity sha512-YWAYOYnJvgvUHu2h3/WUhAiy1xXVYZMZaPj+vxy3MjyVynqyqPRmwjguf+LVEGTpsTenE9dCty9qzj2S8+1Q7A== From a344f24398f8460b226aeb89aa9d069416216901 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Wed, 4 Oct 2023 12:21:49 -0400 Subject: [PATCH 057/204] Fix enum to match client --- .../apicommon/model/report/bed/BedGeneReporter.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedGeneReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedGeneReporter.java index 51f7454ef..a16eaf283 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedGeneReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedGeneReporter.java @@ -21,8 +21,8 @@ public class BedGeneReporter extends BedReporter { private enum SequenceType { - dna_components, - transcript_components, + dna_component, + transcript_component, genomic, spliced_genomic, genomic_features, @@ -49,8 +49,8 @@ private enum SplicedGenomic { public static boolean useCoordinatesOnProteinReference(JSONObject config) throws WdkModelException { SequenceType type = SequenceType.valueOf(config.getString("type")); switch(type){ - case dna_components: - case transcript_components: + case dna_component: + case transcript_component: case genomic: case spliced_genomic: case genomic_features: @@ -145,7 +145,7 @@ private static BedFeatureProvider createFeatureProvider(JSONObject config) throw default: throw new WdkModelException(String.format("Unsupported spliced genomic type: %s", splicedGenomic.name())); } - case dna_components: + case dna_component: DnaComponent dnaComponent = DnaComponent.valueOf(config.getString("dnaComponent")); switch (dnaComponent){ case exon: @@ -155,7 +155,7 @@ private static BedFeatureProvider createFeatureProvider(JSONObject config) throw default: throw new WdkModelException(String.format("Unsupported dnaComponent type: %s", dnaComponent.name())); } - case transcript_components: + case transcript_component: TranscriptComponent transcriptComponent = TranscriptComponent.valueOf(config.getString("transcriptComponent")); switch(transcriptComponent){ case five_prime_utr: From 1b9dc96628f6ee55907d87147442608b48689b9b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 11 Oct 2023 08:57:09 -0400 Subject: [PATCH 058/204] Use standard Content-Type response header (#178) --- .../java/org/apidb/apicommon/model/report/bed/BedReporter.java | 2 +- .../apidb/apicommon/model/report/sequence/SequenceReporter.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedReporter.java index 31261fd39..e68acf425 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/BedReporter.java @@ -80,7 +80,7 @@ protected ContentDisposition getContentDisposition(JSONObject config) { @Override public String getHttpContentType() { - return "text/x-bed"; + return "text/plain"; } @Override diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java index 45349f6ab..0859e3a07 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java @@ -35,7 +35,7 @@ public class SequenceReporter extends AbstractReporter { private static Logger LOG = Logger.getLogger(SequenceReporter.class); - private static final String FASTA_MEDIA_TYPE = "text/x-fasta"; + private static final String FASTA_MEDIA_TYPE = "text/plain"; private static final String BED_REPORTER_NAME = "bed"; private enum SequenceType { From 994db5ddf4b81c87e0c88c5c0aeef25188dfaa86 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 12 Oct 2023 03:29:45 +0000 Subject: [PATCH 059/204] npm: bump @veupathdb/genomics-site from 1.0.81 to 1.0.82 in /Site Bumps @veupathdb/genomics-site from 1.0.81 to 1.0.82. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 03c6a4131..04640c266 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.81" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.81.tgz#9a6055e4b45b887eec2cb90101e08ac2b1e58eaa" - integrity sha512-YWAYOYnJvgvUHu2h3/WUhAiy1xXVYZMZaPj+vxy3MjyVynqyqPRmwjguf+LVEGTpsTenE9dCty9qzj2S8+1Q7A== + version "1.0.82" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.82.tgz#330675d7651f07024daba4901e0649074e1274f7" + integrity sha512-ZtKB/C7kesRp7gh8qDz4KDrvZZ1dQ2zCIgQ2A+OJ/RWALjNxXNEve/I3VePktaswWqQDAHVnFc/6vdY3rNijgQ== From 16725087e85c275fbd985877c0fb8c1680c8a698 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Mon, 16 Oct 2023 11:30:19 -0400 Subject: [PATCH 060/204] Don't discriminate against x-fasta --- .../apicommon/model/report/sequence/SequenceReporter.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java index 0859e3a07..f8841b43d 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java @@ -7,6 +7,7 @@ import java.util.Collections; import java.util.Map; +import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response.Status.Family; import org.apache.log4j.Logger; @@ -145,7 +146,7 @@ public void write(OutputStream out) throws WdkModelException { // make call to sequence retrieval service ResponseFuture responseFuture = ClientUtil.makeAsyncMultiPartPostRequest( - _seqRetSvcRequestUrl, seqRetSvcRequestBody, FASTA_MEDIA_TYPE, Collections.emptyMap()); + _seqRetSvcRequestUrl, seqRetSvcRequestBody, MediaType.WILDCARD, Collections.emptyMap()); // wait for response, then read into an Either Either response = Functions.mapException(() -> responseFuture.getEither(), From 82f1b2b55efc5e9ba7995a6afaccdb029df00a95 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 03:54:28 +0000 Subject: [PATCH 061/204] npm: bump @veupathdb/genomics-site from 1.0.82 to 1.0.83 in /Site Bumps @veupathdb/genomics-site from 1.0.82 to 1.0.83. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 04640c266..0ccd19ff7 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.82" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.82.tgz#330675d7651f07024daba4901e0649074e1274f7" - integrity sha512-ZtKB/C7kesRp7gh8qDz4KDrvZZ1dQ2zCIgQ2A+OJ/RWALjNxXNEve/I3VePktaswWqQDAHVnFc/6vdY3rNijgQ== + version "1.0.83" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.83.tgz#acab9c6d8944b6534c19b99a692b539a28cf54d8" + integrity sha512-xmImF+Gg5g1JtxnmPJFdxuysRQMo+AN8V8J8gB2ULuipSRXHXs2kFoq6R133shxAsUrAp6Ys/XPtdmA51uSa0Q== From 2df0ca22a11cbac3a5d4786049f2e66a63d347c8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 18 Oct 2023 03:52:28 +0000 Subject: [PATCH 062/204] npm: bump @veupathdb/genomics-site from 1.0.83 to 1.0.84 in /Site Bumps @veupathdb/genomics-site from 1.0.83 to 1.0.84. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 0ccd19ff7..630f50ad7 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.83" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.83.tgz#acab9c6d8944b6534c19b99a692b539a28cf54d8" - integrity sha512-xmImF+Gg5g1JtxnmPJFdxuysRQMo+AN8V8J8gB2ULuipSRXHXs2kFoq6R133shxAsUrAp6Ys/XPtdmA51uSa0Q== + version "1.0.84" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.84.tgz#71b7d44d040b604025b30a4198c63778d2736436" + integrity sha512-gyl/VEHAJ/WoM0RFObzf46OPPnof/GZ6vuiG/NbPC+aOn+RQjHIi4XtToyyuuO9lioPsrneA2uMwJaY5lpj/Mg== From e3fdcfa975f35a50936f660f43bd0960e43e9153 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 18 Oct 2023 11:09:25 -0400 Subject: [PATCH 063/204] bed file should be zero based - half open --- .../model/report/bed/util/BedLine.java | 22 ++++++++++++++----- 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java index e3b76ddd2..f7338a89f 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java @@ -17,24 +17,30 @@ public class BedLine { */ private static final String SCORE_FIELD = "0"; + private static Integer locationToZeroBased(Integer loc) { + return new Integer(loc.intValue() - 1); + } + public static List bed6(String featureId, Integer start, Integer end, DeflineBuilder defline, StrandDirection strand){ - return List.of(featureId, start.toString(), end.toString(), defline.toString(), SCORE_FIELD, strand.getSign()); + Integer zeroBasedStart = locationToZeroBased(start); + + return List.of(featureId, zeroBasedStart.toString(), end.toString(), defline.toString(), SCORE_FIELD, strand.getSign()); } + public static List bed12(String featureId, DeflineBuilder defline, StrandDirection strand, List subfeatureStarts, List subfeatureEnds){ Integer start = Collections.min(subfeatureStarts); Integer end = Collections.max(subfeatureEnds); - Integer cdStart = start; - Integer cdEnd = end; String color = "."; Integer numBlocks = subfeatureStarts.size(); - + + // subfeature coords are 1 based closed here (genomic coords). when getting length need to add 1 String blockSizesStr = IntStream.range(0, numBlocks) - .mapToObj(i -> Integer.valueOf(subfeatureEnds.get(i) - subfeatureStarts.get(i)).toString()) + .mapToObj(i -> Integer.valueOf(subfeatureEnds.get(i) - subfeatureStarts.get(i) + 1).toString()) .collect(Collectors.joining(",")); String blockStartsStr = @@ -42,8 +48,12 @@ public static List bed12(String featureId, DeflineBuilder defline, Stran .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString()) .collect(Collectors.joining(",")); + Integer zeroBasedStart = locationToZeroBased(start); + + Integer cdStart = zeroBasedStart; + Integer cdEnd = end; - return List.of(featureId, start.toString(), end.toString(), defline.toString(), SCORE_FIELD, strand.getSign(), cdStart.toString(), cdEnd.toString(), color, numBlocks.toString(), blockSizesStr, blockStartsStr); + return List.of(featureId, zeroBasedStart.toString(), end.toString(), defline.toString(), SCORE_FIELD, strand.getSign(), cdStart.toString(), cdEnd.toString(), color, numBlocks.toString(), blockSizesStr, blockStartsStr); } } From d2933d5cd19c08b54ce185c4f04be1d771934d46 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 18 Oct 2023 11:59:51 -0400 Subject: [PATCH 064/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 630f50ad7..6cf2f62a2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.84" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.84.tgz#71b7d44d040b604025b30a4198c63778d2736436" - integrity sha512-gyl/VEHAJ/WoM0RFObzf46OPPnof/GZ6vuiG/NbPC+aOn+RQjHIi4XtToyyuuO9lioPsrneA2uMwJaY5lpj/Mg== + version "1.0.85" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.85.tgz#dbcdb99249b3a2f76f09d733c4e155785d2fc363" + integrity sha512-CAtfIPXZqc1UfyMzt3ldGldQhhCHvlBE3KBGH2LmdivoPsuQ6M/iUVeyjcX3nhMgyoJRXxi1JCUjD1GtONYq/g== From 2a9339f7703f408ebbd8e59ed3f79a2335b4a453 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Fri, 20 Oct 2023 16:24:30 -0400 Subject: [PATCH 065/204] set startOffset=ONE for standard bed files --- .../apidb/apicommon/model/report/sequence/SequenceReporter.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java index f8841b43d..0630c4802 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java @@ -85,7 +85,7 @@ public SequenceReporter configure(JSONObject config) throws ReporterConfigExcept // FIXME: starting here with synchronous API for proof of concept; convert to async _seqRetSvcRequestUrl = localhost + modelProps.get("SEQUENCE_RETRIEVAL_SERVICE_URL") + - "/sequences/" + sequenceType.name() + "/bed?basesPerLine=" + basesPerLine + "&deflineFormat=QUERYONLY&startOffset=ZERO"; + "/sequences/" + sequenceType.name() + "/bed?basesPerLine=" + basesPerLine + "&deflineFormat=QUERYONLY&startOffset=ONE"; LOG.info("Configured sequence reporter to return FASTA.\n bedFileUrl = " + _bedFileUrl + "\n seqRetSvcUrl = " + _seqRetSvcRequestUrl); return this; From 6e6fed80830d2cae100fda039d9f558e48e5ed7c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 31 Oct 2023 03:14:41 +0000 Subject: [PATCH 066/204] npm: bump @veupathdb/genomics-site from 1.0.85 to 1.0.86 in /Site Bumps @veupathdb/genomics-site from 1.0.85 to 1.0.86. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6cf2f62a2..a527d578e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.85" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.85.tgz#dbcdb99249b3a2f76f09d733c4e155785d2fc363" - integrity sha512-CAtfIPXZqc1UfyMzt3ldGldQhhCHvlBE3KBGH2LmdivoPsuQ6M/iUVeyjcX3nhMgyoJRXxi1JCUjD1GtONYq/g== + version "1.0.86" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.86.tgz#c62509536aa5694ed0e1dfd7d2346210a1230e58" + integrity sha512-9t3mKOY9N4kEq/16SEsD+sgZyZwGPVeM7MXP7JaHc8aIzC8jGRzuI2D9yzMwvC1ZlTdAEwrbww/X46ln4GdnnA== From cd2384fdfb5ac72ad97021bb0ea0064413d7b24f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 2 Nov 2023 03:38:39 +0000 Subject: [PATCH 067/204] npm: bump @veupathdb/genomics-site from 1.0.86 to 1.0.87 in /Site Bumps @veupathdb/genomics-site from 1.0.86 to 1.0.87. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a527d578e..05f538596 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.86" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.86.tgz#c62509536aa5694ed0e1dfd7d2346210a1230e58" - integrity sha512-9t3mKOY9N4kEq/16SEsD+sgZyZwGPVeM7MXP7JaHc8aIzC8jGRzuI2D9yzMwvC1ZlTdAEwrbww/X46ln4GdnnA== + version "1.0.87" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.87.tgz#2a1484957a0f54054664f333e7b099317b20fa0e" + integrity sha512-q2Jc1ifh+INBsxo3SJaX/ZC1ys5BfsTfpbKbRwS1dIeANC97nkMVMaj5OHH/tDA8B1ToxCKfokiweBIVoMmqLg== From 8bef7151eb9adeafa56bd3717641c1171716e113 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 7 Nov 2023 04:26:10 +0000 Subject: [PATCH 068/204] npm: bump @veupathdb/genomics-site from 1.0.87 to 1.0.88 in /Site Bumps @veupathdb/genomics-site from 1.0.87 to 1.0.88. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 05f538596..6bee9b77b 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.87" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.87.tgz#2a1484957a0f54054664f333e7b099317b20fa0e" - integrity sha512-q2Jc1ifh+INBsxo3SJaX/ZC1ys5BfsTfpbKbRwS1dIeANC97nkMVMaj5OHH/tDA8B1ToxCKfokiweBIVoMmqLg== + version "1.0.88" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.88.tgz#7a87f64a0f8baa4722d2fda70aefea5592b0abb0" + integrity sha512-h3yJGrSHHpBTl3KaDZQzvU/Muo3A//Z61Eb7qsNunIcIvynoE4/bLPn5y191O9+grv4H3cwUCuyKKHK4ajePEQ== From 089514dc024eaf705117ae9a2b17c36d87f5e88d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 Nov 2023 04:03:08 +0000 Subject: [PATCH 069/204] npm: bump @veupathdb/genomics-site from 1.0.88 to 1.0.89 in /Site Bumps @veupathdb/genomics-site from 1.0.88 to 1.0.89. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6bee9b77b..820cce78e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.88" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.88.tgz#7a87f64a0f8baa4722d2fda70aefea5592b0abb0" - integrity sha512-h3yJGrSHHpBTl3KaDZQzvU/Muo3A//Z61Eb7qsNunIcIvynoE4/bLPn5y191O9+grv4H3cwUCuyKKHK4ajePEQ== + version "1.0.89" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.89.tgz#befd236cb0278adf167244d70d1ab43471b7ad59" + integrity sha512-9pcXoYmkZioIpdGRMXkembH//2KfU5l9KQ3EqDmOSoqHSyy7TbZ4o4Jf3309wNDE6WaiM+ER93HrkuStoHEhrw== From c1cf8226b7e5c541ac0f110c73899dcdf719ce91 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 10 Nov 2023 04:39:00 +0000 Subject: [PATCH 070/204] npm: bump @veupathdb/genomics-site from 1.0.89 to 1.0.91 in /Site Bumps @veupathdb/genomics-site from 1.0.89 to 1.0.91. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 820cce78e..2136e59cb 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.89" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.89.tgz#befd236cb0278adf167244d70d1ab43471b7ad59" - integrity sha512-9pcXoYmkZioIpdGRMXkembH//2KfU5l9KQ3EqDmOSoqHSyy7TbZ4o4Jf3309wNDE6WaiM+ER93HrkuStoHEhrw== + version "1.0.91" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.91.tgz#860bda676a45592e44ee2e96dd11b283ef44b04a" + integrity sha512-SdcdxDlEZJ50GF059KHgQoyumrR8/j14r+kiP9o26JlW06eSmYmi5nFaXqhmjmJ3iyFZqYuVAhcOi3yzht69Uw== From a1963719a862360965a38bd50d633e209d585120 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 15 Nov 2023 04:22:40 +0000 Subject: [PATCH 071/204] npm: bump @veupathdb/genomics-site from 1.0.91 to 1.0.92 in /Site Bumps @veupathdb/genomics-site from 1.0.91 to 1.0.92. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2136e59cb..61facefd0 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.91" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.91.tgz#860bda676a45592e44ee2e96dd11b283ef44b04a" - integrity sha512-SdcdxDlEZJ50GF059KHgQoyumrR8/j14r+kiP9o26JlW06eSmYmi5nFaXqhmjmJ3iyFZqYuVAhcOi3yzht69Uw== + version "1.0.92" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.92.tgz#d1dbf507e63cd3304f2130ef4f2cb844d103cd9d" + integrity sha512-s/9HLUQFBDYTcak+Ac4+bzxx9POAPf5zIfmQ9JprBXiJd/yOTlTG5w+pkkqGO5UTxhzjtIFPODoRF6T4q1ThiA== From 9b8f1ceef6e55a068b0cb569d608b253fb5552e1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 04:17:16 +0000 Subject: [PATCH 072/204] npm: bump @veupathdb/genomics-site from 1.0.92 to 1.0.93 in /Site Bumps @veupathdb/genomics-site from 1.0.92 to 1.0.93. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 61facefd0..4178a3b04 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.92" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.92.tgz#d1dbf507e63cd3304f2130ef4f2cb844d103cd9d" - integrity sha512-s/9HLUQFBDYTcak+Ac4+bzxx9POAPf5zIfmQ9JprBXiJd/yOTlTG5w+pkkqGO5UTxhzjtIFPODoRF6T4q1ThiA== + version "1.0.93" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.93.tgz#da9c99a157d3ba575dcea455dc8f430ffdc552d9" + integrity sha512-FmpJ5fYYvKCfYRmaXjxW46usYfzJ2HJlgbnqCMOqM8vNgYDTNDW+lxFfwRykvUR9Lu9Csol/vh/y/g6vXBksew== From f66886534ac7b57a9c2defe49865f151b1f42f0a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 18 Nov 2023 04:15:49 +0000 Subject: [PATCH 073/204] npm: bump @veupathdb/genomics-site from 1.0.93 to 1.0.94 in /Site Bumps @veupathdb/genomics-site from 1.0.93 to 1.0.94. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4178a3b04..2820d68f8 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.93" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.93.tgz#da9c99a157d3ba575dcea455dc8f430ffdc552d9" - integrity sha512-FmpJ5fYYvKCfYRmaXjxW46usYfzJ2HJlgbnqCMOqM8vNgYDTNDW+lxFfwRykvUR9Lu9Csol/vh/y/g6vXBksew== + version "1.0.94" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.94.tgz#a680857ee0db39f58b83e42ca2a80960ed839997" + integrity sha512-ogYZd/NrcC5KpM64xQYRGod+SR04hRkohRKEyiKJ7Lv47o8BwuDsEAokhftmjxr7J6vw3gMAJ1xmDcTkHYHSFQ== From 99055167cac056c9aa9a5ef10414ba1925f3bb05 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 21 Nov 2023 13:34:55 -0500 Subject: [PATCH 074/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2820d68f8..a2a3e50d2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.94" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.94.tgz#a680857ee0db39f58b83e42ca2a80960ed839997" - integrity sha512-ogYZd/NrcC5KpM64xQYRGod+SR04hRkohRKEyiKJ7Lv47o8BwuDsEAokhftmjxr7J6vw3gMAJ1xmDcTkHYHSFQ== + version "1.0.96" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.96.tgz#9ad276062d58c920d304a3dbe2bc23cc7c029cfc" + integrity sha512-nyLJI7v28G7KBJio6SLQjazGLWSzymCYFhCofy38n+mZjaKjeZIqFS0+tWayhRQVPH7llWFh2ZPYn6ByIrnHFg== From 7f59f537118308cad38d3a65217e2ff1d7fcfd2e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 21 Nov 2023 15:46:47 -0500 Subject: [PATCH 075/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a2a3e50d2..a9fbf1991 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.96" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.96.tgz#9ad276062d58c920d304a3dbe2bc23cc7c029cfc" - integrity sha512-nyLJI7v28G7KBJio6SLQjazGLWSzymCYFhCofy38n+mZjaKjeZIqFS0+tWayhRQVPH7llWFh2ZPYn6ByIrnHFg== + version "1.0.97" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.97.tgz#c66f22dc8f10e278f9fd211f70ac4cf3c2f6d37a" + integrity sha512-IPFafHnGJf1ziAlpc+xAVvZuKEdWuQdnLuAk3apb2tcDQtZYrXLh94ch47mtqVlS2qXRtm/FHzUAFYMuyWxF1A== From 29240e0c2e870f6e4a40865af2b17bfcdc9c840b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 27 Nov 2023 22:33:43 -0500 Subject: [PATCH 076/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a9fbf1991..f1346b875 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.97" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.97.tgz#c66f22dc8f10e278f9fd211f70ac4cf3c2f6d37a" - integrity sha512-IPFafHnGJf1ziAlpc+xAVvZuKEdWuQdnLuAk3apb2tcDQtZYrXLh94ch47mtqVlS2qXRtm/FHzUAFYMuyWxF1A== + version "1.0.99" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.99.tgz#fbaa950da27749cf777c872be9fd6610cd4b33fd" + integrity sha512-z1FDnFtDV3KaGlgegMjWcEYCzc99bCvas0Bt2HbWjrOK8I9hiFDTFdIZMTWL20Hda+eiRzgsMmrX05BN+XmSfA== From 1534ca5043bc37f5adf93290869f248e6657b85c Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Mon, 27 Nov 2023 23:17:10 -0500 Subject: [PATCH 077/204] block starts for features on reverse strand --- .../model/report/bed/util/BedLine.java | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java index f7338a89f..be0c913db 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java @@ -43,10 +43,19 @@ public static List bed12(String featureId, DeflineBuilder defline, Stran .mapToObj(i -> Integer.valueOf(subfeatureEnds.get(i) - subfeatureStarts.get(i) + 1).toString()) .collect(Collectors.joining(",")); - String blockStartsStr = - IntStream.range(0, numBlocks) - .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString()) - .collect(Collectors.joining(",")); + String blockStartsStr; + if(strand.getSign().equals("-")) { + blockStartsStr = + IntStream.range(0, numBlocks) + .mapToObj(i -> Integer.valueOf(end - subfeatureEnds.get(i)).toString()) + .collect(Collectors.joining(",")); + } + else { + blockStartsStr = + IntStream.range(0, numBlocks) + .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString()) + .collect(Collectors.joining(",")); + } Integer zeroBasedStart = locationToZeroBased(start); From f0151abb23089ab752c0c8a80c226b08e3836214 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Tue, 28 Nov 2023 00:32:35 -0500 Subject: [PATCH 078/204] genomic unspliced, correct offset for negative strand genes --- .../feature/GeneGenomicFeatureProvider.java | 58 ++++++++++++++----- 1 file changed, 42 insertions(+), 16 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java index 55664c36c..a4884e1fe 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java @@ -85,17 +85,26 @@ public List> getRecordAsBedFields(RecordInstance record) throws Wdk int featureEnd = Integer.valueOf(m.group(3)); StrandDirection strand = StrandDirection.fromSign(m.group(4)); - if(_reverseAndComplement) { - strand = strand.opposite(); - } + int fivePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_FIVE_PRIME_UTR_LENGTH); int threePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_THREE_PRIME_UTR_LENGTH); - Integer segmentStart = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength); - Integer segmentEnd = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength); + Integer upstreamPosition = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand); + Integer downstreamPosition = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand); + + Integer segmentStart = upstreamPosition; + Integer segmentEnd = downstreamPosition; + if(strand.getSign().equals("-")) { + segmentStart = downstreamPosition; + segmentEnd = upstreamPosition; + } DeflineBuilder defline = new DeflineBuilder(featureId); + if(_reverseAndComplement) { + strand = strand.opposite(); + } + if(_requestedDeflineFields.contains("organism")){ defline.appendRecordAttribute(record, ATTR_ORGANISM); } @@ -132,18 +141,35 @@ private Matcher matchLocationCoords(RecordInstance record, String key, Pattern p private static int getPositionGenomic( Integer featureStart, Integer featureEnd, int offset, OffsetSign sign, Anchor anchor, - int fivePrimeUtrLength, int threePrimeUtrLength + int fivePrimeUtrLength, int threePrimeUtrLength, + StrandDirection strand ) throws WdkModelException{ - if (sign == OffsetSign.minus) { - offset = - offset; - } - switch(anchor) { - case Start: return featureStart + offset; - case CodeStart: return featureStart + fivePrimeUtrLength + offset; - case End: return featureEnd + offset; - case CodeEnd: return featureEnd - threePrimeUtrLength + offset; - default: throw new WdkModelException("Unsupported anchor type: " + anchor); - } + + if(strand.getSign().equals("-")) { + + if (sign == OffsetSign.plus) { + offset = - offset; + } + switch(anchor) { + case Start: return featureEnd + offset; + case CodeStart: return featureEnd - fivePrimeUtrLength + offset; + case End: return featureStart + offset; + case CodeEnd: return featureStart + threePrimeUtrLength + offset; + default: throw new WdkModelException("Unsupported anchor type: " + anchor); + } + } + else { + if (sign == OffsetSign.minus) { + offset = - offset; + } + switch(anchor) { + case Start: return featureStart + offset; + case CodeStart: return featureStart + fivePrimeUtrLength + offset; + case End: return featureEnd + offset; + case CodeEnd: return featureEnd - threePrimeUtrLength + offset; + default: throw new WdkModelException("Unsupported anchor type: " + anchor); + } + } } private static String getPositionDescGenomic(int offset, OffsetSign sign, Anchor anchor) throws WdkModelException{ From 9fa739959d0a6c7698ee543db5f163989f016ed5 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Tue, 28 Nov 2023 03:24:54 -0500 Subject: [PATCH 079/204] order of subfeatures matter for spliced transcript --- .../model/report/bed/util/BedLine.java | 25 +++++++++---------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java index be0c913db..28d4be68c 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java @@ -1,6 +1,7 @@ package org.apidb.apicommon.model.report.bed.util; import java.util.List; +import java.util.ArrayList; import java.util.Collections; import java.util.stream.Collectors; import java.util.stream.IntStream; @@ -30,6 +31,12 @@ public static List bed6(String featureId, Integer start, Integer end, De public static List bed12(String featureId, DeflineBuilder defline, StrandDirection strand, List subfeatureStarts, List subfeatureEnds){ + + if(strand.getSign().equals("-")) { + Collections.reverse(subfeatureStarts); + Collections.reverse(subfeatureEnds); + } + Integer start = Collections.min(subfeatureStarts); Integer end = Collections.max(subfeatureEnds); @@ -43,19 +50,11 @@ public static List bed12(String featureId, DeflineBuilder defline, Stran .mapToObj(i -> Integer.valueOf(subfeatureEnds.get(i) - subfeatureStarts.get(i) + 1).toString()) .collect(Collectors.joining(",")); - String blockStartsStr; - if(strand.getSign().equals("-")) { - blockStartsStr = - IntStream.range(0, numBlocks) - .mapToObj(i -> Integer.valueOf(end - subfeatureEnds.get(i)).toString()) - .collect(Collectors.joining(",")); - } - else { - blockStartsStr = - IntStream.range(0, numBlocks) - .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString()) - .collect(Collectors.joining(",")); - } + String blockStartsStr = + IntStream.range(0, numBlocks) + .mapToObj(i -> Integer.valueOf(subfeatureStarts.get(i) - start).toString()) + .collect(Collectors.joining(",")); + Integer zeroBasedStart = locationToZeroBased(start); From ae71eb819e52103bcf099052cee2f330c93a376a Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 29 Nov 2023 22:20:07 -0500 Subject: [PATCH 080/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f1346b875..430f53649 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.99" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.99.tgz#fbaa950da27749cf777c872be9fd6610cd4b33fd" - integrity sha512-z1FDnFtDV3KaGlgegMjWcEYCzc99bCvas0Bt2HbWjrOK8I9hiFDTFdIZMTWL20Hda+eiRzgsMmrX05BN+XmSfA== + version "1.0.100" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.100.tgz#ebb7d5a5fcd56d069d101a3ab71797d839b89f8f" + integrity sha512-xGdEKfqMAFOfhDxoIIynU6o7cGIq7xQJri2y0g3fFJNwHnOPavJnwEIADmx81i9vwAHaCAW8GG/r1sLW8pJbLA== From 88dc5690e3f459540c4001155c623569e7d406ca Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Fri, 1 Dec 2023 16:18:41 -0500 Subject: [PATCH 081/204] use a better delimeter --- .../service/services/jbrowse/JBrowseFeatureDataFactory.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java index 4b8038c30..1a3748d34 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseFeatureDataFactory.java @@ -444,7 +444,7 @@ private Optional getBulkSubfeatureSql(String feature, private static void appendAttributes(JSONObject json, ResultSet rs) throws SQLException { String attrsStr = rs.getString("ATTS"); if (rs.wasNull()) return; - String attrs[] = attrsStr.split(";"); + String attrs[] = attrsStr.split(";;"); for (int i = 0; i < attrs.length; i++) { String attr[] = attrs[i].split("="); if (attr.length > 1) { @@ -499,7 +499,7 @@ private Optional getSequenceId(String idColName, String attrsTableName, private static String replaceSqlMacros(String sql, String start, String end, String seqId, Map qp) { sql = sql.replaceAll("\\$base_start", start); sql = sql.replaceAll("\\$rend", end); - sql = sql.replaceAll("\\$dlm",";"); + sql = sql.replaceAll("\\$dlm",";;"); sql = sql.replaceAll("\\$srcfeature_id", seqId); // skip query params we know are used for "control" purposes (not SQL macros) From cd7bea4b9914ac823d4543701328be77c7ec23fe Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Tue, 5 Dec 2023 22:54:44 -0500 Subject: [PATCH 082/204] Fix java warning --- .../java/org/apidb/apicommon/model/report/bed/util/BedLine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java index f7338a89f..b429b135b 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java @@ -18,7 +18,7 @@ public class BedLine { private static final String SCORE_FIELD = "0"; private static Integer locationToZeroBased(Integer loc) { - return new Integer(loc.intValue() - 1); + return Integer.valueOf(loc.intValue() - 1); } public static List bed6(String featureId, Integer start, Integer end, DeflineBuilder defline, StrandDirection strand){ From 6584618bfe21999aa83417df6a65d72121247302 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 6 Dec 2023 04:50:35 +0000 Subject: [PATCH 083/204] npm: bump @veupathdb/genomics-site from 1.0.100 to 1.0.101 in /Site Bumps @veupathdb/genomics-site from 1.0.100 to 1.0.101. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 430f53649..dbc4d76ea 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.100" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.100.tgz#ebb7d5a5fcd56d069d101a3ab71797d839b89f8f" - integrity sha512-xGdEKfqMAFOfhDxoIIynU6o7cGIq7xQJri2y0g3fFJNwHnOPavJnwEIADmx81i9vwAHaCAW8GG/r1sLW8pJbLA== + version "1.0.101" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.101.tgz#3f16409ddd09af28f241561a13f476ab0d63c1e4" + integrity sha512-SWOOGPeB/KoRQBMkhoIPgLndNx1ArZJDUf8p+UCkG0k3domdwonqPlueGg/tIBu6BKM5CJSTLilXGrZfyn3ctA== From 760e6fbe3b50aa146c85ad4f17e2474cc7eaf7bc Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Wed, 6 Dec 2023 00:28:03 -0500 Subject: [PATCH 084/204] Remove unused import --- .../org/apidb/apicommon/model/report/bed/util/BedLine.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java index 0a45121f4..3ab0b62d0 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/util/BedLine.java @@ -1,8 +1,7 @@ package org.apidb.apicommon.model.report.bed.util; -import java.util.List; -import java.util.ArrayList; import java.util.Collections; +import java.util.List; import java.util.stream.Collectors; import java.util.stream.IntStream; From 75b337e79d24aa65bd246ecaa077c4385a2e4676 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 7 Dec 2023 04:36:47 +0000 Subject: [PATCH 085/204] npm: bump @veupathdb/genomics-site from 1.0.101 to 1.0.102 in /Site Bumps @veupathdb/genomics-site from 1.0.101 to 1.0.102. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index dbc4d76ea..85b4be7a9 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.101" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.101.tgz#3f16409ddd09af28f241561a13f476ab0d63c1e4" - integrity sha512-SWOOGPeB/KoRQBMkhoIPgLndNx1ArZJDUf8p+UCkG0k3domdwonqPlueGg/tIBu6BKM5CJSTLilXGrZfyn3ctA== + version "1.0.102" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.102.tgz#1e9d5fc7c46308cd8447cef5e40e5f0b749fc6d3" + integrity sha512-lLDU/KFg0Aeq8v/FSSVm9xZBshSNSCOldXRmd1TAW4NZUY+8cbiSqFoSFqW3E5GuBchN/5l3TL2ttH088paOmQ== From 9e60c48f915863a552c6720a88b5b02622fcc624 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 12 Dec 2023 04:19:09 +0000 Subject: [PATCH 086/204] npm: bump @veupathdb/genomics-site from 1.0.102 to 1.0.103 in /Site Bumps @veupathdb/genomics-site from 1.0.102 to 1.0.103. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 85b4be7a9..0993740e0 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.102" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.102.tgz#1e9d5fc7c46308cd8447cef5e40e5f0b749fc6d3" - integrity sha512-lLDU/KFg0Aeq8v/FSSVm9xZBshSNSCOldXRmd1TAW4NZUY+8cbiSqFoSFqW3E5GuBchN/5l3TL2ttH088paOmQ== + version "1.0.103" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.103.tgz#8f8782321f76f7693a3e4cf20c43b7151757888d" + integrity sha512-wjpioNgS3kl0/5s5LVnViPLWsW3RMfiBeOi9CctEjvCedv+/GacgARKEWbPqY6JcVwXnzmofh9gNfjfy6sKxsQ== From 11a75f92b71f7452335b988aa430bfdb494d53f1 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 14 Dec 2023 23:14:26 -0500 Subject: [PATCH 087/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 0993740e0..ede26dfc4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.103" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.103.tgz#8f8782321f76f7693a3e4cf20c43b7151757888d" - integrity sha512-wjpioNgS3kl0/5s5LVnViPLWsW3RMfiBeOi9CctEjvCedv+/GacgARKEWbPqY6JcVwXnzmofh9gNfjfy6sKxsQ== + version "1.0.104" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.104.tgz#901f805199e78dd3915b911d3613a0df556b9837" + integrity sha512-rKdzb3Uv5pHIUc9m0vDcuC4QwPt7K6kp70SEzxR+1SUinU7WUXsGgeudfbriKwS7wnIX6YWR2dVWILr5TblsyA== From 9e10005ae113d29eb3346f0ca0b26b6a5bf460d2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 19 Dec 2023 04:43:32 +0000 Subject: [PATCH 088/204] npm: bump @veupathdb/genomics-site from 1.0.104 to 1.0.105 in /Site Bumps @veupathdb/genomics-site from 1.0.104 to 1.0.105. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index ede26dfc4..aa462ce53 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.104" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.104.tgz#901f805199e78dd3915b911d3613a0df556b9837" - integrity sha512-rKdzb3Uv5pHIUc9m0vDcuC4QwPt7K6kp70SEzxR+1SUinU7WUXsGgeudfbriKwS7wnIX6YWR2dVWILr5TblsyA== + version "1.0.105" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.105.tgz#5735293f020906fc59a0b6146b882c2985b83c69" + integrity sha512-1QEmYX2gB+2/zdtEnIk8pNscLbvR/x+ZUpQFg5Uh1IEqxUg4FIOD5cjZ7VD46nhy5VoYxdGA4JaHN6qDf0YyEQ== From 5761e9bb08eb564691622fa73c9f3b65a0b1335b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 3 Jan 2024 23:28:03 -0500 Subject: [PATCH 089/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index aa462ce53..4477e527d 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.105" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.105.tgz#5735293f020906fc59a0b6146b882c2985b83c69" - integrity sha512-1QEmYX2gB+2/zdtEnIk8pNscLbvR/x+ZUpQFg5Uh1IEqxUg4FIOD5cjZ7VD46nhy5VoYxdGA4JaHN6qDf0YyEQ== + version "1.0.106" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.106.tgz#6cc4da6598f0169c289a1b8eb71fc095dd546972" + integrity sha512-UfwhshzlICSxERY2UzESdyyB9gXSuMzAG1ByfWgXl8VDXugJKyWYNpJ9Ym6T0TvuTxbv6iVj6xmjbrDMNYk2Jw== From 5fa75b74ac37b931d8b9d5aa677104502603770d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Jan 2024 04:28:48 +0000 Subject: [PATCH 090/204] npm: bump @veupathdb/genomics-site from 1.0.106 to 1.0.107 in /Site Bumps @veupathdb/genomics-site from 1.0.106 to 1.0.107. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4477e527d..5ce78ece2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.106" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.106.tgz#6cc4da6598f0169c289a1b8eb71fc095dd546972" - integrity sha512-UfwhshzlICSxERY2UzESdyyB9gXSuMzAG1ByfWgXl8VDXugJKyWYNpJ9Ym6T0TvuTxbv6iVj6xmjbrDMNYk2Jw== + version "1.0.107" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.107.tgz#20656a5c051cd60ce5443f63e0cd1687b5bf4c87" + integrity sha512-0iGwAc8YHmj4mvWA0wSQCzAlGHZC6YdS+istdCjz9nMnrFyFcR+6FiJE/xa05jjphQZGz6OtZ68afW/JXI6jvA== From 1ea9e1a1ff732baca15d4013c6aa50865a2f0d72 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 16 Jan 2024 23:28:54 -0500 Subject: [PATCH 091/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 5ce78ece2..d18d86f72 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.107" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.107.tgz#20656a5c051cd60ce5443f63e0cd1687b5bf4c87" - integrity sha512-0iGwAc8YHmj4mvWA0wSQCzAlGHZC6YdS+istdCjz9nMnrFyFcR+6FiJE/xa05jjphQZGz6OtZ68afW/JXI6jvA== + version "1.0.108" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.108.tgz#af65ab39a6b4698ca6aef1646441eeaf6048f0b6" + integrity sha512-MWike7HyiCY5kBH+NgAYiX58Xg8iIxO4h2CdciP+lH2CZDxfxgscwWiERdeiZTTkloSTZvBQ3OLzWJL/mfa60w== From 2e8c4f6edefa6c812772e239c92dc3a54717958f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 24 Jan 2024 04:55:47 +0000 Subject: [PATCH 092/204] npm: bump @veupathdb/genomics-site from 1.0.108 to 1.0.109 in /Site Bumps @veupathdb/genomics-site from 1.0.108 to 1.0.109. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index d18d86f72..9bab532b4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.108" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.108.tgz#af65ab39a6b4698ca6aef1646441eeaf6048f0b6" - integrity sha512-MWike7HyiCY5kBH+NgAYiX58Xg8iIxO4h2CdciP+lH2CZDxfxgscwWiERdeiZTTkloSTZvBQ3OLzWJL/mfa60w== + version "1.0.109" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.109.tgz#855e7262b61daccd2e16979fe951885127de069c" + integrity sha512-mrRTL59eN/SS4X9B5sH8GFmeY+CPbKMWXAiKo6xfb2KlJaBD22njx0s8DjBddtYsAkWBYgRtQmd/dVypiSdCKQ== From 2773d941cc1c94259df1cf8795b80e6df6eb0284 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Jan 2024 04:18:21 +0000 Subject: [PATCH 093/204] npm: bump @veupathdb/genomics-site from 1.0.109 to 1.0.110 in /Site Bumps @veupathdb/genomics-site from 1.0.109 to 1.0.110. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 9bab532b4..c804e631a 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.109" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.109.tgz#855e7262b61daccd2e16979fe951885127de069c" - integrity sha512-mrRTL59eN/SS4X9B5sH8GFmeY+CPbKMWXAiKo6xfb2KlJaBD22njx0s8DjBddtYsAkWBYgRtQmd/dVypiSdCKQ== + version "1.0.110" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.110.tgz#5ac7d7aa1f06514878de824c94ca2146e9fdaf8a" + integrity sha512-b7CDPTfJghZdh02HXYlp1QnWvAsGD0I6yUMeJuRaBYZGE41r3N+M9KjjNBx85abxd+kPVopIcb9N2KlNN+XXdg== From 3edbbbb3fa951d4ebac5d8de55de741a78e1a57e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 3 Feb 2024 04:54:33 +0000 Subject: [PATCH 094/204] npm: bump @veupathdb/genomics-site from 1.0.110 to 1.0.111 in /Site Bumps @veupathdb/genomics-site from 1.0.110 to 1.0.111. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index c804e631a..6d13328e3 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.110" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.110.tgz#5ac7d7aa1f06514878de824c94ca2146e9fdaf8a" - integrity sha512-b7CDPTfJghZdh02HXYlp1QnWvAsGD0I6yUMeJuRaBYZGE41r3N+M9KjjNBx85abxd+kPVopIcb9N2KlNN+XXdg== + version "1.0.111" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.111.tgz#a9cd4de3abc047a0fbbe18e9ae33e64ceddd7e75" + integrity sha512-blZHRVBrc/QO4GqUwalRxWa6pkHWv2fSBUzIiAI7B5BDcXY8UAA2whF2aH9bG40dq8bMkPVr0/61BAd2MBdm0w== From d8fa057ddb494016159f1aa7e0d3e4dba7d33ace Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 7 Feb 2024 04:07:05 +0000 Subject: [PATCH 095/204] npm: bump @veupathdb/genomics-site from 1.0.111 to 1.0.112 in /Site Bumps @veupathdb/genomics-site from 1.0.111 to 1.0.112. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6d13328e3..3caa401af 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.111" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.111.tgz#a9cd4de3abc047a0fbbe18e9ae33e64ceddd7e75" - integrity sha512-blZHRVBrc/QO4GqUwalRxWa6pkHWv2fSBUzIiAI7B5BDcXY8UAA2whF2aH9bG40dq8bMkPVr0/61BAd2MBdm0w== + version "1.0.112" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.112.tgz#2105b963b21e81a83dba9f82e4a39e5150c23e6e" + integrity sha512-8y6qRVjB8qu6PCaR76i3od1FkeiAn3myMaRNdXyLcEVwyAJGFAnNF3I7LXkm1fr0+4z/nscOHHnCJgCTJQsJWQ== From a54b8db98cdfea99515a8917b112369bae94c4a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 04:17:44 +0000 Subject: [PATCH 096/204] npm: bump @veupathdb/genomics-site from 1.0.112 to 1.0.113 in /Site Bumps @veupathdb/genomics-site from 1.0.112 to 1.0.113. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 3caa401af..7e3545004 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.112" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.112.tgz#2105b963b21e81a83dba9f82e4a39e5150c23e6e" - integrity sha512-8y6qRVjB8qu6PCaR76i3od1FkeiAn3myMaRNdXyLcEVwyAJGFAnNF3I7LXkm1fr0+4z/nscOHHnCJgCTJQsJWQ== + version "1.0.113" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.113.tgz#072f61a8f68965b81f5c38b1a3c91befcec4338e" + integrity sha512-S2L/jkUm8x/OB8l2Ekui8VzegpoYdAbtD+PsNAqLMAIp4kgOZg8ZJtw39R9nBkNoJyBXdWspoogac7Dev+UNdQ== From 6891139b4b8d6238211b236bd7e50aec4e934d43 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 13 Feb 2024 23:52:19 -0500 Subject: [PATCH 097/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7e3545004..54b44bafe 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.113" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.113.tgz#072f61a8f68965b81f5c38b1a3c91befcec4338e" - integrity sha512-S2L/jkUm8x/OB8l2Ekui8VzegpoYdAbtD+PsNAqLMAIp4kgOZg8ZJtw39R9nBkNoJyBXdWspoogac7Dev+UNdQ== + version "1.0.114" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.114.tgz#60e18c72235fa0abf029e14754cdad54cbaaa670" + integrity sha512-+MJbZTjnYPwqNRNwr57yeY5PRDS75PLNv/79D+LWM/kEDNyxXk9ZraEWWllK0BwO/wj3m2Cn73Riuu38vvujeQ== From a6881f5dc7cc9d8b5f8d6e4feaa7b56024d0c030 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 15 Feb 2024 23:16:05 -0500 Subject: [PATCH 098/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 54b44bafe..e52765820 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.114" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.114.tgz#60e18c72235fa0abf029e14754cdad54cbaaa670" - integrity sha512-+MJbZTjnYPwqNRNwr57yeY5PRDS75PLNv/79D+LWM/kEDNyxXk9ZraEWWllK0BwO/wj3m2Cn73Riuu38vvujeQ== + version "1.0.116" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.116.tgz#1330bd9954343e177b1bd8c41efd4938f2affbe9" + integrity sha512-EP/j+ONcCrTEDIMA5lgDPjyO6/is2WdVhiMsQOU3HNk1/LcHrXk+U4hlhtDxZH0/CZpBA2ZWkvnPoMUgmmea3A== From 5e67da91ab06887a1bf492575bfafc89b96c1e9e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 16 Feb 2024 09:50:41 -0500 Subject: [PATCH 099/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index e52765820..6aab60790 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.116" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.116.tgz#1330bd9954343e177b1bd8c41efd4938f2affbe9" - integrity sha512-EP/j+ONcCrTEDIMA5lgDPjyO6/is2WdVhiMsQOU3HNk1/LcHrXk+U4hlhtDxZH0/CZpBA2ZWkvnPoMUgmmea3A== + version "1.0.117" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.117.tgz#7e73070a3321c88deff352ce26fde446374c040a" + integrity sha512-6jIppUt50EbwKdJMjHCg2731iS8XXuRtFN4Fw4NVPoCdtpwFPeFyklKkCosT6QUNLvv8YJoKGuAX9XZ5aex+PQ== From 9803c565931995650cd1903c97a607d9d7d39833 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 17 Feb 2024 04:17:27 +0000 Subject: [PATCH 100/204] npm: bump @veupathdb/genomics-site from 1.0.117 to 1.0.118 in /Site Bumps @veupathdb/genomics-site from 1.0.117 to 1.0.118. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6aab60790..43c60893e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.117" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.117.tgz#7e73070a3321c88deff352ce26fde446374c040a" - integrity sha512-6jIppUt50EbwKdJMjHCg2731iS8XXuRtFN4Fw4NVPoCdtpwFPeFyklKkCosT6QUNLvv8YJoKGuAX9XZ5aex+PQ== + version "1.0.118" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.118.tgz#b597bf9eb4737c81c776093200a3a44486149a5a" + integrity sha512-ARnOnp48O+dlHZIp0+f+teLYNC4h+ihF+UmJwftlZbxB0iJ7FtM3WVkOUzzQqQS0rNyhqLDj9KZyQJR1lrrLLw== From 9b31ec40d31e6ffe08607f16da2643295bbd8fdf Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Mon, 19 Feb 2024 09:33:43 -0500 Subject: [PATCH 101/204] only use one : in defline --- .../report/bed/feature/GenomicTableFieldFeatureProvider.java | 2 +- .../report/bed/feature/ProteinInterproFeatureProvider.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GenomicTableFieldFeatureProvider.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GenomicTableFieldFeatureProvider.java index 98b9cdc3c..c4c46b137 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GenomicTableFieldFeatureProvider.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GenomicTableFieldFeatureProvider.java @@ -43,7 +43,7 @@ protected List createFeatureRow(RecordInstance record, Map> getRecordAsBedFields(RecordInstance record) throws Wdk */ for (String transcriptId : interproRow.get("transcript_ids").toString().split(", ")){ String chrom = transcriptId; - DeflineBuilder defline = new DeflineBuilder(chrom + "::" + segmentStart + "-" + segmentEnd); + DeflineBuilder defline = new DeflineBuilder(chrom + ":" + segmentStart + "-" + segmentEnd); if(_requestedDeflineFields.contains("organism")){ defline.appendRecordAttribute(record, ATTR_ORGANISM); } From b4777c84745f224264227251fec7cf6b3897897b Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 19 Feb 2024 17:46:49 -0500 Subject: [PATCH 102/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 43c60893e..1263d23a1 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.118" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.118.tgz#b597bf9eb4737c81c776093200a3a44486149a5a" - integrity sha512-ARnOnp48O+dlHZIp0+f+teLYNC4h+ihF+UmJwftlZbxB0iJ7FtM3WVkOUzzQqQS0rNyhqLDj9KZyQJR1lrrLLw== + version "1.0.119" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.119.tgz#9afb89ea3c24986cc56c8258a552b55d30b74841" + integrity sha512-K+58bh5Nmy1bRU9irFvZHNwMHUfoAq/ZPVmxKf+RntRoaawaN4Tlvi0A30yBMQErVG5izPu41AMHcNMo2oovJQ== From b92159ff764d7ea779d9116b1960c2df872d0d18 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 20 Feb 2024 16:53:08 -0500 Subject: [PATCH 103/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 1263d23a1..84f29ca11 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.119" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.119.tgz#9afb89ea3c24986cc56c8258a552b55d30b74841" - integrity sha512-K+58bh5Nmy1bRU9irFvZHNwMHUfoAq/ZPVmxKf+RntRoaawaN4Tlvi0A30yBMQErVG5izPu41AMHcNMo2oovJQ== + version "1.0.120" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.120.tgz#3f4b3ab757e6f88b3502468c28657a50f83a0301" + integrity sha512-UwZA/zMXG213T28fEpYQlfjGdZQZKrCHbXuNwdlayM0ptNEVxC5dDgIZuDEZ1wyaP6DJWh06YT6k5XktBXymMQ== From 80ea9c4afcc329690c292653804a859566fb86b6 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 22 Feb 2024 15:21:01 -0500 Subject: [PATCH 104/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 84f29ca11..0e64ca8db 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.120" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.120.tgz#3f4b3ab757e6f88b3502468c28657a50f83a0301" - integrity sha512-UwZA/zMXG213T28fEpYQlfjGdZQZKrCHbXuNwdlayM0ptNEVxC5dDgIZuDEZ1wyaP6DJWh06YT6k5XktBXymMQ== + version "1.0.121" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.121.tgz#b6444d0c278aec38e98113a8413d17d26ce4e89b" + integrity sha512-9w3Swl36fu/zgLyDR+EJSWNf9ogRa82Rno+QHD4jT4EKU4L0x3s6NNxqCWNBkxOgmMycJSo5efcAQP67RNsF1A== From 10deb9fb80160264064e05ef06945ef270c6da92 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 22 Feb 2024 15:24:55 -0500 Subject: [PATCH 105/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 0e64ca8db..43dfa9d7b 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.121" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.121.tgz#b6444d0c278aec38e98113a8413d17d26ce4e89b" - integrity sha512-9w3Swl36fu/zgLyDR+EJSWNf9ogRa82Rno+QHD4jT4EKU4L0x3s6NNxqCWNBkxOgmMycJSo5efcAQP67RNsF1A== + version "1.0.122" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.122.tgz#ab8cb7dac2a79d90b839edb2da96e8d968fb16dc" + integrity sha512-9xRW9D7jVwNy+ZXjkKPt+Kt0DNEXTZvYeXOPqCh3lAsVWwuYwkGFyZqFG9DxzABF3n0mN4NiSvvcra/bToT77A== From 8b8f8574f92c3222351e513c0c4bd64f9e97eb62 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 22 Feb 2024 15:56:18 -0500 Subject: [PATCH 106/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 43dfa9d7b..051dfd473 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.122" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.122.tgz#ab8cb7dac2a79d90b839edb2da96e8d968fb16dc" - integrity sha512-9xRW9D7jVwNy+ZXjkKPt+Kt0DNEXTZvYeXOPqCh3lAsVWwuYwkGFyZqFG9DxzABF3n0mN4NiSvvcra/bToT77A== + version "1.0.123" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.123.tgz#e42e7c7d297f56ea57bdb22e781f1112ec635214" + integrity sha512-uZBXS7+CIvqs5akJPAKtwkcX/e0FzhxXI8awK4gOVI6QHwsgONjWyP7yGOq1+zoususXWWA0dI+IOtRt2ExFgw== From c3adc212d6c365ae06617f24b284f5f330d7dfec Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 24 Feb 2024 04:05:27 +0000 Subject: [PATCH 107/204] npm: bump @veupathdb/genomics-site from 1.0.123 to 1.0.124 in /Site Bumps @veupathdb/genomics-site from 1.0.123 to 1.0.124. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 051dfd473..da1fa0bb4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.123" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.123.tgz#e42e7c7d297f56ea57bdb22e781f1112ec635214" - integrity sha512-uZBXS7+CIvqs5akJPAKtwkcX/e0FzhxXI8awK4gOVI6QHwsgONjWyP7yGOq1+zoususXWWA0dI+IOtRt2ExFgw== + version "1.0.124" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.124.tgz#12a92e6bce637bcba87e69bffd5aa2e59b86f961" + integrity sha512-78NfJmneRx0LKGzSEeo2DQgl/7VC/S671kaEVpKvLBIjN12ozVfuHr5vVPRVcSXwVG5BSR+GIOQPuexeqsuJuQ== From 81ff5d77c858c695247b8fba0705589d31454281 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Tue, 27 Feb 2024 16:45:53 -0500 Subject: [PATCH 108/204] API changes to support bearer tokens --- .../apicommon/controller/ApiSiteSetup.java | 25 ++++--- .../comment/CommentAlertEmailFormatter.java | 6 +- .../model/comment/CommentFactory.java | 66 +++++++++++++++---- .../apicommon/model/comment/pojo/Author.java | 10 ++- .../comment/repo/InsertCommentQuery.java | 10 +-- .../test/SingleTableRecordStreamTest.java | 3 +- .../service/services/ApiBasketService.java | 2 +- .../service/services/ApiProjectService.java | 2 +- .../services/OrganismMetricsService.java | 2 +- .../services/TranscriptToggleService.java | 2 +- .../comments/AbstractUserCommentService.java | 11 ++-- .../jbrowse/JBrowseUserDatasetsService.java | 2 +- 12 files changed, 88 insertions(+), 53 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/controller/ApiSiteSetup.java b/Model/src/main/java/org/apidb/apicommon/controller/ApiSiteSetup.java index 91fe21d28..1d5e20732 100644 --- a/Model/src/main/java/org/apidb/apicommon/controller/ApiSiteSetup.java +++ b/Model/src/main/java/org/apidb/apicommon/controller/ApiSiteSetup.java @@ -1,12 +1,11 @@ package org.apidb.apicommon.controller; -import java.util.Map; - import org.apidb.apicommon.model.comment.CommentFactory; import org.apidb.apicommon.model.comment.pojo.Author; -import org.gusdb.fgputil.accountdb.UserProfile; import org.gusdb.fgputil.events.Event; import org.gusdb.fgputil.events.Events; +import org.gusdb.oauth2.client.veupathdb.User; +import org.gusdb.oauth2.client.veupathdb.UserProperty; import org.gusdb.wdk.events.UserProfileUpdateEvent; import org.gusdb.wdk.model.WdkModel; import org.gusdb.wdk.model.WdkModelException; @@ -36,13 +35,11 @@ private static void userProfileUpdateListener(Event event) UserProfileUpdateEvent updateEvent = (UserProfileUpdateEvent) event; // check to see if any of the property text fields changed - Map userProps = updateEvent.getNewProfile().getProperties(); - Map oldProfileProps = updateEvent.getOldProfile() - .getProperties(); boolean commentSearchTextUpdateRequired = false; - - for (String key : oldProfileProps.keySet()) { - if (!oldProfileProps.get(key).equals(userProps.get(key))) { + String[] commentProps = new String[] { "firstName", "lastName", "organization" }; + for (String key : commentProps) { + UserProperty prop = User.USER_PROPERTIES.get(key); + if (!prop.getValue(updateEvent.getOldUser()).equals(prop.getValue(updateEvent.getNewUser()))) { commentSearchTextUpdateRequired = true; } } @@ -54,12 +51,12 @@ private static void userProfileUpdateListener(Event event) // need to write updated text to comment search field CommentFactory commentFactory = CommentFactoryManager.getCommentFactory( updateEvent.getWdkModel().getProjectId()); - UserProfile profile = updateEvent.getNewProfile(); + User user = updateEvent.getNewUser(); commentFactory.updateAuthor(new Author() - .setFirstName(profile.getProperties().get("firstName")) - .setLastName(profile.getProperties().get("lastName")) - .setOrganization(profile.getProperties().get("organization")) - .setUserId(profile.getUserId())); + .setFirstName(user.getFirstName()) + .setLastName(user.getLastName()) + .setOrganization(user.getOrganization()) + .setUserId(user.getUserId())); } } diff --git a/Model/src/main/java/org/apidb/apicommon/model/comment/CommentAlertEmailFormatter.java b/Model/src/main/java/org/apidb/apicommon/model/comment/CommentAlertEmailFormatter.java index 6463070f1..1abed42dc 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/comment/CommentAlertEmailFormatter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/comment/CommentAlertEmailFormatter.java @@ -1,14 +1,14 @@ package org.apidb.apicommon.model.comment; +import java.util.Collection; +import java.util.stream.Collectors; + import org.apidb.apicommon.model.comment.pojo.CommentRequest; import org.apidb.apicommon.model.comment.pojo.ExternalDatabase; import org.gusdb.fgputil.FormatUtil; import org.gusdb.wdk.model.WdkModel; import org.gusdb.wdk.model.user.User; -import java.util.Collection; -import java.util.stream.Collectors; - public class CommentAlertEmailFormatter { private static final String FIELD_COMMENT_ID = "Comment Id", diff --git a/Model/src/main/java/org/apidb/apicommon/model/comment/CommentFactory.java b/Model/src/main/java/org/apidb/apicommon/model/comment/CommentFactory.java index 34af7306f..038db2b17 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/comment/CommentFactory.java +++ b/Model/src/main/java/org/apidb/apicommon/model/comment/CommentFactory.java @@ -1,28 +1,66 @@ package org.apidb.apicommon.model.comment; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.ObjectMapper; -import org.apidb.apicommon.model.comment.pojo.*; -import org.apidb.apicommon.model.comment.repo.*; -import org.gusdb.fgputil.db.pool.DatabaseInstance; -import org.gusdb.fgputil.runtime.InstanceManager; -import org.gusdb.fgputil.runtime.Manageable; -import org.gusdb.wdk.model.WdkModel; -import org.gusdb.wdk.model.WdkModelException; -import org.gusdb.wdk.model.config.ModelConfigUserDB; -import org.gusdb.wdk.model.user.User; +import static org.apidb.apicommon.model.comment.ReferenceType.ACCESSION; +import static org.apidb.apicommon.model.comment.ReferenceType.AUTHOR; +import static org.apidb.apicommon.model.comment.ReferenceType.DIGITAL_OBJECT_ID; +import static org.apidb.apicommon.model.comment.ReferenceType.PUB_MED; -import javax.sql.DataSource; import java.io.IOException; import java.net.URL; import java.sql.Connection; import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.Optional; +import java.util.Set; + +import javax.sql.DataSource; + +import org.apidb.apicommon.model.comment.pojo.Attachment; +import org.apidb.apicommon.model.comment.pojo.Author; +import org.apidb.apicommon.model.comment.pojo.Category; +import org.apidb.apicommon.model.comment.pojo.Comment; +import org.apidb.apicommon.model.comment.pojo.CommentRequest; +import org.apidb.apicommon.model.comment.pojo.ExternalDatabase; +import org.apidb.apicommon.model.comment.pojo.Project; +import org.apidb.apicommon.model.comment.pojo.PubMedReference; +import org.apidb.apicommon.model.comment.repo.DeleteAttachmentQuery; +import org.apidb.apicommon.model.comment.repo.FindCommentQuery; +import org.apidb.apicommon.model.comment.repo.GetAllAttachmentsQuery; +import org.apidb.apicommon.model.comment.repo.GetAttachmentQuery; +import org.apidb.apicommon.model.comment.repo.GetAuthorQuery; +import org.apidb.apicommon.model.comment.repo.GetCategoriesQuery; +import org.apidb.apicommon.model.comment.repo.GetCommentExistsQuery; +import org.apidb.apicommon.model.comment.repo.GetCommentQuery; +import org.apidb.apicommon.model.comment.repo.GetExternalDatabaseQuery; +import org.apidb.apicommon.model.comment.repo.HideCommentQuery; +import org.apidb.apicommon.model.comment.repo.InsertAttachmentQuery; +import org.apidb.apicommon.model.comment.repo.InsertAuthorQuery; +import org.apidb.apicommon.model.comment.repo.InsertCategoryQuery; +import org.apidb.apicommon.model.comment.repo.InsertCommentQuery; +import org.apidb.apicommon.model.comment.repo.InsertExternalDatabaseLinkQuery; +import org.apidb.apicommon.model.comment.repo.InsertExternalDatabaseQuery; +import org.apidb.apicommon.model.comment.repo.InsertLocationQuery; +import org.apidb.apicommon.model.comment.repo.InsertReferencesQuery; +import org.apidb.apicommon.model.comment.repo.InsertSequenceQuery; +import org.apidb.apicommon.model.comment.repo.InsertStableIdQuery; +import org.apidb.apicommon.model.comment.repo.Table; +import org.apidb.apicommon.model.comment.repo.UpdateAttachmentQuery; +import org.apidb.apicommon.model.comment.repo.UpdateAuthorQuery; import org.eupathdb.sitesearch.data.comments.UserCommentUpdater; +import org.gusdb.fgputil.db.pool.DatabaseInstance; +import org.gusdb.fgputil.runtime.InstanceManager; +import org.gusdb.fgputil.runtime.Manageable; +import org.gusdb.wdk.model.WdkModel; +import org.gusdb.wdk.model.WdkModelException; +import org.gusdb.wdk.model.config.ModelConfigUserDB; +import org.gusdb.wdk.model.user.User; -import static org.apidb.apicommon.model.comment.ReferenceType.*; +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; /** * Manages user comments on WDK records diff --git a/Model/src/main/java/org/apidb/apicommon/model/comment/pojo/Author.java b/Model/src/main/java/org/apidb/apicommon/model/comment/pojo/Author.java index fa72c35df..660a45d3a 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/comment/pojo/Author.java +++ b/Model/src/main/java/org/apidb/apicommon/model/comment/pojo/Author.java @@ -2,9 +2,8 @@ import org.gusdb.wdk.model.user.User; -import java.util.Map; - public class Author { + private String _firstName; private String _lastName; @@ -50,11 +49,10 @@ public Author setUserId(long userId) { } public static Author fromUser(final User user) { - final Map props = user.getProfileProperties(); return new Author() .setUserId(user.getUserId()) - .setFirstName(props.get("firstName")) - .setLastName(props.get("lastName")) - .setOrganization(props.get("organization")); + .setFirstName(user.getFirstName()) + .setLastName(user.getLastName()) + .setOrganization(user.getOrganization()); } } diff --git a/Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java b/Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java index edfe4be01..86842284a 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java +++ b/Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java @@ -1,5 +1,11 @@ package org.apidb.apicommon.model.comment.repo; +import static java.sql.Types.BIGINT; +import static java.sql.Types.CLOB; +import static java.sql.Types.VARCHAR; + +import java.io.StringReader; + import org.apidb.apicommon.model.comment.ReviewStatus; import org.apidb.apicommon.model.comment.pojo.CommentRequest; import org.apidb.apicommon.model.comment.pojo.Project; @@ -7,10 +13,6 @@ import org.gusdb.fgputil.db.runner.SQLRunner; import org.gusdb.wdk.model.user.User; -import java.io.StringReader; - -import static java.sql.Types.*; - /** * Insert a new comment record. */ diff --git a/Model/src/main/java/org/apidb/apicommon/test/SingleTableRecordStreamTest.java b/Model/src/main/java/org/apidb/apicommon/test/SingleTableRecordStreamTest.java index bb70274ff..fb3aa7f5c 100644 --- a/Model/src/main/java/org/apidb/apicommon/test/SingleTableRecordStreamTest.java +++ b/Model/src/main/java/org/apidb/apicommon/test/SingleTableRecordStreamTest.java @@ -30,7 +30,6 @@ import org.gusdb.wdk.model.record.attribute.AttributeField; import org.gusdb.wdk.model.record.attribute.AttributeValue; import org.gusdb.wdk.model.user.Step; -import org.gusdb.wdk.model.user.UnregisteredUser.UnregisteredUserType; import org.gusdb.wdk.model.user.User; import org.gusdb.wdk.model.user.UserCache; import org.json.JSONObject; @@ -105,7 +104,7 @@ public static void main(String[] args) throws Exception { /*%%%%%%%%%%%%%%%%%%%%%%%%%%% helper functions %%%%%%%%%%%%%%%%%%%%%%%%%%%*/ private static RunnableObj createStep(WdkModel model) throws WdkModelException { - User user = model.getUserFactory().createUnregistedUser(UnregisteredUserType.GUEST); + User user = model.getSystemUser(); return Step.builder(model, user.getUserId(), model.getStepFactory().getNewStepId()) .setAnswerSpec(AnswerSpec.builder(model) .setQuestionFullName(QUESTION_NAME) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/ApiBasketService.java b/Service/src/main/java/org/apidb/apicommon/service/services/ApiBasketService.java index a841c5bf3..4cb42b9a8 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/ApiBasketService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/ApiBasketService.java @@ -86,7 +86,7 @@ protected RevisedRequest translatePatchRequest( return new RevisedRequest<>( getTranscriptRecordClass(getWdkModel()), new BasketActions(actions.getAction(), Collections.emptyList()) - .setRunnableAnswerSpec(newSpec.buildRunnable(getSessionUser(), step.get().getContainer()))); + .setRunnableAnswerSpec(newSpec.buildRunnable(getRequestingUser(), step.get().getContainer()))); } // translate IDs to gene PKs if necessary diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/ApiProjectService.java b/Service/src/main/java/org/apidb/apicommon/service/services/ApiProjectService.java index 87a277bf1..b52a780f8 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/ApiProjectService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/ApiProjectService.java @@ -41,7 +41,7 @@ protected JSONObject addSupplementalProjectInfo(JSONObject projectJson) throws W // get all organisms in vocabulary of org param of taxon question Question taxonQuestion = model.getQuestionByName(TAXON_QUESTION_NAME).get(); DisplayablyValid spec = QuestionService.getDisplayableAnswerSpec( - TAXON_QUESTION_NAME, model, getSessionUser(), name -> taxonQuestion); + TAXON_QUESTION_NAME, model, getRequestingUser(), name -> taxonQuestion); AbstractEnumParam orgParam = (AbstractEnumParam)taxonQuestion.getParamMap().get(ORGANISM_PARAM_NAME); List organisms = orgParam.getVocabInstance(AnswerSpec.getValidQueryInstanceSpec(spec)).getVocabTreeLeafTerms(); diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java b/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java index b0e63d166..315b21aad 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java @@ -110,7 +110,7 @@ private String resolveOrganism(String recordClassUrlSegment, String primaryKeyVa throw new BadRequestException("Record type with url segment '" + recordClassUrlSegment + "' does not contain an '" + ORGANISM_ATTRIBUTE + "' attribute."); } PrimaryKeyValue pkValue = getPkValue(recordClass, primaryKeyValues); - List records = RecordClass.getRecordInstances(getSessionUser(), pkValue); + List records = RecordClass.getRecordInstances(getRequestingUser(), pkValue); if (records.isEmpty()) { throw new BadRequestException("Primary Key '" + primaryKeyValues + "' does not map to any records of type '" + recordClassUrlSegment + "'."); } diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/TranscriptToggleService.java b/Service/src/main/java/org/apidb/apicommon/service/services/TranscriptToggleService.java index 4fb689e39..f8949612a 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/TranscriptToggleService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/TranscriptToggleService.java @@ -36,7 +36,7 @@ public void setTranscriptFlag(@PathParam("stepId") Integer stepId, String body) LOG.info("Action is to turn filter: " + filterTurnedOn); Step step = getWdkModel().getStepFactory().getStepByIdAndUserId( - stepId, getSessionUser().getUserId(), ValidationLevel.SYNTACTIC) + stepId, getRequestingUser().getUserId(), ValidationLevel.SYNTACTIC) .orElseThrow(() -> new NotFoundException("No step exists with ID " + stepId)); AnswerSpecBuilder newSpec = AnswerSpec.builder(step.getAnswerSpec()); diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/comments/AbstractUserCommentService.java b/Service/src/main/java/org/apidb/apicommon/service/services/comments/AbstractUserCommentService.java index 177df6cdf..11b1fa96d 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/comments/AbstractUserCommentService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/comments/AbstractUserCommentService.java @@ -1,5 +1,10 @@ package org.apidb.apicommon.service.services.comments; +import java.util.function.Supplier; + +import javax.ws.rs.NotAuthorizedException; +import javax.ws.rs.NotFoundException; + import org.apidb.apicommon.controller.CommentFactoryManager; import org.apidb.apicommon.model.comment.CommentFactory; import org.apidb.apicommon.model.comment.pojo.Comment; @@ -7,17 +12,13 @@ import org.gusdb.wdk.model.user.User; import org.gusdb.wdk.service.service.AbstractWdkService; -import javax.ws.rs.NotAuthorizedException; -import javax.ws.rs.NotFoundException; -import java.util.function.Supplier; - public abstract class AbstractUserCommentService extends AbstractWdkService { protected CommentFactory getCommentFactory() { return CommentFactoryManager.getCommentFactory(getWdkModel().getProjectId()); } protected User fetchUser() { - final User out = getSessionUser(); + final User out = getRequestingUser(); if (out.isGuest()) throw new NotAuthorizedException("you must login before performing this action"); return out; diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java index 33a416e17..65c83e6d2 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java @@ -55,7 +55,7 @@ public JSONObject getAllUserDatasetsJBrowse(@PathParam("organism") String public catch (Exception e) { tracks = new JSONArray(); Exception e2 = new WdkModelException("Unable to load JBrowse user datasets for user with ID " + - getSessionUser().getUserId() + ", organism " + publicOrganismAbbrev, e); + getRequestingUser().getUserId() + ", organism " + publicOrganismAbbrev, e); LOG.error("Could not load JBrowse user datasets", e2); Events.trigger(new ErrorEvent(new ServerErrorBundle(e2), getErrorContext(ErrorLocation.WDK_SERVICE))); } From 65bf6e730f1b7cae24c7d91c784958ed17080e87 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 1 Mar 2024 04:50:15 +0000 Subject: [PATCH 109/204] npm: bump @veupathdb/genomics-site from 1.0.124 to 1.0.125 in /Site Bumps @veupathdb/genomics-site from 1.0.124 to 1.0.125. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index da1fa0bb4..2bd445f08 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.124" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.124.tgz#12a92e6bce637bcba87e69bffd5aa2e59b86f961" - integrity sha512-78NfJmneRx0LKGzSEeo2DQgl/7VC/S671kaEVpKvLBIjN12ozVfuHr5vVPRVcSXwVG5BSR+GIOQPuexeqsuJuQ== + version "1.0.125" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.125.tgz#b25c5a1bb78b7615e53fb47ebcc4748b93827833" + integrity sha512-itwf4VyvlZ7LFm08yIi0rJ1N55p9vFgT6W38z/yqP+JBKZ47ai5bjuELuJOt0NvzNeH5Pa3CLvfk3MSH2v6O6Q== From 14e6e721fe4332362c2f9711390ce15947191032 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 5 Mar 2024 15:39:44 -0500 Subject: [PATCH 110/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2bd445f08..53b23839f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.125" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.125.tgz#b25c5a1bb78b7615e53fb47ebcc4748b93827833" - integrity sha512-itwf4VyvlZ7LFm08yIi0rJ1N55p9vFgT6W38z/yqP+JBKZ47ai5bjuELuJOt0NvzNeH5Pa3CLvfk3MSH2v6O6Q== + version "1.0.126" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.126.tgz#8a3432006b0aefc8b5e604ad4df338c52ca7fb41" + integrity sha512-Se4+KAi4bWyDMcYqBKJf70r/aVf5uV8AoJJ+VJfXztqLayEiRhz92Eis8zC8cWX/r0kAAE5YlUXHCKm67J8LmA== From 76f40aef10d65606951f6864cd29cc82f19248ed Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 12 Mar 2024 14:32:27 -0400 Subject: [PATCH 111/204] use coding start/end explicitly, instead of trying to calculate it. - refs #53727 --- .../feature/GeneGenomicFeatureProvider.java | 22 ++++++++++++------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java index a4884e1fe..46f9decab 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java @@ -31,6 +31,8 @@ private enum Anchor { private static final Pattern LOCATION_TEXT_PATTERN = Pattern.compile("^(.*):(\\d+)..(\\d+)\\((\\+|-)\\)$"); private static final String ATTR_LOCATION_TEXT = "location_text"; + private static final String ATTR_CODING_START = "coding_start"; + private static final String ATTR_CODING_END = "coding_end"; private static final String ATTR_THREE_PRIME_UTR_LENGTH = "three_prime_utr_length"; private static final String ATTR_FIVE_PRIME_UTR_LENGTH = "five_prime_utr_length"; private static final String ATTR_ORGANISM = "organism"; @@ -66,7 +68,7 @@ public String getRequiredRecordClassFullName() { @Override public String[] getRequiredAttributeNames() { - return new String[] { ATTR_LOCATION_TEXT , ATTR_ORGANISM, ATTR_THREE_PRIME_UTR_LENGTH, ATTR_FIVE_PRIME_UTR_LENGTH, ATTR_GENE_NAME, ATTR_GENE_PRODUCT}; + return new String[] { ATTR_LOCATION_TEXT , ATTR_ORGANISM, ATTR_CODING_START, ATTR_CODING_END, ATTR_THREE_PRIME_UTR_LENGTH, ATTR_FIVE_PRIME_UTR_LENGTH, ATTR_GENE_NAME, ATTR_GENE_PRODUCT}; } @Override @@ -86,11 +88,14 @@ public List> getRecordAsBedFields(RecordInstance record) throws Wdk StrandDirection strand = StrandDirection.fromSign(m.group(4)); + int codingStart = integerValueWithZeroForEmpty(record, ATTR_CODING_START); + int codingEnd = integerValueWithZeroForEmpty(record, ATTR_CODING_END); + int fivePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_FIVE_PRIME_UTR_LENGTH); int threePrimeUtrLength = integerValueWithZeroForEmpty(record, ATTR_THREE_PRIME_UTR_LENGTH); - Integer upstreamPosition = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand); - Integer downstreamPosition = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, fivePrimeUtrLength, threePrimeUtrLength, strand); + Integer upstreamPosition = getPositionGenomic(featureStart, featureEnd, _upstreamOffset, _upstreamSign, _upstreamAnchor, codingStart, codingEnd, fivePrimeUtrLength, threePrimeUtrLength, strand); + Integer downstreamPosition = getPositionGenomic(featureStart, featureEnd, _downstreamOffset, _downstreamSign, _downstreamAnchor, codingStart, codingEnd, fivePrimeUtrLength, threePrimeUtrLength, strand); Integer segmentStart = upstreamPosition; Integer segmentEnd = downstreamPosition; @@ -141,6 +146,7 @@ private Matcher matchLocationCoords(RecordInstance record, String key, Pattern p private static int getPositionGenomic( Integer featureStart, Integer featureEnd, int offset, OffsetSign sign, Anchor anchor, + Integer codingStart, Integer codingEnd, int fivePrimeUtrLength, int threePrimeUtrLength, StrandDirection strand ) throws WdkModelException{ @@ -152,9 +158,9 @@ private static int getPositionGenomic( } switch(anchor) { case Start: return featureEnd + offset; - case CodeStart: return featureEnd - fivePrimeUtrLength + offset; + case CodeStart: return codingEnd; case End: return featureStart + offset; - case CodeEnd: return featureStart + threePrimeUtrLength + offset; + case CodeEnd: return codingStart; default: throw new WdkModelException("Unsupported anchor type: " + anchor); } } @@ -163,10 +169,10 @@ private static int getPositionGenomic( offset = - offset; } switch(anchor) { - case Start: return featureStart + offset; - case CodeStart: return featureStart + fivePrimeUtrLength + offset; + case Start: return featureStart + offset; + case CodeStart: return codingStart; case End: return featureEnd + offset; - case CodeEnd: return featureEnd - threePrimeUtrLength + offset; + case CodeEnd: return codingEnd; default: throw new WdkModelException("Unsupported anchor type: " + anchor); } } From f41b83ec51b4ea5922e018ea680db049cecc3748 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 13 Mar 2024 03:15:20 +0000 Subject: [PATCH 112/204] npm: bump @veupathdb/genomics-site from 1.0.126 to 1.0.127 in /Site Bumps @veupathdb/genomics-site from 1.0.126 to 1.0.127. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 53b23839f..4ee6ee182 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.126" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.126.tgz#8a3432006b0aefc8b5e604ad4df338c52ca7fb41" - integrity sha512-Se4+KAi4bWyDMcYqBKJf70r/aVf5uV8AoJJ+VJfXztqLayEiRhz92Eis8zC8cWX/r0kAAE5YlUXHCKm67J8LmA== + version "1.0.127" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.127.tgz#11bd72b5de3f1e4db07614c0a0c71f1289eb92ce" + integrity sha512-b3JuTmEr5+3/8+Y5PCSvNsjc8SmphNSKIKun7bBfRX1KcXDBg46gpuUpJ5d82EjRklM9ztjw6zLKK2GDsvbi3g== From deb7c684edb521ec16fc9327d9073649616b7e4c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:26:43 +0000 Subject: [PATCH 113/204] npm: bump @veupathdb/genomics-site from 1.0.127 to 1.0.128 in /Site Bumps @veupathdb/genomics-site from 1.0.127 to 1.0.128. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4ee6ee182..2c8ab7d7c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.127" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.127.tgz#11bd72b5de3f1e4db07614c0a0c71f1289eb92ce" - integrity sha512-b3JuTmEr5+3/8+Y5PCSvNsjc8SmphNSKIKun7bBfRX1KcXDBg46gpuUpJ5d82EjRklM9ztjw6zLKK2GDsvbi3g== + version "1.0.128" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.128.tgz#afcff59a36fb1159f1edbbaa8ff0d14952282bc8" + integrity sha512-2QXVfIW/XwdP1rbcDbhnvipyrFYgLWxgL/Q+mtcNWZENnn4fiLwPmmAsK7Dexi9uickI0xBF1QDVi46iiA56Hw== From d02a919b1b6f39e3baeb702505ecde85567d2193 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 19 Mar 2024 03:21:00 +0000 Subject: [PATCH 114/204] npm: bump @veupathdb/genomics-site from 1.0.128 to 1.0.129 in /Site Bumps @veupathdb/genomics-site from 1.0.128 to 1.0.129. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2c8ab7d7c..cff53cf92 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.128" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.128.tgz#afcff59a36fb1159f1edbbaa8ff0d14952282bc8" - integrity sha512-2QXVfIW/XwdP1rbcDbhnvipyrFYgLWxgL/Q+mtcNWZENnn4fiLwPmmAsK7Dexi9uickI0xBF1QDVi46iiA56Hw== + version "1.0.129" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.129.tgz#02f0247932aa04a43149add839977c3da24d83c6" + integrity sha512-h1md/pMdrVc7qHZFGg9dYCv2WFTV7s7VWVOyq8DQR6ZwswTjaCmpju1V4nik0d3LwUXdC1wOIDBBUHv8Tk4OEw== From 8e0233f23cca19a8acd97e98f8c1894599e16151 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 20 Mar 2024 03:53:17 +0000 Subject: [PATCH 115/204] npm: bump @veupathdb/genomics-site from 1.0.129 to 1.0.130 in /Site Bumps @veupathdb/genomics-site from 1.0.129 to 1.0.130. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index cff53cf92..1d37f25de 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.129" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.129.tgz#02f0247932aa04a43149add839977c3da24d83c6" - integrity sha512-h1md/pMdrVc7qHZFGg9dYCv2WFTV7s7VWVOyq8DQR6ZwswTjaCmpju1V4nik0d3LwUXdC1wOIDBBUHv8Tk4OEw== + version "1.0.130" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.130.tgz#b4ad32b15741cbbd3471cbaca306ec5cd66ea124" + integrity sha512-eu7vZutYgSzJGYNd9jWohEJNZIAqcz/j1xHBHtDN0dDG4QKpjvE/r4DNeYMEAQ2mCl74ydXOTYnE0dQAyWLCng== From 141f3cb247c193133b93c9d193abe2a90c6121b3 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Fri, 22 Mar 2024 12:51:50 -0400 Subject: [PATCH 116/204] fix the codind start/end, which were ignoring the offset! -refs #53932 --- .../report/bed/feature/GeneGenomicFeatureProvider.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java index 46f9decab..96a3e7508 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/bed/feature/GeneGenomicFeatureProvider.java @@ -158,9 +158,9 @@ private static int getPositionGenomic( } switch(anchor) { case Start: return featureEnd + offset; - case CodeStart: return codingEnd; + case CodeStart: return codingEnd + offset; case End: return featureStart + offset; - case CodeEnd: return codingStart; + case CodeEnd: return codingStart + offset; default: throw new WdkModelException("Unsupported anchor type: " + anchor); } } @@ -170,9 +170,9 @@ private static int getPositionGenomic( } switch(anchor) { case Start: return featureStart + offset; - case CodeStart: return codingStart; + case CodeStart: return codingStart + offset; case End: return featureEnd + offset; - case CodeEnd: return codingEnd; + case CodeEnd: return codingEnd + offset; default: throw new WdkModelException("Unsupported anchor type: " + anchor); } } From 8e953f91a1e7885d51a807bf0016356172b48273 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Mar 2024 03:15:03 +0000 Subject: [PATCH 117/204] npm: bump @veupathdb/genomics-site from 1.0.130 to 1.0.131 in /Site Bumps @veupathdb/genomics-site from 1.0.130 to 1.0.131. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 1d37f25de..c9199a0a2 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.130" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.130.tgz#b4ad32b15741cbbd3471cbaca306ec5cd66ea124" - integrity sha512-eu7vZutYgSzJGYNd9jWohEJNZIAqcz/j1xHBHtDN0dDG4QKpjvE/r4DNeYMEAQ2mCl74ydXOTYnE0dQAyWLCng== + version "1.0.131" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.131.tgz#f0445a6050b41907d1ad827685bdc6e368126a63" + integrity sha512-yMy97Gtm89bH//ycXqgAVZioAB0Czzs6Pi7PCADTY6jqCsjCEyN+WBi2qnAr6rrDu38vh2rl7KnC5jRjVaNMXw== From bb842c99949feaf3b48c9c9fbda9638bfbc5c12d Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 26 Mar 2024 10:56:42 -0400 Subject: [PATCH 118/204] fix width of hsapREF_Dewi_Roryzae_2021_ebi_rnaSeq_RSRC graph - refs #52689 --- View/lib/perl/GraphPackage/Templates/RNASeq.pm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/RNASeq.pm b/View/lib/perl/GraphPackage/Templates/RNASeq.pm index 97c6935c5..505437b89 100644 --- a/View/lib/perl/GraphPackage/Templates/RNASeq.pm +++ b/View/lib/perl/GraphPackage/Templates/RNASeq.pm @@ -1790,6 +1790,14 @@ sub getPlotWidth { return 550; } 1; +# host - hsapREF_Dewi_Roryzae_2021_ebi_rnaSeq_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_abeab0974c; + +sub getPlotWidth { return 750; } + +1; + + # vect - aaegLVP_AGWG_SRP034735_ebi_rnaSeq_RSRC package ApiCommonWebsite::View::GraphPackage::Templates::RNASeq::DS_f279b1d0f8; From 9be3ed3d3318faccb3820cd85b311cdcf1608efb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 29 Mar 2024 03:53:26 +0000 Subject: [PATCH 119/204] npm: bump @veupathdb/genomics-site from 1.0.131 to 1.0.132 in /Site Bumps @veupathdb/genomics-site from 1.0.131 to 1.0.132. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index c9199a0a2..7611ad7a6 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.131" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.131.tgz#f0445a6050b41907d1ad827685bdc6e368126a63" - integrity sha512-yMy97Gtm89bH//ycXqgAVZioAB0Czzs6Pi7PCADTY6jqCsjCEyN+WBi2qnAr6rrDu38vh2rl7KnC5jRjVaNMXw== + version "1.0.132" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.132.tgz#d984d7e9a3d14863f38f176949b696d8bdad6345" + integrity sha512-O+xrzLJ+Tq/ki+b/VpaDm40/oL657HVG8y0Oilw23Tb8FFBKNmC5QhbSFjvfpxlVGIxsxMX/63uVA5YPxhxVqA== From 140633a9321698729a33d232120275929a1d2ec5 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Mon, 1 Apr 2024 15:06:50 -0400 Subject: [PATCH 120/204] Add OAuth values to template --- .../roles/conifer/templates/ApiCommonWebsite/container_env.j2 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Model/lib/conifer/roles/conifer/templates/ApiCommonWebsite/container_env.j2 b/Model/lib/conifer/roles/conifer/templates/ApiCommonWebsite/container_env.j2 index 8c789f83c..109fc4756 100644 --- a/Model/lib/conifer/roles/conifer/templates/ApiCommonWebsite/container_env.j2 +++ b/Model/lib/conifer/roles/conifer/templates/ApiCommonWebsite/container_env.j2 @@ -14,3 +14,7 @@ SITE_BASE_URL=https://{{ hostname }}/{{ webapp_ctx }} PROJECT_ID={{ project }} COHORT={{ cohort }} + +OAUTH_URL={{ modelconfig_oauthUrl }} +OAUTH_CLIENT_ID={{ modelconfig_oauthClientId }} +OAUTH_CLIENT_SECRET={{ modelconfig_oauthClientSecret }} From 66252ff60595471fbc99840f2411d1c3e6999628 Mon Sep 17 00:00:00 2001 From: Dan Galdi Date: Fri, 5 Apr 2024 13:18:50 -0400 Subject: [PATCH 121/204] jbrowse vdi (#195) --- .../services/jbrowse/JBrowseService.java | 15 +- .../jbrowse/JBrowseUserDatasetsService.java | 268 +++++++++++------- .../jbrowse/model/JBrowseDatasetResponse.java | 19 ++ .../services/jbrowse/model/JBrowseTrack.java | 180 ++++++++++++ .../jbrowse/model/VDIDatasetReference.java | 43 +++ .../jbrowse/model/VDIDatasetType.java | 31 ++ 6 files changed, 441 insertions(+), 115 deletions(-) create mode 100644 Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseDatasetResponse.java create mode 100644 Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java create mode 100644 Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetReference.java create mode 100644 Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetType.java diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java index 36db811e4..ead28e03a 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java @@ -240,15 +240,18 @@ public Response getJbrowseChIPSeqTracks(@PathParam("organismAbbrev") String orga public Response getJBrowseStore(@QueryParam("data") String data, @HeaderParam("Range") String fileRange) throws WdkModelException { - String projectId = getWdkModel().getProjectId(); String buildNumber = getWdkModel().getBuildNumber(); - String webservicesDir = getWdkModel().getProperties().get("WEBSERVICEMIRROR"); + String udDir = getWdkModel().getProperties().get("UD_DIR"); + // New WDK property: UserDatasetFiles. This is located in /var/www/Common/userDatasets String path = checkPath( - webservicesDir + "/" + - projectId + "/" + - "build-" + buildNumber + "/" + - data); + udDir + "/" + + "build-" + buildNumber + "/" + + data); + + if (path.contains("..") || path.contains("$")) { + throw new NotFoundException(formatNotFound("*")); + } return getFileChunkResponse(Paths.get(path), parseRangeHeaderValue(fileRange)); } diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java index 65c83e6d2..9d0587b29 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java @@ -1,161 +1,211 @@ package org.apidb.apicommon.service.services.jbrowse; import javax.ws.rs.GET; +import javax.ws.rs.HeaderParam; +import javax.ws.rs.NotFoundException; import javax.ws.rs.Path; import javax.ws.rs.PathParam; import javax.ws.rs.Produces; +import javax.ws.rs.QueryParam; import javax.ws.rs.core.MediaType; import org.apache.log4j.Logger; +import org.apidb.apicommon.service.services.jbrowse.model.JBrowseDatasetResponse; +import org.apidb.apicommon.service.services.jbrowse.model.JBrowseTrack; +import org.apidb.apicommon.service.services.jbrowse.model.VDIDatasetReference; +import org.apidb.apicommon.service.services.jbrowse.model.VDIDatasetType; +import org.gusdb.fgputil.db.runner.SQLRunner; import org.gusdb.fgputil.events.Events; import org.gusdb.wdk.errors.ErrorContext.ErrorLocation; import org.gusdb.wdk.errors.ServerErrorBundle; import org.gusdb.wdk.events.ErrorEvent; import org.gusdb.wdk.model.WdkModelException; import javax.ws.rs.ForbiddenException; -import org.gusdb.wdk.model.user.dataset.UserDataset; -import org.gusdb.wdk.model.user.dataset.UserDatasetDependency; -import org.gusdb.wdk.model.user.dataset.UserDatasetFile; -import org.gusdb.wdk.model.user.dataset.UserDatasetInfo; -import org.gusdb.wdk.model.user.dataset.UserDatasetMeta; -import org.gusdb.wdk.model.user.dataset.UserDatasetSession; -import org.gusdb.wdk.model.user.dataset.UserDatasetType; -import org.gusdb.wdk.service.formatter.UserDatasetsFormatter; -import org.gusdb.wdk.service.service.user.UserDatasetService; +import javax.ws.rs.core.Response; + import org.gusdb.wdk.service.service.user.UserService; -import org.json.JSONArray; -import org.json.JSONObject; + +import java.io.File; +import java.nio.file.Paths; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.Locale; +import java.util.Optional; +import java.util.stream.Collectors; + +import static org.gusdb.wdk.service.FileRanges.getFileChunkResponse; +import static org.gusdb.wdk.service.FileRanges.parseRangeHeaderValue; public class JBrowseUserDatasetsService extends UserService { private static final Logger LOG = Logger.getLogger(JBrowseUserDatasetsService.class); + private static final String VDI_DATASET_DIR_KEY = "VDI_DATASETS_DIRECTORY"; + private static final String VDI_CONTROL_SCHEMA_KEY ="VDI_CONTROL_SCHEMA"; + private static final String VDI_DATASET_SCHEMA_KEY ="VDI_DATASETS_SCHEMA"; public JBrowseUserDatasetsService(@PathParam(USER_ID_PATH_PARAM) String uid) { super(uid); } + + /** + * This endpoint exposes user dataset track files with the intent of JBrowse using it to retrieve file ranges. + * Any installed file for a dataset owned by the user can be fetched by this endpoint. + * + * URLs to hit this endpoint are constructed by this service when the JBrowse application asks for the user's available + * tracks. + */ @GET - @Path("user-datasets-jbrowse/{organism}") + @Path("user-datasets-jbrowse/data") @Produces(MediaType.APPLICATION_JSON) - public JSONObject getAllUserDatasetsJBrowse(@PathParam("organism") String publicOrganismAbbrev) { + public Response getAllUserDatasetFileJBrowse(@QueryParam("data") String data, + @QueryParam("datasetID") String datasetID, + @HeaderParam("Range") String fileRange) throws WdkModelException { + String buildNumber = getWdkModel().getBuildNumber(); + String udDir = getWdkModel().getProperties().get(VDI_DATASET_DIR_KEY); + String schemaKey = getWdkModel().getProperties().get(VDI_DATASET_SCHEMA_KEY).toLowerCase(Locale.ROOT); + + // Verify that the dataset belongs to user. Random people should not be able to download anyone's files, even + // though they are protected by obscurity. + if (!datasetBelongsToUser(getPrivateRegisteredUser().getUserId(), datasetID)) { + throw new NotFoundException("Unable to find dataset with ID " + datasetID); + } + + String path = String.format("%s/%s/build-%s/%s/%s/%s", udDir, schemaKey, buildNumber, getWdkModel().getProjectId(), datasetID, data); + + LOG.info("Looking up jbrowse files for dataset {} in directory " + path); + + if (path.contains("..") || path.contains("$")) { + throw new NotFoundException(formatNotFound("*")); + } + + return getFileChunkResponse(Paths.get(path), parseRangeHeaderValue(fileRange)); + } + + @GET + @Path("user-datasets-jbrowse/{organism}") + @Produces(MediaType.APPLICATION_JSON) + public Response getAllUserDatasetsJBrowse(@PathParam("organism") String publicOrganismAbbrev) { LOG.debug("\nservice user-datasets-jbrowse has been called ---gets all jbrowse configuration for user datasets\n"); + final JBrowseDatasetResponse jBrowseDatasetResponse = new JBrowseDatasetResponse(); - JSONArray tracks; try { - tracks = UserDatasetService.getAllUserDatasetsJson(getWdkModel(), - getPrivateRegisteredUser(), - new JBrowseUserDatasetFormatter(publicOrganismAbbrev)); + List datasets = queryVisibleDatasets(getPrivateRegisteredUser().getUserId()); + LOG.info("Found " + datasets.size() + " datasets for user " + getPrivateRegisteredUser().getUserId()); + + // Any tracks that are in the installed dataset dir on the filesystem are installed in this project, fetch + // them indiscriminately! + List tracks = datasets.stream() + .flatMap(dataset -> fetchTracksFromFilesystem(dataset).stream()) + .collect(Collectors.toList()); + + LOG.info("Found " + tracks.size() + " tracks for user " + getPrivateRegisteredUser().getUserId()); + jBrowseDatasetResponse.setTracks(tracks); } // if the user isn't logged in, just return an empty array catch (ForbiddenException e) { - tracks = new JSONArray(); + jBrowseDatasetResponse.setTracks(Collections.emptyList()); } // if any other exception occurs, log and send email, but return empty array so UI is not hosed catch (Exception e) { - tracks = new JSONArray(); + jBrowseDatasetResponse.setTracks(Collections.emptyList()); Exception e2 = new WdkModelException("Unable to load JBrowse user datasets for user with ID " + getRequestingUser().getUserId() + ", organism " + publicOrganismAbbrev, e); LOG.error("Could not load JBrowse user datasets", e2); Events.trigger(new ErrorEvent(new ServerErrorBundle(e2), getErrorContext(ErrorLocation.WDK_SERVICE))); } - return new JSONObject().put("tracks", tracks); + return Response.ok(jBrowseDatasetResponse).build(); } - private static class JBrowseUserDatasetFormatter implements UserDatasetsFormatter { - - private final String _publicOrganismAbbrev; - - public JBrowseUserDatasetFormatter(String publicOrganismAbbrev) { - _publicOrganismAbbrev = publicOrganismAbbrev; - } - - @Override - public void addUserDatasetInfoToJsonArray(UserDatasetInfo dataset, - JSONArray datasetsJson, UserDatasetSession dsSession) throws WdkModelException { - JSONArray samples = getSamplesJsonForDataset(dataset); - if (dataset.isInstalled() && dataset.getUserDatasetCompatibility().isCompatible()) - for (int i = 0 ; i < samples.length(); i++) { - datasetsJson.put(samples.getJSONObject(i)); - } - } - - - private JSONArray getBigwigSampleConfiguration(UserDataset dataset, String subcategory) throws WdkModelException { - JSONArray samplesJson = new JSONArray(); - - int maxScore = 1000; - Long datasetId = dataset.getUserDatasetId(); - UserDatasetMeta datasetMeta = dataset.getMeta(); - String datasetName = datasetMeta.getName(); - String datasetSummary = datasetMeta.getSummary(); - - for (UserDatasetFile file : dataset.getFiles().values()) { - String fileName = file.getFileName(); - if(!fileName.toUpperCase().endsWith(".BW")) - continue ; - - String urlTemplate = "/a/service/users/current/user-datasets/" + datasetId + "/user-datafiles/" + fileName; - - JSONObject json = new JSONObject(); - json.put("storeClass", "JBrowse/Store/SeqFeature/BigWig"); - json.put("urlTemplate", urlTemplate); - json.put("yScalePosition", "left"); - json.put("key", datasetName + " " + fileName); - json.put("label", datasetName + " " + fileName); - json.put("type", "JBrowse/View/Track/Wiggle/XYPlot"); - json.put("category", "My Data from Galaxy"); - json.put("min_score", 0); - json.put("max_score", maxScore); - - JSONObject style = new JSONObject(); - style.put("pos_color", "#5B2C6F"); + /** + * Fetch all tracks from the filesystem for a given dataset reference. If the dataset has no installed files in this + * project an empty list is returned. + */ + private List fetchTracksFromFilesystem(VDIDatasetReference vdiDatasetReference) { + final String vdiDatasetsDir = getWdkModel().getProperties().get(VDI_DATASET_DIR_KEY); + String schemaKey = getWdkModel().getProperties().get(VDI_DATASET_SCHEMA_KEY).toLowerCase(Locale.ROOT); + final String buildNumber = getWdkModel().getBuildNumber(); + final java.nio.file.Path datasetDir = Paths.get(vdiDatasetsDir, schemaKey, "build-" + buildNumber, getWdkModel().getProjectId(), vdiDatasetReference.getId()); + LOG.info("Looking for tracks in " + datasetDir); + return Arrays.stream(Optional.ofNullable(datasetDir.toFile().listFiles()).orElse(new File[0])) + .map(jbrowseFile -> { + final JBrowseTrack jBrowseTrack = new JBrowseTrack(); + + jBrowseTrack.setKey(vdiDatasetReference.getName() + " " + jbrowseFile.getName()); + jBrowseTrack.setLabel(vdiDatasetReference.getName() + " " + jbrowseFile.getName()); + jBrowseTrack.setUrlTemplate(String.format("/a/service/users/current/user-datasets-jbrowse/data?datasetID=%s&data=%s", + vdiDatasetReference.getId(), jbrowseFile.getName())); + + JBrowseTrack.Metadata metadata = new JBrowseTrack.Metadata(); + + final String subCategory = VDIDatasetType.fromVDIName(vdiDatasetReference.getType()).getJbrowseSubcategoryName(); + jBrowseTrack.setSubcategory(subCategory); + metadata.setSubcategory(subCategory); + + metadata.setDataset(vdiDatasetReference.getName()); + metadata.setMdescription(vdiDatasetReference.getDescription()); + + jBrowseTrack.setMetadata(metadata); + jBrowseTrack.setStyle(new JBrowseTrack.Style()); + + return jBrowseTrack; + }) + .collect(Collectors.toList()); + } - JSONObject metadata = new JSONObject(); - metadata.put("subcategory", subcategory); - metadata.put("dataset", datasetName); - metadata.put("trackType", "Coverage"); - metadata.put("mdescription", datasetSummary); + private boolean datasetBelongsToUser(long userID, String datasetID) { + final String schema = getWdkModel().getProperties().get(VDI_CONTROL_SCHEMA_KEY); + String sql = String.format( + "SELECT user_dataset_id FROM %s.AvailableUserDatasets da WHERE da.user_id = ? AND da.user_dataset_id = ?", + schema.toLowerCase(Locale.ROOT) + ); + return new SQLRunner(getWdkModel().getAppDb().getDataSource(), sql) + .executeQuery(new Object[] { userID, datasetID }, ResultSet::next); + } - json.put("metadata", metadata); - json.put("style", style); - samplesJson.put(json); + /** + * Query the visible datasets according the VDI control schema's visible datasets view. + * + * Note that this view is specifically designed and intended for use by applications to know which datasets are available + * to a particular user. + * + * @param userID UserID to retrieve visible datasets for. + * @return List of visible datasets. + */ + private List queryVisibleDatasets(long userID) { + final String schema = getWdkModel().getProperties().get(VDI_CONTROL_SCHEMA_KEY); + String sql = String.format( + "SELECT user_dataset_id, type, name, description FROM %s.AvailableUserDatasets da WHERE da.user_id = ?", + schema + ); + LOG.debug("Querying visible datasets: " + sql); + return new SQLRunner(getWdkModel().getAppDb().getDataSource(), sql) + .executeQuery(new Object[] { userID }, rs -> { + List vdiDatasets = new ArrayList<>(); + while (rs.next()) { + vdiDatasets.add(datasetFromResultSet(rs)); } - return samplesJson; - } - - - private JSONArray getSamplesJsonForDataset(UserDatasetInfo datasetInfo) throws WdkModelException { - - JSONArray samplesJson = new JSONArray(); - - String genomeSuffix = "_" + _publicOrganismAbbrev + "_Genome"; - - UserDataset dataset = datasetInfo.getDataset(); - - boolean matchesOrganismAbbrev = false; - - for (UserDatasetDependency dependency : dataset.getDependencies()) { - if(dependency.getResourceIdentifier().endsWith(genomeSuffix)) - matchesOrganismAbbrev = true; - } - - if(!matchesOrganismAbbrev) - return samplesJson; - - UserDatasetType type = dataset.getType(); - String datasetType = type.getName(); - - if(datasetType.equals("RnaSeq")) { - return getBigwigSampleConfiguration(dataset, "RNASeq"); - } - if(datasetType.equals("BigwigFiles")) { - return getBigwigSampleConfiguration(dataset, "Bigwig Files From User"); - } + return vdiDatasets; + }); + } - return samplesJson; - } + /** + * Constructs a {@link VDIDatasetReference} from a ResultSet produced by a query of the visible datasets view. + */ + private VDIDatasetReference datasetFromResultSet(ResultSet resultSet) throws SQLException { + VDIDatasetReference row = new VDIDatasetReference(); + row.setDescription(resultSet.getString("description")); + row.setId(resultSet.getString("user_dataset_id")); + row.setType(resultSet.getString("type")); + row.setDescription(resultSet.getString("description")); + row.setName(resultSet.getString("name")); + return row; } } diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseDatasetResponse.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseDatasetResponse.java new file mode 100644 index 000000000..ef3747320 --- /dev/null +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseDatasetResponse.java @@ -0,0 +1,19 @@ +package org.apidb.apicommon.service.services.jbrowse.model; + +import java.util.List; + +public class JBrowseDatasetResponse { + private List tracks; + + public JBrowseDatasetResponse() { + + } + + public void setTracks(List tracks) { + this.tracks = tracks; + } + + public List getTracks() { + return tracks; + } +} diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java new file mode 100644 index 000000000..4296306c3 --- /dev/null +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java @@ -0,0 +1,180 @@ +package org.apidb.apicommon.service.services.jbrowse.model; + +import com.fasterxml.jackson.annotation.JsonProperty; + +/** + * + */ +public class JBrowseTrack { + // Fields with defaults + private String storeClass = "JBrowse/Store/SeqFeature/BigWig"; + private String yScalePosition = "left"; + private String type = "JBrowse/View/Track/Wiggle/XYPlot"; + private String category = "My Data from Galaxy"; + + @JsonProperty("min_score") + private int minScore = 0; + @JsonProperty("max_score") + private int maxScore = 1000; + + + // Fields without defaults + private String key; + private String label; + private String urlTemplate; + private Metadata metadata; + private Style style; + private String subcategory; + + // No Args constructor for jackson + public JBrowseTrack() { + + } + + public String getStoreClass() { + return storeClass; + } + + public void setStoreClass(String storeClass) { + this.storeClass = storeClass; + } + + public String getyScalePosition() { + return yScalePosition; + } + + public void setyScalePosition(String yScalePosition) { + this.yScalePosition = yScalePosition; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getLabel() { + return label; + } + + public void setLabel(String label) { + this.label = label; + } + + public String getUrlTemplate() { + return urlTemplate; + } + + public void setUrlTemplate(String urlTemplate) { + this.urlTemplate = urlTemplate; + } + + public Metadata getMetadata() { + return metadata; + } + + public void setMetadata(Metadata metadata) { + this.metadata = metadata; + } + + public Style getStyle() { + return style; + } + + public void setStyle(Style style) { + this.style = style; + } + + public int getMinScore() { + return minScore; + } + + public void setMinScore(int minScore) { + this.minScore = minScore; + } + + public int getMaxScore() { + return maxScore; + } + + public void setMaxScore(int maxScore) { + this.maxScore = maxScore; + } + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public void setSubcategory(String subcategory) { + this.subcategory = subcategory; + } + + public String getSubcategory() { + return subcategory; + } + + public static class Style { + @JsonProperty("pos_color") + private String posColor = "#5B2C6F"; + + public Style() { + } + + public String getPosColor() { + return posColor; + } + + public void setPosColor(String posColor) { + this.posColor = posColor; + } + } + + public static class Metadata { + private String trackType = "Coverage"; + + private String subcategory; + private String dataset; + private String mdescription; + + public Metadata() { + } + + public String getTrackType() { + return trackType; + } + + public void setTrackType(String trackType) { + this.trackType = trackType; + } + + public String getSubcategory() { + return subcategory; + } + + public void setSubcategory(String subcategory) { + this.subcategory = subcategory; + } + + public String getDataset() { + return dataset; + } + + public void setDataset(String dataset) { + this.dataset = dataset; + } + + public String getMdescription() { + return mdescription; + } + + public void setMdescription(String mdescription) { + this.mdescription = mdescription; + } + } +} diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetReference.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetReference.java new file mode 100644 index 000000000..fed07a5d2 --- /dev/null +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetReference.java @@ -0,0 +1,43 @@ +package org.apidb.apicommon.service.services.jbrowse.model; + +/** + * + */ +public class VDIDatasetReference { + private String id; + private String name; + private String type; + private String description; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } +} diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetType.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetType.java new file mode 100644 index 000000000..71abbb6b9 --- /dev/null +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/VDIDatasetType.java @@ -0,0 +1,31 @@ +package org.apidb.apicommon.service.services.jbrowse.model; + +import java.util.Arrays; + +public enum VDIDatasetType { + RNA_SEQ("RNASeq", "RNASeq"), + BIGWIG("BigwigFiles", "Bigwig Files From User"); + + private String vdiName; + private String jbrowseSubcategoryName; + + VDIDatasetType(String vdiName, String jbrowseSubcategoryName) { + this.vdiName = vdiName; + this.jbrowseSubcategoryName = jbrowseSubcategoryName; + } + + public String getVdiName() { + return vdiName; + } + + public String getJbrowseSubcategoryName() { + return jbrowseSubcategoryName; + } + + public static VDIDatasetType fromVDIName(String vdiName) { + return Arrays.stream(values()) + .filter(val -> val.vdiName.equalsIgnoreCase(vdiName)) + .findFirst() + .orElseThrow(); + } +} From 8a4e8d749ff6a714526c6775a2d1d2756fa606b6 Mon Sep 17 00:00:00 2001 From: Jeremy Myers Date: Fri, 5 Apr 2024 14:24:49 -0400 Subject: [PATCH 122/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7611ad7a6..2b136e587 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.132" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.132.tgz#d984d7e9a3d14863f38f176949b696d8bdad6345" - integrity sha512-O+xrzLJ+Tq/ki+b/VpaDm40/oL657HVG8y0Oilw23Tb8FFBKNmC5QhbSFjvfpxlVGIxsxMX/63uVA5YPxhxVqA== + version "1.0.133" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.133.tgz#e4cb809c02af8530da151327dca8412a40a35e53" + integrity sha512-4yMHIjujVfmqiJAYf1gFItT0nnfAwEFa2z6m1mRl2+EXMrktGy9+aaIVTBG/CdwQTgDqD8tMbQWH2lRJadpJDg== From d6e5ffafdbfb606a97982db5af13dd1091105571 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Mon, 8 Apr 2024 18:34:24 -0400 Subject: [PATCH 123/204] production default in site repo --- .../vars/ApiCommon/production/default.yml | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 1ed11f83d..1df3e80b5 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -13,7 +13,27 @@ modelconfig_commentdb.maxIdle: 10 commentconfig_solrUrl: "https://solr-sitesearch-{{ sitesearchsolr_env_map[prefix]|default(sitesearchsolr_env_map['default']) }}.local.apidb.org:8443/solr/site_search/" +vdi_control_env_map: + w1_prefix: VDI_CONTROL_PROD_S + b1_prefix: VDI_CONTROL_BETA_S + q1_prefix: VDI_CONTROL_QA_S + w2_prefix: VDI_CONTROL_PROD_N + b2_prefix: VDI_CONTROL_BETA_N + q2_prefix: VDI_CONTROL_QA_N + default: VDI_CONTROL_QA_N + +vdi_datasets_env_map: + w1_prefix: VDI_DATASETS_PROD_S + b1_prefix: VDI_DATASETS_BETA_S + q1_prefix: VDI_DATASETS_QA_S + w2_prefix: VDI_DATASETS_PROD_N + b2_prefix: VDI_DATASETS_BETA_N + q2_prefix: VDI_DATASETS_QA_N + default: VDI_DATASETS_QA_N + modelprop: + VDI_CONTROL_SCHEMA: "{{ vdi_control_env_map[prefix_vdi]|default(vdi_control_env_map['default']) }}" + VDI_DATASETS_SCHEMA: "{{ vdi_datasets_env_map[prefix_vdi]|default(vdi_datasets_env_map['default']) }}" GOOGLE_ANALYTICS_ID: "{{ lookup('euparc', 'attr=google_analytics_id xpath=sites/site[@hostname=\"{}\"] default='.format( hostname|swap_hostname(_host_frontends) ) ) From 97465df76c3032e241ab855fff4c0ff9db9a4bb8 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 06:57:43 -0400 Subject: [PATCH 124/204] vdi config --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 1df3e80b5..408bfe72c 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -12,6 +12,7 @@ modelconfig_userDb_maxIdle: 10 modelconfig_commentdb.maxIdle: 10 commentconfig_solrUrl: "https://solr-sitesearch-{{ sitesearchsolr_env_map[prefix]|default(sitesearchsolr_env_map['default']) }}.local.apidb.org:8443/solr/site_search/" +prefix_vdi: "{{ hostname | regex_replace('^([a-z][0-9]).*','1_prefix') }}" vdi_control_env_map: w1_prefix: VDI_CONTROL_PROD_S From f19a0affe4487ca26b55ba9131e78ff5a47f597d Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 08:18:56 -0400 Subject: [PATCH 125/204] printing conifer hostname --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 408bfe72c..1a95d6bc6 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -33,6 +33,7 @@ vdi_datasets_env_map: default: VDI_DATASETS_QA_N modelprop: + HOSTNAME: "{{ hostname }}" VDI_CONTROL_SCHEMA: "{{ vdi_control_env_map[prefix_vdi]|default(vdi_control_env_map['default']) }}" VDI_DATASETS_SCHEMA: "{{ vdi_datasets_env_map[prefix_vdi]|default(vdi_datasets_env_map['default']) }}" GOOGLE_ANALYTICS_ID: "{{ lookup('euparc', From 8ab3e4587d5d42f8036082e88bb0902d9b72937a Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 09:37:36 -0400 Subject: [PATCH 126/204] printing conifer prefix_vdi --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 1a95d6bc6..464963b29 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -34,6 +34,7 @@ vdi_datasets_env_map: modelprop: HOSTNAME: "{{ hostname }}" + PREFIX_VDI: "{{ prefix_vdi }}" VDI_CONTROL_SCHEMA: "{{ vdi_control_env_map[prefix_vdi]|default(vdi_control_env_map['default']) }}" VDI_DATASETS_SCHEMA: "{{ vdi_datasets_env_map[prefix_vdi]|default(vdi_datasets_env_map['default']) }}" GOOGLE_ANALYTICS_ID: "{{ lookup('euparc', From dbfa06e0e183ee98fe1961e6c2ed671f5a0384be Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 09:59:08 -0400 Subject: [PATCH 127/204] printing conifer prefix --- .../roles/conifer/vars/ApiCommon/production/default.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 464963b29..f664ee9d7 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -12,7 +12,7 @@ modelconfig_userDb_maxIdle: 10 modelconfig_commentdb.maxIdle: 10 commentconfig_solrUrl: "https://solr-sitesearch-{{ sitesearchsolr_env_map[prefix]|default(sitesearchsolr_env_map['default']) }}.local.apidb.org:8443/solr/site_search/" -prefix_vdi: "{{ hostname | regex_replace('^([a-z][0-9]).*','1_prefix') }}" +prefix_vdi: "{{ hostname | regex_replace('^([a-z][0-9]).*','\\1_prefix') }}" vdi_control_env_map: w1_prefix: VDI_CONTROL_PROD_S @@ -35,6 +35,7 @@ vdi_datasets_env_map: modelprop: HOSTNAME: "{{ hostname }}" PREFIX_VDI: "{{ prefix_vdi }}" + PREFIX: "{{ prefix }"} VDI_CONTROL_SCHEMA: "{{ vdi_control_env_map[prefix_vdi]|default(vdi_control_env_map['default']) }}" VDI_DATASETS_SCHEMA: "{{ vdi_datasets_env_map[prefix_vdi]|default(vdi_datasets_env_map['default']) }}" GOOGLE_ANALYTICS_ID: "{{ lookup('euparc', From 1b4314945fb3051ca44c7d37362ebc150f984d30 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 10:06:13 -0400 Subject: [PATCH 128/204] printing conifer prefix --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index f664ee9d7..443c1b4f6 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -35,7 +35,7 @@ vdi_datasets_env_map: modelprop: HOSTNAME: "{{ hostname }}" PREFIX_VDI: "{{ prefix_vdi }}" - PREFIX: "{{ prefix }"} + PREFIX: "{{ prefix }}" VDI_CONTROL_SCHEMA: "{{ vdi_control_env_map[prefix_vdi]|default(vdi_control_env_map['default']) }}" VDI_DATASETS_SCHEMA: "{{ vdi_datasets_env_map[prefix_vdi]|default(vdi_datasets_env_map['default']) }}" GOOGLE_ANALYTICS_ID: "{{ lookup('euparc', From a73ff5bf99fd2fb867214115774418a0c3531bd2 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 9 Apr 2024 12:30:37 -0400 Subject: [PATCH 129/204] add veupathdb as analysis author --- Model/lib/conifer/roles/conifer/vars/ApiCommon/VectorBase.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/VectorBase.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/VectorBase.yml index 752caeace..5671800b7 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/VectorBase.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/VectorBase.yml @@ -5,7 +5,7 @@ modelprop: FACEBOOK_URL: https://facebook.com/pages/VectorBase/189608142260 eda: enabled: "true" # this will enable it for dev sites - example_analyses_author: 854899613 + example_analyses_author: 854899613,1926010 single_app_mode: pass user_datasets_workspace: enabled: "true" From daadbb6a50f82638f3d4715f30b8e77a4ca3cd3c Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Tue, 9 Apr 2024 12:54:39 -0400 Subject: [PATCH 130/204] Revert change meant to address user datasets -> VDI --- .../service/services/jbrowse/JBrowseService.java | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java index ead28e03a..36db811e4 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseService.java @@ -240,18 +240,15 @@ public Response getJbrowseChIPSeqTracks(@PathParam("organismAbbrev") String orga public Response getJBrowseStore(@QueryParam("data") String data, @HeaderParam("Range") String fileRange) throws WdkModelException { + String projectId = getWdkModel().getProjectId(); String buildNumber = getWdkModel().getBuildNumber(); - String udDir = getWdkModel().getProperties().get("UD_DIR"); - // New WDK property: UserDatasetFiles. This is located in /var/www/Common/userDatasets + String webservicesDir = getWdkModel().getProperties().get("WEBSERVICEMIRROR"); String path = checkPath( - udDir + "/" + - "build-" + buildNumber + "/" + - data); - - if (path.contains("..") || path.contains("$")) { - throw new NotFoundException(formatNotFound("*")); - } + webservicesDir + "/" + + projectId + "/" + + "build-" + buildNumber + "/" + + data); return getFileChunkResponse(Paths.get(path), parseRangeHeaderValue(fileRange)); } From acb155b6052986c43b2cc444e5a4b010067eb3b4 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 9 Apr 2024 17:02:17 -0400 Subject: [PATCH 131/204] add Pk graph -refs #53740 --- .../GraphPackage/Templates/PhenotypeScore.pm | 27 +++++++++++++++++++ .../Templates/Proteomics/LogRatio.pm | 18 +++++++++++++ 2 files changed, 45 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm index b6d4b8636..9caf219ff 100644 --- a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm +++ b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm @@ -69,6 +69,7 @@ sub makePhenotypeGraphObject { 1; +# pfal3D7_phenotype_pB_mutagenesis_MIS_MFS_RSRC package ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore::DS_1cc763e9d0; use strict; use vars qw( @ISA ); @@ -107,6 +108,32 @@ sub declareParts { 1; +# pknoH_phenotype_piggyBac_mutagenesis_HME_MIS_OIS_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore::DS_6d7ee15b4a; +use strict; +use vars qw( @ISA ); + +@ISA = qw(ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore ); + +sub getPhenotypeSpecs { + return [ {abbrev => "HMS", + name => "Hybrid model score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Hybrid model score'" + }, + {abbrev => "OIS", + name => "Occupancy index score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Occupancy index score'" + }, + {abbrev => "MIS", + name => "Mutagenesis index score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Mutagenesis index score'" + }, + ]; +} + +1; + + package ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore::DS_90eea17ef6; use strict; use vars qw( @ISA ); diff --git a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm index cc376d437..0ca0eed98 100644 --- a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm +++ b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm @@ -100,6 +100,24 @@ sub finalProfileAdjustments { 1; +# Host +package ApiCommonWebsite::View::GraphPackage::Templates::Proteomics::LogRatio::DS_74ac747eab; + +sub finalProfileAdjustments { + my ($self, $profile) = @_; + + my $legend = ['haha']; + my $colors = ['gray']; + $profile->setLegendLabels($legend); + $profile->setColors($colors); +} + +1; + + + + + #package ApiCommonWebsite::View::GraphPackage::Templates::Proteomics::LogRatio::DS_8e133ba94b; #sub finalProfileAdjustments { From 96261ad1229f8c57bbf77d766dd56bae5b017605 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 9 Apr 2024 17:39:38 -0400 Subject: [PATCH 132/204] minor ordering fix for Pk phenotypegraph -refs #53740 --- View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm index 9caf219ff..7aea87e51 100644 --- a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm +++ b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm @@ -120,14 +120,14 @@ sub getPhenotypeSpecs { name => "Hybrid model score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Hybrid model score'" }, - {abbrev => "OIS", - name => "Occupancy index score", - query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Occupancy index score'" - }, {abbrev => "MIS", name => "Mutagenesis index score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Mutagenesis index score'" }, + {abbrev => "OIS", + name => "Occupancy index score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Occupancy index score'" + }, ]; } From 678dc188744491d4dfdadda6599c8ed56b0d045f Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Wed, 10 Apr 2024 16:29:17 -0400 Subject: [PATCH 133/204] fix legend --- View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm index 0ca0eed98..3573e48c4 100644 --- a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm +++ b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm @@ -106,7 +106,7 @@ package ApiCommonWebsite::View::GraphPackage::Templates::Proteomics::LogRatio::D sub finalProfileAdjustments { my ($self, $profile) = @_; - my $legend = ['haha']; + my $legend = ['Cpar_infected_over_control']; my $colors = ['gray']; $profile->setLegendLabels($legend); $profile->setColors($colors); From 94eaa57515a2816bb8ac4f72a68e6c4a225055c3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Apr 2024 03:39:33 +0000 Subject: [PATCH 134/204] npm: bump @veupathdb/genomics-site from 1.0.133 to 1.0.134 in /Site Bumps @veupathdb/genomics-site from 1.0.133 to 1.0.134. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 2b136e587..a149a9641 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.133" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.133.tgz#e4cb809c02af8530da151327dca8412a40a35e53" - integrity sha512-4yMHIjujVfmqiJAYf1gFItT0nnfAwEFa2z6m1mRl2+EXMrktGy9+aaIVTBG/CdwQTgDqD8tMbQWH2lRJadpJDg== + version "1.0.134" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.134.tgz#ceaca33965ae74b6ed361b60b6c04af74dbb7e15" + integrity sha512-NZANC9Mr/wjtrO2OYcYwQ6WA+aXN7f3/GvYgBaKpQRd1iiZVK934cfE5neC3c58jwuKTGvfJ9A6wrbU+sBXl5Q== From c121d8f4ba164cda3616d89f7e08174889ee8bac Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Thu, 11 Apr 2024 16:13:59 -0400 Subject: [PATCH 135/204] graphs for 2 toxo quantProt datasets -refs #51916 #51903 --- .../Templates/Proteomics/LogRatio.pm | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm index 3573e48c4..d0f85e665 100644 --- a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm +++ b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm @@ -115,6 +115,31 @@ sub finalProfileAdjustments { 1; +# toxo - tgonME49_quantitativeMassSpec_Hanggeli_SAG1_iTop3_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::Proteomics::LogRatio::DS_bf624abaf0; + +sub finalProfileAdjustments { + my ($self, $profile) = @_; + +# my $legend = ['C18_v_WT_iTop3','C33_v_WT_iTop3','C30_v_WT_iTop3','C6_v_WT_iTop3','C30_v_C18_iTop3','C6_v_C18_iTop3','C30_v_C33_iTop3','C6_v_C33_iTop3','C33_v_C18_iTop3,''C6_v_30_iTop3']; + my $colors = ['gray', 'gray', 'gray','gray', 'gray', 'gray','gray', 'gray', 'gray','gray',]; +# $profile->setLegendLabels($legend); + $profile->setColors($colors); +} +1; + +# toxo - tgonME49_quantitativeMassSpec_Hanggeli_4Clones_iTop3_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::Proteomics::LogRatio::DS_9ee5f5fb72; + +sub finalProfileAdjustments { + my ($self, $profile) = @_; + +# my $legend = ['C18_v_WT_iLFQ','C33_v_WT_iLFQ','C30_v_WT_iLFQ','C6_v_WT_iLFQ','C30_v_C18_iLFQ','C6_v_C18_iLFQ','C30_v_C33_iLFQ','C6_v_C33_iLFQ','C33_v_C18_iLFQ','C6_v_C30_iLFQ']; + my $colors = ['gray', 'gray', 'gray','gray', 'gray', 'gray','gray', 'gray', 'gray','gray',]; +# $profile->setLegendLabels($legend); + $profile->setColors($colors); +} +1; From 03838ff6c7f7a217bce25a0fc991777fa0b53949 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Apr 2024 03:14:10 +0000 Subject: [PATCH 136/204] npm: bump @veupathdb/genomics-site from 1.0.134 to 1.0.135 in /Site Bumps @veupathdb/genomics-site from 1.0.134 to 1.0.135. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a149a9641..277c7b4cc 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.134" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.134.tgz#ceaca33965ae74b6ed361b60b6c04af74dbb7e15" - integrity sha512-NZANC9Mr/wjtrO2OYcYwQ6WA+aXN7f3/GvYgBaKpQRd1iiZVK934cfE5neC3c58jwuKTGvfJ9A6wrbU+sBXl5Q== + version "1.0.135" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.135.tgz#f4d8ddc629f577f4343b4611fd7c6e177c619c23" + integrity sha512-/MTxzKvwwXIDWC2vRlJKz1dpONwEjRQtXELax4ibr2r4Pl1DpbkZ2CfBiMDc7f03XtIPPLwQB1OhEiu0poMJFQ== From cdf13c0b6c0bd17c2aecf57febf155019e858547 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 13 Apr 2024 03:11:59 +0000 Subject: [PATCH 137/204] npm: bump @veupathdb/genomics-site from 1.0.135 to 1.0.136 in /Site Bumps @veupathdb/genomics-site from 1.0.135 to 1.0.136. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 277c7b4cc..e6eb0b72c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.135" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.135.tgz#f4d8ddc629f577f4343b4611fd7c6e177c619c23" - integrity sha512-/MTxzKvwwXIDWC2vRlJKz1dpONwEjRQtXELax4ibr2r4Pl1DpbkZ2CfBiMDc7f03XtIPPLwQB1OhEiu0poMJFQ== + version "1.0.136" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.136.tgz#1cd886187d1359fde1f66c1f9e428dd474d1b99c" + integrity sha512-LGHdRUX0YW9vLAEvBJoUtETd5CK+3AqPWpFvmpsVmvPG0hCbxt8/UZaMmnt805OGZNaCClv+TA7vBs2gOCuQwQ== From f7fb83fb2e29deadd89b7b745bed44428a5e3f91 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Apr 2024 03:11:29 +0000 Subject: [PATCH 138/204] npm: bump @veupathdb/genomics-site from 1.0.136 to 1.0.137 in /Site Bumps @veupathdb/genomics-site from 1.0.136 to 1.0.137. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index e6eb0b72c..793e7b014 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.136" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.136.tgz#1cd886187d1359fde1f66c1f9e428dd474d1b99c" - integrity sha512-LGHdRUX0YW9vLAEvBJoUtETd5CK+3AqPWpFvmpsVmvPG0hCbxt8/UZaMmnt805OGZNaCClv+TA7vBs2gOCuQwQ== + version "1.0.137" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.137.tgz#cad934a317cc175bd8967b16d4fda92ccd1c223b" + integrity sha512-y0GvpdWx18WWNpZvU8hrYCqPcYXRUx7IvUf036JJSsXnAeUCXraNeBnuLDd8JVQwLf3fXlLxO1utFn0MGHYf6g== From 1cdc2543259386b2246565893f55cf71123b3b73 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 16 Apr 2024 15:06:25 -0400 Subject: [PATCH 139/204] remove "MIS" sample point from pknoH_phenotype_piggyBac_mutagenesis_HME_MIS_OIS_RSRC graph -refs #53740 --- View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm | 4 ---- 1 file changed, 4 deletions(-) diff --git a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm index 7aea87e51..2cb12bd67 100644 --- a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm +++ b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm @@ -120,10 +120,6 @@ sub getPhenotypeSpecs { name => "Hybrid model score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Hybrid model score'" }, - {abbrev => "MIS", - name => "Mutagenesis index score", - query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Mutagenesis index score'" - }, {abbrev => "OIS", name => "Occupancy index score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Occupancy index score'" From cfe59a268de4ba26362a02b7a198a45c9f96f4ee Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 17 Apr 2024 03:52:39 +0000 Subject: [PATCH 140/204] npm: bump @veupathdb/genomics-site from 1.0.137 to 1.0.138 in /Site Bumps @veupathdb/genomics-site from 1.0.137 to 1.0.138. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 793e7b014..f0b663c3d 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.137" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.137.tgz#cad934a317cc175bd8967b16d4fda92ccd1c223b" - integrity sha512-y0GvpdWx18WWNpZvU8hrYCqPcYXRUx7IvUf036JJSsXnAeUCXraNeBnuLDd8JVQwLf3fXlLxO1utFn0MGHYf6g== + version "1.0.138" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.138.tgz#abbd7a567fc7768c1aa73d95f3937527096ea30a" + integrity sha512-u16g74NH9WqBxb0QpbFr/VATfmMWPcOQzIBnSviyc+ZvsFE9TFZyHsmT8ADlhJfhh6f9gVPbN2MK7HJOAilYPw== From 8e4571c49ca9f965ac263f7a1cb41dca19ccaafe Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Apr 2024 03:50:13 +0000 Subject: [PATCH 141/204] npm: bump @veupathdb/genomics-site from 1.0.138 to 1.0.139 in /Site Bumps @veupathdb/genomics-site from 1.0.138 to 1.0.139. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f0b663c3d..57485a8ea 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.138" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.138.tgz#abbd7a567fc7768c1aa73d95f3937527096ea30a" - integrity sha512-u16g74NH9WqBxb0QpbFr/VATfmMWPcOQzIBnSviyc+ZvsFE9TFZyHsmT8ADlhJfhh6f9gVPbN2MK7HJOAilYPw== + version "1.0.139" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.139.tgz#afc04e19923ec423a05f87465feef09477c2387c" + integrity sha512-CkpBd5wmZebFuVET37XCLOS2GDpx6GDsfIyvhh9yEzVe+mtGyJWxMxACDZM6dgmTXDqV4yU77L3WrWk64/NEVA== From fee083861117ffc15b12af89b70a01d74fe2518f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Apr 2024 03:28:07 +0000 Subject: [PATCH 142/204] npm: bump @veupathdb/genomics-site from 1.0.139 to 1.0.140 in /Site Bumps @veupathdb/genomics-site from 1.0.139 to 1.0.140. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 57485a8ea..c92e0d9d0 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.139" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.139.tgz#afc04e19923ec423a05f87465feef09477c2387c" - integrity sha512-CkpBd5wmZebFuVET37XCLOS2GDpx6GDsfIyvhh9yEzVe+mtGyJWxMxACDZM6dgmTXDqV4yU77L3WrWk64/NEVA== + version "1.0.140" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.140.tgz#473b7172716e65eeec1e734cf53b19b14c016024" + integrity sha512-L19wzO7kwjx0+udHzM0KhOC2/sd5ohyP6+hlz0LJ9agY9RcTkhgVjRPvOuJkm6Y/kYp/8HAao2ySHMjq0qCzMg== From c4b93d5015eb8347d4f947bd8d0e90b06973fced Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 20 Apr 2024 03:29:54 +0000 Subject: [PATCH 143/204] npm: bump @veupathdb/genomics-site from 1.0.140 to 1.0.141 in /Site Bumps @veupathdb/genomics-site from 1.0.140 to 1.0.141. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index c92e0d9d0..1068615d8 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.140" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.140.tgz#473b7172716e65eeec1e734cf53b19b14c016024" - integrity sha512-L19wzO7kwjx0+udHzM0KhOC2/sd5ohyP6+hlz0LJ9agY9RcTkhgVjRPvOuJkm6Y/kYp/8HAao2ySHMjq0qCzMg== + version "1.0.141" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.141.tgz#a5706207ffdab84137ac79b9f24eeb1c42befbe4" + integrity sha512-sE46RoEbCXmt5lYQnJaqgVT8oWERGjNh8/nW0TFL9jl/4RUVivNu1jvWAs5yee2FqoLiJId4/kJKFtbSz2XN6w== From 987f1bdfff011e97a36d9c2d6013c2a226d136a9 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Mon, 22 Apr 2024 10:00:56 -0400 Subject: [PATCH 144/204] fix y axis label - refs #53995 --- View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm | 1 + 1 file changed, 1 insertion(+) diff --git a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm index d0f85e665..f0232fce2 100644 --- a/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm +++ b/View/lib/perl/GraphPackage/Templates/Proteomics/LogRatio.pm @@ -108,6 +108,7 @@ sub finalProfileAdjustments { my $legend = ['Cpar_infected_over_control']; my $colors = ['gray']; + $profile->setYaxisLabel('Relative Abundance'); $profile->setLegendLabels($legend); $profile->setColors($colors); } From 70e5cb106a3768cf36407c259c19ad03f83123a2 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Mon, 22 Apr 2024 22:25:21 -0400 Subject: [PATCH 145/204] Return more sensical error to users when proxy timeout occurs --- .../apicommon/model/report/sequence/SequenceReporter.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java index 0630c4802..51afeeadb 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java +++ b/Model/src/main/java/org/apidb/apicommon/model/report/sequence/SequenceReporter.java @@ -172,7 +172,11 @@ public void write(OutputStream out) throws WdkModelException { } else { LOG.error("Received 5xx response from sequence retrieval service with body: \n" + failure.getResponseBody()); - throw new RuntimeException(failure.getResponseBody()); + String failureResponseBody = failure.getResponseBody(); + if (failureResponseBody.contains("502 Proxy Error")) { + throw new PostValidationUserException("This request has timed out. If this problem persists, please contact us."); + } + throw new RuntimeException(failureResponseBody); } }); } From 26d3a622c73e615f90bc039d8f7724cffa31126d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 23 Apr 2024 03:07:03 +0000 Subject: [PATCH 146/204] npm: bump @veupathdb/genomics-site from 1.0.141 to 1.0.142 in /Site Bumps @veupathdb/genomics-site from 1.0.141 to 1.0.142. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 1068615d8..19c2191ab 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.141" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.141.tgz#a5706207ffdab84137ac79b9f24eeb1c42befbe4" - integrity sha512-sE46RoEbCXmt5lYQnJaqgVT8oWERGjNh8/nW0TFL9jl/4RUVivNu1jvWAs5yee2FqoLiJId4/kJKFtbSz2XN6w== + version "1.0.142" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.142.tgz#032543b41802a56245d2d4716942d855dc3f33bd" + integrity sha512-BjIQ2Tr0hUh9wEkKY5/+DMF/14vZ+gUZRRMilFDClQjeYlRb00ohH3emkPv45bq8chGvfuK90Wkp2JaBwYzwhg== From 64f31d72fd5a8919cc3abeb1acc959e3aa80f6db Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 23 Apr 2024 11:21:26 -0400 Subject: [PATCH 147/204] testing vdi prod with qa plasmo --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 443c1b4f6..9fb8192c5 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_QA_N + q2_prefix: VDI_CONTROL_PROD_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_QA_N + q2_prefix: VDI_DATASETS_PROD_N default: VDI_DATASETS_QA_N modelprop: From 8f763213131ebfa8e5ee92a6548250aa1a925687 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 23 Apr 2024 11:31:49 -0400 Subject: [PATCH 148/204] Add default value for showUnreleasedData --- .../roles/conifer/vars/ApiCommon/default.yml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml index 684b3ec04..ceb99476d 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml @@ -92,3 +92,20 @@ fisherexacttestconfig_dbLogin: '{{ modelconfig_appDb_login }}' fisherexacttestconfig_dbPassword: '{{ modelconfig_appDb_password }}' fisherexacttestconfig_perlExec: /usr/bin/perl fisherexacttestconfig_connectionUrl: "{{ '' if modelconfig_userDb_connectionUrl.startswith('=c=') else modelconfig_appDb_connectionUrl|jdbc2Dbi }}" + +_showUnreleasedDataByHostnamePrefix: + a: false + b: false + w: false + +# Construct a prefix from hostname, like "w" or "a". +# +# This will only match when a hostname starts with a single letter, followed by a single number, followed by a period: +# "a1.plasmodb.org" => "a" +# "b2.veupathdb.org" => "b" +# "joeuser.plasmodb.org" => "joeuser.plasmodb.org" +# +# When a Hostname does not match, the original will be returned. +hostname_prefix: "{{ hostname | regex_replace('^([a-z])[0-9][.].*','\\1') }}" + +showUnreleasedData: "{{ _showUnreleasedDataByHostnamePrefix[hostname_prefix] | default('true') }}" From 10118504163f0fe953f0a0146afeef80007e3a0a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 24 Apr 2024 03:16:32 +0000 Subject: [PATCH 149/204] npm: bump @veupathdb/genomics-site from 1.0.142 to 1.0.143 in /Site Bumps @veupathdb/genomics-site from 1.0.142 to 1.0.143. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 19c2191ab..91aad5f46 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.142" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.142.tgz#032543b41802a56245d2d4716942d855dc3f33bd" - integrity sha512-BjIQ2Tr0hUh9wEkKY5/+DMF/14vZ+gUZRRMilFDClQjeYlRb00ohH3emkPv45bq8chGvfuK90Wkp2JaBwYzwhg== + version "1.0.143" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.143.tgz#503cb072cb3e073e29fff24c8e0733035e76e577" + integrity sha512-Cl0CO4LSy5r0zqX8bSGWd5FXd731/Iunf+6SANfjs5Rg9v6I5tmQAGaNqpSkXhLDudnehj8wPqP05JlpvqEVKA== From db1c6b664432ed13d75d4e761de6a5057d5e3ed8 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Wed, 24 Apr 2024 09:49:31 -0400 Subject: [PATCH 150/204] testing vdi prod with qa plasmo --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 9fb8192c5..443c1b4f6 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_PROD_N + q2_prefix: VDI_CONTROL_QA_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_PROD_N + q2_prefix: VDI_DATASETS_QA_N default: VDI_DATASETS_QA_N modelprop: From 08f52d6248101786e2945448d029ec2acf69c65a Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Wed, 24 Apr 2024 12:58:46 -0400 Subject: [PATCH 151/204] addx axis label for Host quant prot graph -refs #53997 --- View/lib/perl/GraphPackage/Templates/Proteomics/NonRatio.pm | 1 + 1 file changed, 1 insertion(+) diff --git a/View/lib/perl/GraphPackage/Templates/Proteomics/NonRatio.pm b/View/lib/perl/GraphPackage/Templates/Proteomics/NonRatio.pm index 006466b47..470b30b73 100644 --- a/View/lib/perl/GraphPackage/Templates/Proteomics/NonRatio.pm +++ b/View/lib/perl/GraphPackage/Templates/Proteomics/NonRatio.pm @@ -68,6 +68,7 @@ sub finalProfileAdjustments { my $legend = ['GT1 0 to 16 hr','ME49 0 to 16 hr','ME49 0 to 44 hr', 'RH 0 to 36 hr', 'VEG 0 to 16 hr', 'VEG 0 to 44 hr']; $profile->setHasExtraLegend(1); + $profile->setXaxisLabel("Time Point (hours post infection)"); $profile->setLegendLabels($legend); return $self; } From ac77c0ae1fb051107fd8775bf6d16040d7116257 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Apr 2024 03:32:13 +0000 Subject: [PATCH 152/204] npm: bump @veupathdb/genomics-site from 1.0.143 to 1.0.144 in /Site Bumps @veupathdb/genomics-site from 1.0.143 to 1.0.144. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 91aad5f46..21f5303be 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.143" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.143.tgz#503cb072cb3e073e29fff24c8e0733035e76e577" - integrity sha512-Cl0CO4LSy5r0zqX8bSGWd5FXd731/Iunf+6SANfjs5Rg9v6I5tmQAGaNqpSkXhLDudnehj8wPqP05JlpvqEVKA== + version "1.0.144" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.144.tgz#f9c495a4c8a445a9a627a9dc960c07d5f5852246" + integrity sha512-NGzV+tvUhfdW5KSBt2YOwZDngPwW7sRKFpacB+rPB9uJvjo7DYwr9u+kzY+ziYLSYFI5KTfjX5yJ4p6EhV1tLQ== From bddd58179e5432dc96dbe130d018dd60582600ee Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 25 Apr 2024 23:19:54 -0400 Subject: [PATCH 153/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 21f5303be..d6d260379 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.144" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.144.tgz#f9c495a4c8a445a9a627a9dc960c07d5f5852246" - integrity sha512-NGzV+tvUhfdW5KSBt2YOwZDngPwW7sRKFpacB+rPB9uJvjo7DYwr9u+kzY+ziYLSYFI5KTfjX5yJ4p6EhV1tLQ== + version "1.0.145" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.145.tgz#e8cd3faee9321e6f8ebd957c3163282bd0947cf0" + integrity sha512-4rs01uEiwkUUqZ3qZSVy2OtrPuMmqfaURs4l3QsvUdsqWLhs2SViT76MOLUuVPE93D0woTNTd/7jWwDjJfq0Rg== From a949e00fc87be6689254b819579f51cbc030f048 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 27 Apr 2024 03:18:54 +0000 Subject: [PATCH 154/204] npm: bump @veupathdb/genomics-site from 1.0.145 to 1.0.146 in /Site Bumps @veupathdb/genomics-site from 1.0.145 to 1.0.146. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index d6d260379..20b4df960 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.145" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.145.tgz#e8cd3faee9321e6f8ebd957c3163282bd0947cf0" - integrity sha512-4rs01uEiwkUUqZ3qZSVy2OtrPuMmqfaURs4l3QsvUdsqWLhs2SViT76MOLUuVPE93D0woTNTd/7jWwDjJfq0Rg== + version "1.0.146" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.146.tgz#3fef71270f08a45396e1ca0249a26493c373cb32" + integrity sha512-hcrHlZLaWlELpZJyIpZtd57uLatpuI+4O8x4LnLc7aAPVrzGa6AYCix7hoEeM0JU1EH4KK2RNebe/9ORvIcQqw== From 5e3365387aa96fa31a9ce7821836906efd427cc5 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Mon, 29 Apr 2024 12:03:51 -0400 Subject: [PATCH 155/204] qa.plasmo used to test vdi_prod uder datasets --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 443c1b4f6..9fb8192c5 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_QA_N + q2_prefix: VDI_CONTROL_PROD_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_QA_N + q2_prefix: VDI_DATASETS_PROD_N default: VDI_DATASETS_QA_N modelprop: From 95269b932f685afa323b10cdd5e43db391cd331a Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Mon, 29 Apr 2024 14:40:26 -0400 Subject: [PATCH 156/204] qa.plasmo used to test vdi_prod uder datasets --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 9fb8192c5..443c1b4f6 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_PROD_N + q2_prefix: VDI_CONTROL_QA_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_PROD_N + q2_prefix: VDI_DATASETS_QA_N default: VDI_DATASETS_QA_N modelprop: From be7ee80e8304c3696ab6544084e69183c9aee2ab Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 30 Apr 2024 03:45:19 +0000 Subject: [PATCH 157/204] npm: bump @veupathdb/genomics-site from 1.0.146 to 1.0.147 in /Site Bumps @veupathdb/genomics-site from 1.0.146 to 1.0.147. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... 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z9J848#qye+eJCERY0Vq{?pny!gdk99+XI@5wfnG4^cj#T+0(AFexk$bKD=P~r=#h+#ms&$VN#4F~gXKVk3v3U`$K8Yqb0J${r3 X5FkK-0t5sMuh}F^tL6Uy>%afm*@h$R literal 0 HcmV?d00001 From 4e6ce81b7ddc4c3569027f2032f43b74b4c6f1d6 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Tue, 30 Apr 2024 17:16:13 -0400 Subject: [PATCH 159/204] add graph for Adams piggybac dataset -refs #54156 --- .../GraphPackage/Templates/PhenotypeScore.pm | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm index 2cb12bd67..316513d40 100644 --- a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm +++ b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm @@ -130,6 +130,35 @@ sub getPhenotypeSpecs { 1; + +# pknoA1H1_phenotype_piggyBac_mutagenesis_MIS_MFS_RSRC +package ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore::DS_66b6e821e7; +use strict; +use vars qw( @ISA ); + +@ISA = qw(ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore ); + +sub getPhenotypeSpecs { + return [ {abbrev => "MIS", + name => "MIS score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MIS'" + }, + {abbrev => "MIS plus", + name => "MIS+ score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MIS plus'" + }, + {abbrev => "MFS", + name => "MFS score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MFS'" + }, + ]; +} + +1; + + + + package ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore::DS_90eea17ef6; use strict; use vars qw( @ISA ); From 8e65308ba31cfbc58283f40e62788b067b349bac Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 1 May 2024 03:09:33 +0000 Subject: [PATCH 160/204] npm: bump @veupathdb/genomics-site from 1.0.147 to 1.0.148 in /Site Bumps @veupathdb/genomics-site from 1.0.147 to 1.0.148. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 3f7859808..dcf95e81f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.147" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.147.tgz#2cbd3457a2034d23b08767c2482c3679c57df3e2" - integrity sha512-onHpZ3ZblXsQcxmW9bh5656+xmzeNWd9AVayXBLATHPXHSa9m8wGP4iv4ej3E6HMXCOirOemHVoXZkX1cY0nUw== + version "1.0.148" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.148.tgz#51f18145c42e08bce31777434db63afff07f29ef" + integrity sha512-4ZpAr8iPrH5aSTEBbFnXSBtqBi+p8dCIt+tTdo8Yr/naxhgLgixHpFYpYjykCWYMAC5r3wqy7XhqFQ4c4BdZeg== From 8c0ba2b0659eb4dc2c4155549613831e3ed30e26 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 1 May 2024 13:19:05 -0400 Subject: [PATCH 161/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index dcf95e81f..834595432 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.148" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.148.tgz#51f18145c42e08bce31777434db63afff07f29ef" - integrity sha512-4ZpAr8iPrH5aSTEBbFnXSBtqBi+p8dCIt+tTdo8Yr/naxhgLgixHpFYpYjykCWYMAC5r3wqy7XhqFQ4c4BdZeg== + version "1.0.149" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.149.tgz#3842fb696c5498132f91a9bf6bdb2555134c59f3" + integrity sha512-8lLJ/R+I1Szudr9OYWM1GDiOEdhvoA4LIbbshKF/HoeAep3DA4Hpjn9+12pCz4AUMSR7ZJxgCGf+XKie3lzkBg== From 3583797b1248a4dbcb5dad41e01b608c7e21090d Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Wed, 1 May 2024 13:52:41 -0400 Subject: [PATCH 162/204] conifer qa site using prod schema --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 443c1b4f6..9fb8192c5 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_QA_N + q2_prefix: VDI_CONTROL_PROD_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_QA_N + q2_prefix: VDI_DATASETS_PROD_N default: VDI_DATASETS_QA_N modelprop: From 9ae8758ae6fa516afc6c714f3ec1650208068a71 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 3 May 2024 03:52:56 +0000 Subject: [PATCH 163/204] npm: bump @veupathdb/genomics-site from 1.0.149 to 1.0.150 in /Site Bumps @veupathdb/genomics-site from 1.0.149 to 1.0.150. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 834595432..4d14d28f5 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.149" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.149.tgz#3842fb696c5498132f91a9bf6bdb2555134c59f3" - integrity sha512-8lLJ/R+I1Szudr9OYWM1GDiOEdhvoA4LIbbshKF/HoeAep3DA4Hpjn9+12pCz4AUMSR7ZJxgCGf+XKie3lzkBg== + version "1.0.150" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.150.tgz#c92670e0570daba6331327a43912fbcface83190" + integrity sha512-K/3Il3xXhutfQa5OFyGD3c5B2Ge6WAC8KgHgf1es0OVPdYVrfn8QcKoN917ZPKDNSB0do/tdXocT2B6zCvyNdg== From 491fab8400809259bcc6dafd5e52226c23d18436 Mon Sep 17 00:00:00 2001 From: Bindu Gajria Date: Fri, 3 May 2024 09:44:35 -0400 Subject: [PATCH 164/204] reordering of samples for 2 plasmo datasets - refs #54156 --- .../GraphPackage/Templates/PhenotypeScore.pm | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm index 316513d40..91d8ab762 100644 --- a/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm +++ b/View/lib/perl/GraphPackage/Templates/PhenotypeScore.pm @@ -116,14 +116,14 @@ use vars qw( @ISA ); @ISA = qw(ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore ); sub getPhenotypeSpecs { - return [ {abbrev => "HMS", - name => "Hybrid model score", - query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Hybrid model score'" - }, - {abbrev => "OIS", + return [ {abbrev => "OIS", name => "Occupancy index score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Occupancy index score'" }, + {abbrev => "HMS", + name => "Hybrid model score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'Hybrid model score'" + }, ]; } @@ -139,14 +139,14 @@ use vars qw( @ISA ); @ISA = qw(ApiCommonWebsite::View::GraphPackage::Templates::PhenotypeScore ); sub getPhenotypeSpecs { - return [ {abbrev => "MIS", - name => "MIS score", - query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MIS'" - }, - {abbrev => "MIS plus", + return [ {abbrev => "MIS plus", name => "MIS+ score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MIS plus'" }, + {abbrev => "MIS", + name => "MIS score", + query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MIS'" + }, {abbrev => "MFS", name => "MFS score", query => "select ga.source_id, r.score as value from apidb.phenotypescore r, apidbtuning.geneattributes ga where ga.na_feature_id = r.na_feature_id and r.score_type = 'MFS'" From 5645a0f0882c576d045e4d7f4ea5f997ef7166f1 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 6 May 2024 23:09:07 -0400 Subject: [PATCH 165/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4d14d28f5..8f60d0a0a 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.150" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.150.tgz#c92670e0570daba6331327a43912fbcface83190" - integrity sha512-K/3Il3xXhutfQa5OFyGD3c5B2Ge6WAC8KgHgf1es0OVPdYVrfn8QcKoN917ZPKDNSB0do/tdXocT2B6zCvyNdg== + version "1.0.151" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.151.tgz#a8972d1113e19951d01efb6a9fd6bfc932e6e79b" + integrity sha512-proRpTArbQA1irUxy8ac1eaUODGlTRGIJl19YWRoVOObK0x/W1KDY+UuJUN76uq4IYTHOsaCB6lN7cXEeE3qOA== From ed6916cb579834edfad060d6cec695a4e28a55d8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 9 May 2024 03:50:29 +0000 Subject: [PATCH 166/204] npm: bump @veupathdb/genomics-site from 1.0.151 to 1.0.152 in /Site Bumps @veupathdb/genomics-site from 1.0.151 to 1.0.152. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 8f60d0a0a..0b493438f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.151" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.151.tgz#a8972d1113e19951d01efb6a9fd6bfc932e6e79b" - integrity sha512-proRpTArbQA1irUxy8ac1eaUODGlTRGIJl19YWRoVOObK0x/W1KDY+UuJUN76uq4IYTHOsaCB6lN7cXEeE3qOA== + version "1.0.152" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.152.tgz#3ddcf1e572cd686a87625affc38bf53335d14c5a" + integrity sha512-oV+dGrV3iylv1eX3zjzXQY585vq0g+VRM2MXMKRxX5lK33Y1aFaNx4YLjK790v8+4/NOI6DAIMI9m1i+AIr8fw== From 86e25bb4d4c509355f106be9df7a17f87fdadd4b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 10 May 2024 03:11:41 +0000 Subject: [PATCH 167/204] npm: bump @veupathdb/genomics-site from 1.0.152 to 1.0.153 in /Site Bumps @veupathdb/genomics-site from 1.0.152 to 1.0.153. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 0b493438f..8156489bc 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.152" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.152.tgz#3ddcf1e572cd686a87625affc38bf53335d14c5a" - integrity sha512-oV+dGrV3iylv1eX3zjzXQY585vq0g+VRM2MXMKRxX5lK33Y1aFaNx4YLjK790v8+4/NOI6DAIMI9m1i+AIr8fw== + version "1.0.153" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.153.tgz#140678cfc9fabe996231d88eb16e4394cbf5b0c6" + integrity sha512-TFRhls/c8z5IdU9lrAUxUo4CYflLc2qZQwW4G7eTE2jzBbhxMu/v5wGMy/sCwdlolPK1DMe6uME/HJZC4dKRpA== From 0b3354c439cef98ba3e13d3e1cd060b3894952a1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 11 May 2024 03:10:02 +0000 Subject: [PATCH 168/204] npm: bump @veupathdb/genomics-site from 1.0.153 to 1.0.154 in /Site Bumps @veupathdb/genomics-site from 1.0.153 to 1.0.154. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 8156489bc..883fe8976 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.153" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.153.tgz#140678cfc9fabe996231d88eb16e4394cbf5b0c6" - integrity sha512-TFRhls/c8z5IdU9lrAUxUo4CYflLc2qZQwW4G7eTE2jzBbhxMu/v5wGMy/sCwdlolPK1DMe6uME/HJZC4dKRpA== + version "1.0.154" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.154.tgz#da9e0c3c4dc887a4be1c9373686e748fffa22be8" + integrity sha512-n2UhFn+FTp0ATbht+cHe5gqrHDWZ6jm00eOrvAjLMV6kas8Vdnz5xS3iF4LGs1lnDg9z6OGvayl6idjGfTlTpw== From e2b62cd447198375dd47aabb19a76c729ebe7cc0 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Mon, 13 May 2024 16:16:21 -0400 Subject: [PATCH 169/204] correct vdi schema for qa sites --- .../roles/conifer/vars/ApiCommon/production/default.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 9fb8192c5..443c1b4f6 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -20,7 +20,7 @@ vdi_control_env_map: q1_prefix: VDI_CONTROL_QA_S w2_prefix: VDI_CONTROL_PROD_N b2_prefix: VDI_CONTROL_BETA_N - q2_prefix: VDI_CONTROL_PROD_N + q2_prefix: VDI_CONTROL_QA_N default: VDI_CONTROL_QA_N vdi_datasets_env_map: @@ -29,7 +29,7 @@ vdi_datasets_env_map: q1_prefix: VDI_DATASETS_QA_S w2_prefix: VDI_DATASETS_PROD_N b2_prefix: VDI_DATASETS_BETA_N - q2_prefix: VDI_DATASETS_PROD_N + q2_prefix: VDI_DATASETS_QA_N default: VDI_DATASETS_QA_N modelprop: From 513c95089a5c4690191c0bf1376b3d6dfe04ac9b Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Tue, 14 May 2024 13:29:35 -0400 Subject: [PATCH 170/204] dataplotter user dataset queries to use VDI schema --- .../dataPlotter/ProfileSetService.java | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java b/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java index 3f74395eb..8847e1f90 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java @@ -18,6 +18,7 @@ import org.gusdb.fgputil.db.stream.ResultSetToJsonConverter; import org.gusdb.fgputil.functional.Functions; import org.gusdb.wdk.model.WdkModelException; +import org.gusdb.wdk.model.WdkModel; import org.gusdb.wdk.service.service.AbstractWdkService; import org.json.JSONArray; import org.json.JSONObject; @@ -66,6 +67,8 @@ public Response getProfileSetIds( String projectId = getWdkModel().getProjectId(); String sql = DataPlotterQueries.getQueryMap(projectId).get("profile_set_ids"); sql = sql.replaceAll("\\$datasetId", datasetId); + String vdiSchema = getWdkModel().getProperties().get("VDI_DATASETS_SCHEMA"); + sql = sql.replaceAll("@VDI_DATASETS_SCHEMA@", vdiSchema); return getStreamingResponse(sql, "getProfileSetIds", "Failed running SQL to fetch user dataset profile set ids."); } @@ -270,7 +273,7 @@ public Response getPlotData( "plotData", "Failed running SQL to fetch plot data."); } - private static String getProfileSetSql(String projectId, String profileSetName, String profileType, String sourceId, String displayName, int order) { + private String getProfileSetSql(String projectId, String profileSetName, String profileType, String sourceId, String displayName, int order) { String colsToReturn = order + " as profile_order, name, value, samplenames.profile_set_name, samplenames.profile_type, samplenames.element_order"; if (displayName != null) { @@ -286,7 +289,7 @@ private static String getProfileSetSql(String projectId, String profileSetName, return sql; } - private static String getProfileSetByECSql(String projectId, String profileSetName, String profileType, String sourceId, int order) { + private String getProfileSetByECSql(String projectId, String profileSetName, String profileType, String sourceId, int order) { String sql = DataPlotterQueries.getQueryMap(projectId).get("profile_set_by_ec"); sql = sql.replaceAll("\\$order", Integer.toString(order)); @@ -297,7 +300,7 @@ private static String getProfileSetByECSql(String projectId, String profileSetNa return sql; } - private static String getProfileSetWithMetadataSql(String projectId, String profileSetName, String profileType, String facet, String xAxis, String sourceId, int order) { + private String getProfileSetWithMetadataSql(String projectId, String profileSetName, String profileType, String facet, String xAxis, String sourceId, int order) { String sql = DataPlotterQueries.getQueryMap(projectId).get("profile_set_with_metadata"); sql = sql.replaceAll("\\$order", Integer.toString(order)); @@ -310,7 +313,7 @@ private static String getProfileSetWithMetadataSql(String projectId, String prof return sql; } - private static String getProfileSetNamesSql(String projectId, String datasetPresenterId, String sourceId) { + private String getProfileSetNamesSql(String projectId, String datasetPresenterId, String sourceId) { String sql = sourceId.equals("none") ? DataPlotterQueries.getQueryMap(projectId).get("profile_set_names") : DataPlotterQueries.getQueryMap(projectId).get("profile_set_names_by_source_id"); @@ -321,7 +324,7 @@ private static String getProfileSetNamesSql(String projectId, String datasetPres return sql; } - private static String getRankedValuesSql(String projectId, String sqlName, String sourceIdValueQuery, String sourceId, String N, String name, int order) { + private String getRankedValuesSql(String projectId, String sqlName, String sourceIdValueQuery, String sourceId, String N, String name, int order) { String columnsToReturn = ""; String columnsInDat = "source_id, value"; if (sqlName.equals("RankedNthSourceIdNames")) { @@ -347,19 +350,21 @@ private static String getRankedValuesSql(String projectId, String sqlName, Strin return sql; } - private static String getUserDatasetsSql(String projectId, String profileSetId, String sourceId, String name, int order) { + private String getUserDatasetsSql(String projectId, String profileSetId, String sourceId, String name, int order) { String sql = DataPlotterQueries.getQueryMap(projectId).get("user_datasets"); sql = sql.replaceAll("\\$order", Integer.toString(order)); sql = sql.replaceAll("\\$name", name); sql = sql.replaceAll("\\$sourceId", sourceId); sql = sql.replaceAll("\\$profileSetId", profileSetId); + String vdiSchema = getWdkModel().getProperties().get("VDI_DATASETS_SCHEMA"); + sql = sql.replaceAll("@VDI_DATASETS_SCHEMA@", vdiSchema); return sql; } //TODO figure adding antisense result to return plot ready data - private static String getSenseAntisenseSql(String projectId, String senseProfileSetId, String antisenseProfileSetId, String sourceId, String floor) { + private String getSenseAntisenseSql(String projectId, String senseProfileSetId, String antisenseProfileSetId, String sourceId, String floor) { String sql = DataPlotterQueries.getQueryMap(projectId).get("sense_antisense"); sql = sql.replaceAll("\\$floor", floor); @@ -371,7 +376,7 @@ private static String getSenseAntisenseSql(String projectId, String senseProfile } - private static String getPathwayGeneraSql(String projectId, String generaSql, String sourceId) { + private String getPathwayGeneraSql(String projectId, String generaSql, String sourceId) { String sql = DataPlotterQueries.getQueryMap(projectId).get("pathway_genera"); sql = sql.replaceAll("\\$generaSql", generaSql); @@ -381,7 +386,7 @@ private static String getPathwayGeneraSql(String projectId, String generaSql, St } //some of these nameless params may be null.. consider better ways to do this - private static String getSql(String projectId, String sqlName, String param1, String param2, String param3, String param4, String param5, int order) { + private String getSql(String projectId, String sqlName, String param1, String param2, String param3, String param4, String param5, int order) { switch(sqlName) { case "ProfileSetNames": return getProfileSetNamesSql(projectId, param1, param2); From 28aecafb0826c0879ac5dce2d3607d0bed5674e6 Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Thu, 16 May 2024 11:14:38 -0400 Subject: [PATCH 171/204] new prop for UD files --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index 443c1b4f6..d0626a921 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -33,6 +33,7 @@ vdi_datasets_env_map: default: VDI_DATASETS_QA_N modelprop: + VDI_DATASETS_DIRECTORY: "/var/www/Common/userDatasets" HOSTNAME: "{{ hostname }}" PREFIX_VDI: "{{ prefix_vdi }}" PREFIX: "{{ prefix }}" From 9cab5e61e9172fb25aaa93fc0c90f97797c6f8af Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 22 May 2024 03:46:58 +0000 Subject: [PATCH 172/204] --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 883fe8976..f1adb9399 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.154" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.154.tgz#da9e0c3c4dc887a4be1c9373686e748fffa22be8" - integrity sha512-n2UhFn+FTp0ATbht+cHe5gqrHDWZ6jm00eOrvAjLMV6kas8Vdnz5xS3iF4LGs1lnDg9z6OGvayl6idjGfTlTpw== + version "1.0.155" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.155.tgz#b26f945ae685f3b440759ad7abae4f73a07f34a9" + integrity sha512-IZeGUYd03LlWBA5Pn5Ky40pnqf494lWYYP/Wr6+EM82iDfdXSx7pfF0DLyrnvwvV8uBJn0Fn/DywtGy3dwrQjg== From 5e36eafe098279e1f74fd2e8776298a38381da62 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 24 Jun 2024 11:34:33 -0400 Subject: [PATCH 173/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index f1adb9399..a365c26ff 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.155" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.155.tgz#b26f945ae685f3b440759ad7abae4f73a07f34a9" - integrity sha512-IZeGUYd03LlWBA5Pn5Ky40pnqf494lWYYP/Wr6+EM82iDfdXSx7pfF0DLyrnvwvV8uBJn0Fn/DywtGy3dwrQjg== + version "1.0.158" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.158.tgz#68c9d5bffa0c1ad1039e15730bfff59224db99fc" + integrity sha512-8Vlvy+JhRQqJNDRXdhHo73kaxijOIVE6j9mHK4hz8w4yALv2bu9YMzT4Iga2butmP1cU1Hz00V7PVqVjaxI5RA== From d7894d8152d2cef49a9f94d47f75c564642d59b7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 26 Jun 2024 03:33:12 +0000 Subject: [PATCH 174/204] npm: bump @veupathdb/genomics-site from 1.0.158 to 1.0.159 in /Site Bumps @veupathdb/genomics-site from 1.0.158 to 1.0.159. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index a365c26ff..7cc7ffead 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.158" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.158.tgz#68c9d5bffa0c1ad1039e15730bfff59224db99fc" - integrity sha512-8Vlvy+JhRQqJNDRXdhHo73kaxijOIVE6j9mHK4hz8w4yALv2bu9YMzT4Iga2butmP1cU1Hz00V7PVqVjaxI5RA== + version "1.0.159" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.159.tgz#30f9562f22c3251266f6271017e0cdfab4804ac0" + integrity sha512-9QSoDDjFTBZ0OdmpXfy0nuB5ZsSwRfaHM1QfZZdc6LBJZIsQXYO6BVLYVQEGmZAJ0gUuVO+cx8hGOstgEClz6g== From 333cee062a89745645d69e3123a05a0514f29104 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Fri, 28 Jun 2024 15:55:53 -0400 Subject: [PATCH 175/204] add legend for antismash colors --- 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deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7cc7ffead..b10d29999 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.159" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.159.tgz#30f9562f22c3251266f6271017e0cdfab4804ac0" - integrity sha512-9QSoDDjFTBZ0OdmpXfy0nuB5ZsSwRfaHM1QfZZdc6LBJZIsQXYO6BVLYVQEGmZAJ0gUuVO+cx8hGOstgEClz6g== + version "1.0.160" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.160.tgz#6504a20fdbbb21bb7564e134d67a242ac7b60756" + integrity sha512-m/pNkuidUIG3Iubi0Gv9oMf5xOUkaTyYRY9DrIcw91tbuh1GbXRIgSYw/SxM8bS3b28EZn6ZuQzhXtaiqVlzAw== From 7e085b5b9078bee1d97c0bfe892a2aa668fe3764 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jul 2024 03:49:41 +0000 Subject: [PATCH 177/204] npm: bump @veupathdb/genomics-site from 1.0.160 to 1.0.161 in /Site Bumps @veupathdb/genomics-site from 1.0.160 to 1.0.161. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index b10d29999..6e20ebfb5 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.160" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.160.tgz#6504a20fdbbb21bb7564e134d67a242ac7b60756" - integrity sha512-m/pNkuidUIG3Iubi0Gv9oMf5xOUkaTyYRY9DrIcw91tbuh1GbXRIgSYw/SxM8bS3b28EZn6ZuQzhXtaiqVlzAw== + version "1.0.161" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.161.tgz#efedf76e815b80e21183b45c4263bbdd38c44a82" + integrity sha512-crrU3m6VhpUhvuMQuwZ3pvTV+vkVK/jykmDv9xeIZAvs5YW9Jqvvlvu87e1LN/3l7hfAZeVUMd7evNng82gTcw== From b79dc99345dffe3981329b7a826e17533eb55dfb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Jul 2024 03:32:52 +0000 Subject: [PATCH 178/204] npm: bump @veupathdb/genomics-site from 1.0.161 to 1.0.162 in /Site Bumps @veupathdb/genomics-site from 1.0.161 to 1.0.162. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 6e20ebfb5..bbe425d0c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.161" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.161.tgz#efedf76e815b80e21183b45c4263bbdd38c44a82" - integrity sha512-crrU3m6VhpUhvuMQuwZ3pvTV+vkVK/jykmDv9xeIZAvs5YW9Jqvvlvu87e1LN/3l7hfAZeVUMd7evNng82gTcw== + version "1.0.162" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.162.tgz#c8d71ad2f355421e822e7f3b5bc2bd7aaa0a703b" + integrity sha512-Hipy+80yr8HtWmPa7/87gz/lRH4tttfVaFtNIy5ws7qNErXomqpL1+vTHy7e0Oz+sNGKRHBU43wg6VYqDXbqrA== From ba5d92221094058be5c58e384bb35ce46f295565 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 03:49:22 +0000 Subject: [PATCH 179/204] npm: bump @veupathdb/genomics-site from 1.0.162 to 1.0.163 in /Site Bumps @veupathdb/genomics-site from 1.0.162 to 1.0.163. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index bbe425d0c..bb3d4a6b1 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.162" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.162.tgz#c8d71ad2f355421e822e7f3b5bc2bd7aaa0a703b" - integrity sha512-Hipy+80yr8HtWmPa7/87gz/lRH4tttfVaFtNIy5ws7qNErXomqpL1+vTHy7e0Oz+sNGKRHBU43wg6VYqDXbqrA== + version "1.0.163" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.163.tgz#07153aade85f986ec5c29d4cc0ed179713973406" + integrity sha512-muBMPwbO1nv2iUzTw7TNGUmyWmtdNYzkoN8Ui8eoYg9hyKepAIbSfVNEECcig5R8/j8ZEQSc8Jz2YygMPKmC8Q== From 11a8e7083890a8d7f0a6e33059a38d426fc55581 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 27 Jul 2024 03:45:02 +0000 Subject: [PATCH 180/204] npm: bump @veupathdb/genomics-site from 1.0.163 to 1.0.165 in /Site Bumps @veupathdb/genomics-site from 1.0.163 to 1.0.165. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index bb3d4a6b1..cc335e16f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.163" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.163.tgz#07153aade85f986ec5c29d4cc0ed179713973406" - integrity sha512-muBMPwbO1nv2iUzTw7TNGUmyWmtdNYzkoN8Ui8eoYg9hyKepAIbSfVNEECcig5R8/j8ZEQSc8Jz2YygMPKmC8Q== + version "1.0.165" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.165.tgz#6c09da816110d13356a2dd5c96766f49736655ae" + integrity sha512-P0bUpM5+kK8TJpkBH3esJUJGnWZSPRPt+bawAE+EGEkCzdIGnhqwPxAHZbqh9xN0JQ92xTkHmFmNBTzswbAaTA== From f1b92aef3ca86268f937cdb2d871ee9ad63679af Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 31 Jul 2024 03:24:38 +0000 Subject: [PATCH 181/204] npm: bump @veupathdb/genomics-site from 1.0.165 to 1.0.166 in /Site Bumps @veupathdb/genomics-site from 1.0.165 to 1.0.166. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index cc335e16f..1b25a3a63 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.165" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.165.tgz#6c09da816110d13356a2dd5c96766f49736655ae" - integrity sha512-P0bUpM5+kK8TJpkBH3esJUJGnWZSPRPt+bawAE+EGEkCzdIGnhqwPxAHZbqh9xN0JQ92xTkHmFmNBTzswbAaTA== + version "1.0.166" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.166.tgz#678b0d755b6613753d93d0c2bfef5fd751a7c955" + integrity sha512-Ye7JVUtI8ID/x9w/F2NRkbcQWMV6b5DaiOFnBfqqjtsAlVWxjbzbcJp439Cn7+kbWjCFdnVtwcB9TCB3N+Ks1A== From 7a1c1556c01ad759a0d78dec1739d93fb9f37f1f Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Sat, 3 Aug 2024 13:30:38 -0400 Subject: [PATCH 182/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 1b25a3a63..37d007475 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.0.166" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.0.166.tgz#678b0d755b6613753d93d0c2bfef5fd751a7c955" - integrity sha512-Ye7JVUtI8ID/x9w/F2NRkbcQWMV6b5DaiOFnBfqqjtsAlVWxjbzbcJp439Cn7+kbWjCFdnVtwcB9TCB3N+Ks1A== + version "1.1.0" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.0.tgz#03c989ff77d50ec0d275205c6c0022769ddd0f1c" + integrity sha512-fz3ZQXYUg8wPyuZNz0zTmUWthQfpMHSeIHawgNq8rStC02vWzINseXuzZtQl4nYTez7LejgafMW1DuQ2IsvSYw== From 72c7720730e7e64ded71b9f159701aa7b8366f56 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 5 Aug 2024 22:30:59 -0400 Subject: [PATCH 183/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 37d007475..c568b7b75 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.1.0" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.0.tgz#03c989ff77d50ec0d275205c6c0022769ddd0f1c" - integrity sha512-fz3ZQXYUg8wPyuZNz0zTmUWthQfpMHSeIHawgNq8rStC02vWzINseXuzZtQl4nYTez7LejgafMW1DuQ2IsvSYw== + version "1.1.1" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.1.tgz#cfa4dcfa3e5840af51115385ba96049314d5a95a" + integrity sha512-D/It4QPqUj3X2T56KLXRQJB2ZJFK8KmA6ixSr+ux5yO34NX/FcsD5qHaRF64FBlPtSv9nvLbEuM3++E5V9agKg== From 341d2567d937a620a62d7eb51bbd46a73690ce9a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 7 Aug 2024 03:20:57 +0000 Subject: [PATCH 184/204] npm: bump @veupathdb/genomics-site from 1.1.1 to 1.1.2 in /Site Bumps @veupathdb/genomics-site from 1.1.1 to 1.1.2. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index c568b7b75..1c8aa3ca4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.1.1" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.1.tgz#cfa4dcfa3e5840af51115385ba96049314d5a95a" - integrity sha512-D/It4QPqUj3X2T56KLXRQJB2ZJFK8KmA6ixSr+ux5yO34NX/FcsD5qHaRF64FBlPtSv9nvLbEuM3++E5V9agKg== + version "1.1.2" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.2.tgz#94096e540ea5f82341977f962a0f4a46e5cd26af" + integrity sha512-Abomqz5GNtQOhm+4825+wKiXxlDwX1tllq5PdbLrxNDp2VPzn48EmT7WNrvCwEdP1WQHyBRo2aJEi47gLHYjZA== From 4c78326a7456cba05551b9560dc0de2ff8193fff Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Fri, 9 Aug 2024 16:43:47 -0400 Subject: [PATCH 185/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 1c8aa3ca4..3d2e5b06c 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.1.2" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.2.tgz#94096e540ea5f82341977f962a0f4a46e5cd26af" - integrity sha512-Abomqz5GNtQOhm+4825+wKiXxlDwX1tllq5PdbLrxNDp2VPzn48EmT7WNrvCwEdP1WQHyBRo2aJEi47gLHYjZA== + version "1.1.3" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.3.tgz#2cbeb192fdf0c1037217adb1e11487b77442fed9" + integrity sha512-bC7OIe8g42ZlUGr0Fe2H/R92YUN7DRHwG0RuDc498Z67SSASYnfOG8VIasE1qmwB+j/D/QCocdWIVlTjFT074g== From 9b69ce716902967e2274fb8ffd9651afeeff1d06 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 12 Aug 2024 14:32:57 -0400 Subject: [PATCH 186/204] Add dispatchers for UrlRewriteFilter --- Site/webapp/WEB-INF/web.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Site/webapp/WEB-INF/web.xml b/Site/webapp/WEB-INF/web.xml index 4add40db9..aa5ab0d6c 100644 --- a/Site/webapp/WEB-INF/web.xml +++ b/Site/webapp/WEB-INF/web.xml @@ -97,6 +97,8 @@ UrlRewriteFilter /* + REQUEST + FORWARD @@ -196,4 +198,3 @@ - From c750443845cd873d046202ccf691af691d6b8e21 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 12 Aug 2024 15:17:15 -0400 Subject: [PATCH 187/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 3d2e5b06c..88c764cd8 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.1.3" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.3.tgz#2cbeb192fdf0c1037217adb1e11487b77442fed9" - integrity sha512-bC7OIe8g42ZlUGr0Fe2H/R92YUN7DRHwG0RuDc498Z67SSASYnfOG8VIasE1qmwB+j/D/QCocdWIVlTjFT074g== + version "1.1.6" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.6.tgz#b42484160f9d03d984b8255e013b5b4ddf9b3d4d" + integrity sha512-3YQRc4IYqZc+EEQTLmF5159hkfxlRhbl5LNtQebRdFfL3Fuz70taMxUX2NTfjNECNp7EZOxJmr/OwMDv5Qf1Cw== From a785254a942993fa2d5d89c1a3246505e23f2fbe Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 13 Aug 2024 23:47:06 -0400 Subject: [PATCH 188/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 88c764cd8..327a93ccf 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.0.49": - version "1.1.6" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.6.tgz#b42484160f9d03d984b8255e013b5b4ddf9b3d4d" - integrity sha512-3YQRc4IYqZc+EEQTLmF5159hkfxlRhbl5LNtQebRdFfL3Fuz70taMxUX2NTfjNECNp7EZOxJmr/OwMDv5Qf1Cw== + version "1.1.7" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.7.tgz#f3b6a1de5581ada650eeee8f3a181d3887d76cf5" + integrity sha512-TEwkyDCqMEv5AxAaptZEIy8ERLfNnc3ej8BO1KVIyfBV/1FPjpfrBzSNZ6StxBPjz2HR0tmy5OccFDnGKOHJ9w== From 2390200da1ea8c69adbd6d9020fb0b3d9f29bffa Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 26 Aug 2024 09:51:07 -0400 Subject: [PATCH 189/204] upgrade client code --- Site/package.json | 2 +- Site/yarn.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Site/package.json b/Site/package.json index 4c9119477..cd9466b68 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "^1.0.49" + "@veupathdb/genomics-site": "1.1.0" } } diff --git a/Site/yarn.lock b/Site/yarn.lock index 327a93ccf..ff7ccb04a 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@^1.0.49": - version "1.1.7" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.7.tgz#f3b6a1de5581ada650eeee8f3a181d3887d76cf5" - integrity sha512-TEwkyDCqMEv5AxAaptZEIy8ERLfNnc3ej8BO1KVIyfBV/1FPjpfrBzSNZ6StxBPjz2HR0tmy5OccFDnGKOHJ9w== +"@veupathdb/genomics-site@1.1.0": + version "1.1.0" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.0.tgz#03c989ff77d50ec0d275205c6c0022769ddd0f1c" + integrity sha512-fz3ZQXYUg8wPyuZNz0zTmUWthQfpMHSeIHawgNq8rStC02vWzINseXuzZtQl4nYTez7LejgafMW1DuQ2IsvSYw== From 174673f6372a58d61d33b1537e7096da5a6aba63 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 26 Aug 2024 10:12:54 -0400 Subject: [PATCH 190/204] upgrade client code --- Site/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Site/package.json b/Site/package.json index cd9466b68..792863bed 100644 --- a/Site/package.json +++ b/Site/package.json @@ -2,6 +2,6 @@ "name": "genomics-site-deployer", "private": true, "dependencies": { - "@veupathdb/genomics-site": "1.1.0" + "@veupathdb/genomics-site": "^1.1.0" } } From c039e6d557f89add71e7c486807bb30da803913f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 27 Aug 2024 03:49:05 +0000 Subject: [PATCH 191/204] npm: bump @veupathdb/genomics-site from 1.1.0 to 1.1.8 in /Site Bumps @veupathdb/genomics-site from 1.1.0 to 1.1.8. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index ff7ccb04a..fc607361e 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -2,7 +2,7 @@ # yarn lockfile v1 -"@veupathdb/genomics-site@1.1.0": - version "1.1.0" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.0.tgz#03c989ff77d50ec0d275205c6c0022769ddd0f1c" - integrity sha512-fz3ZQXYUg8wPyuZNz0zTmUWthQfpMHSeIHawgNq8rStC02vWzINseXuzZtQl4nYTez7LejgafMW1DuQ2IsvSYw== +"@veupathdb/genomics-site@^1.1.0": + version "1.1.8" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.8.tgz#4aae90c2e08e8d9b15ba965c21405857a9b37331" + integrity sha512-lBOBJcu9NY6eBMhHughnEBdKbUYOxJ1sI3N7cV42Q/PPyo0D7gh0oLO3NhjwVzZLCEZYyB5yg97eqMenZRW/lg== From 42724895e0d9fad1f7d8bb32410a2793503c35b4 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 27 Aug 2024 09:51:05 -0400 Subject: [PATCH 192/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index fc607361e..109c61e10 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.8" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.8.tgz#4aae90c2e08e8d9b15ba965c21405857a9b37331" - integrity sha512-lBOBJcu9NY6eBMhHughnEBdKbUYOxJ1sI3N7cV42Q/PPyo0D7gh0oLO3NhjwVzZLCEZYyB5yg97eqMenZRW/lg== + version "1.1.9" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.9.tgz#6ba7f9cca0e7e8dec4502573cd991d12ef266265" + integrity sha512-hjopmdM6pbnCP4QzVVmzR9h6MhyTb7yoqIALpeHc74GncxRFJxBZtpn7lSDbtqDxoInbNOpGYwpmiul4xhRc0A== From cf0ffd467de7db8a726fa9c959e4f4578236b14e Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Thu, 29 Aug 2024 16:33:55 -0400 Subject: [PATCH 193/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 109c61e10..c9983a516 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.9" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.9.tgz#6ba7f9cca0e7e8dec4502573cd991d12ef266265" - integrity sha512-hjopmdM6pbnCP4QzVVmzR9h6MhyTb7yoqIALpeHc74GncxRFJxBZtpn7lSDbtqDxoInbNOpGYwpmiul4xhRc0A== + version "1.1.10" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.10.tgz#a63548dae04e2b5f239be84c5e3e22f8db1cd32c" + integrity sha512-FVzV9Dfw9wduOLKCJgLv+SAefryxUUgqI+Sd/1VnkY5OY+EUAV+eZwEzyJ67j+wtOpOLBTaWGjX/R0jRzb7Pqg== From 8f489e0ac989a0d6d29e6a4bb249b66abfbb89cb Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Thu, 12 Sep 2024 13:12:22 -0400 Subject: [PATCH 194/204] Clean up compiler warnings --- .../service/services/dataPlotter/ProfileSetService.java | 1 - .../service/services/jbrowse/model/JBrowseTrack.java | 4 ---- 2 files changed, 5 deletions(-) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java b/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java index 8847e1f90..5f1db6411 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java @@ -18,7 +18,6 @@ import org.gusdb.fgputil.db.stream.ResultSetToJsonConverter; import org.gusdb.fgputil.functional.Functions; import org.gusdb.wdk.model.WdkModelException; -import org.gusdb.wdk.model.WdkModel; import org.gusdb.wdk.service.service.AbstractWdkService; import org.json.JSONArray; import org.json.JSONObject; diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java index 4296306c3..93853fdb3 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/model/JBrowseTrack.java @@ -2,15 +2,11 @@ import com.fasterxml.jackson.annotation.JsonProperty; -/** - * - */ public class JBrowseTrack { // Fields with defaults private String storeClass = "JBrowse/Store/SeqFeature/BigWig"; private String yScalePosition = "left"; private String type = "JBrowse/View/Track/Wiggle/XYPlot"; - private String category = "My Data from Galaxy"; @JsonProperty("min_score") private int minScore = 0; From 2492c82077b8bdb34417f87137a7fcaecb58f9ec Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 17 Sep 2024 10:05:05 -0400 Subject: [PATCH 195/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index c9983a516..b8960aff4 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.10" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.10.tgz#a63548dae04e2b5f239be84c5e3e22f8db1cd32c" - integrity sha512-FVzV9Dfw9wduOLKCJgLv+SAefryxUUgqI+Sd/1VnkY5OY+EUAV+eZwEzyJ67j+wtOpOLBTaWGjX/R0jRzb7Pqg== + version "1.1.11" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.11.tgz#209d37fe7393ee15c25c112e4cbdd7c4d4d992a6" + integrity sha512-RHtdiPeohyYdtg7y98Gp3/IUtvla0ZzXoB5dmnDu2OU2/T05PINj6gW4wXUz3df7M/2enqf7TygIKG6J4QEiAw== From 8efee430fa0e5102af1fb77ba17cbd0f5212f33b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 21 Sep 2024 03:52:58 +0000 Subject: [PATCH 196/204] npm: bump @veupathdb/genomics-site from 1.1.11 to 1.1.12 in /Site Bumps @veupathdb/genomics-site from 1.1.11 to 1.1.12. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index b8960aff4..7228a6eb6 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.11" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.11.tgz#209d37fe7393ee15c25c112e4cbdd7c4d4d992a6" - integrity sha512-RHtdiPeohyYdtg7y98Gp3/IUtvla0ZzXoB5dmnDu2OU2/T05PINj6gW4wXUz3df7M/2enqf7TygIKG6J4QEiAw== + version "1.1.12" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.12.tgz#3cea4d6ba6a25d5c2ef18537a6268ad6d1cacd64" + integrity sha512-S9jMDtdJVrqUwpvLRQ2Eqt189wNG2TlppUkc1pshh1dGAaFW9N2WR/vczkhIbGTuBx3tjTEKdgz8fRFbJYDtzw== From 39d69a049fa26ca3a84f683603f5a26444cbe9ae Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 24 Sep 2024 10:26:48 -0400 Subject: [PATCH 197/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7228a6eb6..7547e8b9f 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.12" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.12.tgz#3cea4d6ba6a25d5c2ef18537a6268ad6d1cacd64" - integrity sha512-S9jMDtdJVrqUwpvLRQ2Eqt189wNG2TlppUkc1pshh1dGAaFW9N2WR/vczkhIbGTuBx3tjTEKdgz8fRFbJYDtzw== + version "1.1.13" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.13.tgz#1ac5cf50dcbe3502466dba5551aa676b09f53ff8" + integrity sha512-JlIYK9J4DhIh3XkoxpwHCrfkGzMw6ZCzX3TZlMXnnbiMh1SzU/ZW5WmF9VWaTeAB0BdolmKduzSSOqiQlPi5Yw== From 8ba65eeb45b3e2d45fabf6f12edb875fc451045c Mon Sep 17 00:00:00 2001 From: aurreco-uga Date: Tue, 24 Sep 2024 12:00:23 -0400 Subject: [PATCH 198/204] genomic sites require login (cherry picked from commit c23a9724432db29f825367714b7025d85fc87761) --- .../conifer/roles/conifer/vars/ApiCommon/production/default.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml index d0626a921..9fb0d6b23 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml @@ -12,6 +12,8 @@ modelconfig_userDb_maxIdle: 10 modelconfig_commentdb.maxIdle: 10 commentconfig_solrUrl: "https://solr-sitesearch-{{ sitesearchsolr_env_map[prefix]|default(sitesearchsolr_env_map['default']) }}.local.apidb.org:8443/solr/site_search/" +requireLogin: "true" + prefix_vdi: "{{ hostname | regex_replace('^([a-z][0-9]).*','\\1_prefix') }}" vdi_control_env_map: From cf81d3df35f18f2458ca82c05dbcd81564173688 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Tue, 24 Sep 2024 14:38:47 -0400 Subject: [PATCH 199/204] Add project_id label to organism metrics --- .../apicommon/service/services/OrganismMetricsService.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java b/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java index 315b21aad..11a2c6695 100644 --- a/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java +++ b/Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java @@ -48,7 +48,7 @@ public class OrganismMetricsService extends AbstractWdkService { private static final Counter ORGANISM_COUNTER = Counter.build() .name("page_access_by_organism") .help("Times a page related to each organism is accessed.") - .labelNames("organism") + .labelNames("project_id", "organism") .register(); // lazy loaded constant list of valid org names @@ -72,7 +72,7 @@ public Response incrementOrganismCount( } // found a valid organism name in this request; increment counter for that org - ORGANISM_COUNTER.labels(organism).inc(); + ORGANISM_COUNTER.labels(getWdkModel().getProjectId(), organism).inc(); return Response.noContent().build(); } From ec1e1b80c8c98359873e9e0f55c29b07d59d4df1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 27 Sep 2024 03:10:33 +0000 Subject: [PATCH 200/204] npm: bump @veupathdb/genomics-site from 1.1.13 to 1.1.14 in /Site Bumps @veupathdb/genomics-site from 1.1.13 to 1.1.14. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 7547e8b9f..db2c13ec5 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.13" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.13.tgz#1ac5cf50dcbe3502466dba5551aa676b09f53ff8" - integrity sha512-JlIYK9J4DhIh3XkoxpwHCrfkGzMw6ZCzX3TZlMXnnbiMh1SzU/ZW5WmF9VWaTeAB0BdolmKduzSSOqiQlPi5Yw== + version "1.1.14" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.14.tgz#23fa3b6b6acad113d31f5a92e1005c531e120a9c" + integrity sha512-+2BzAfebKXCtkAwDTMXOlcjlxUJGiLs6vgVgccqteWYv4OAmWegrC5fm+O408/rgkTOiU8NZC7jRNv34hI0kKg== From 098a7e3acc88401f88fd4c423ca5e76ec6889f5c Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Mon, 30 Sep 2024 23:49:09 -0400 Subject: [PATCH 201/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index db2c13ec5..d5e5416d1 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.14" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.14.tgz#23fa3b6b6acad113d31f5a92e1005c531e120a9c" - integrity sha512-+2BzAfebKXCtkAwDTMXOlcjlxUJGiLs6vgVgccqteWYv4OAmWegrC5fm+O408/rgkTOiU8NZC7jRNv34hI0kKg== + version "1.1.15" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.15.tgz#e132837d2068caf5e1efbba45d9affab4d8d5a52" + integrity sha512-HSXRtc1CJtwD7sbZo5gyn555/z8ylPCktj5Jn6KIQcfth/yaZjRQnx7Seks2EWgY8YGFM3BL5z/R+JJ06smZig== From 632256330ad0074db051db36f8468087ee0f45b8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 1 Oct 2024 03:49:10 +0000 Subject: [PATCH 202/204] npm: bump @veupathdb/genomics-site from 1.1.14 to 1.1.15 in /Site Bumps @veupathdb/genomics-site from 1.1.14 to 1.1.15. --- updated-dependencies: - dependency-name: "@veupathdb/genomics-site" dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index db2c13ec5..d5e5416d1 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.14" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.14.tgz#23fa3b6b6acad113d31f5a92e1005c531e120a9c" - integrity sha512-+2BzAfebKXCtkAwDTMXOlcjlxUJGiLs6vgVgccqteWYv4OAmWegrC5fm+O408/rgkTOiU8NZC7jRNv34hI0kKg== + version "1.1.15" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.15.tgz#e132837d2068caf5e1efbba45d9affab4d8d5a52" + integrity sha512-HSXRtc1CJtwD7sbZo5gyn555/z8ylPCktj5Jn6KIQcfth/yaZjRQnx7Seks2EWgY8YGFM3BL5z/R+JJ06smZig== From 63560e0995f0de64471cd9a2f8ee08cbc0b51af0 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Tue, 1 Oct 2024 16:36:57 -0400 Subject: [PATCH 203/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index d5e5416d1..4cb1a4b82 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.15" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.15.tgz#e132837d2068caf5e1efbba45d9affab4d8d5a52" - integrity sha512-HSXRtc1CJtwD7sbZo5gyn555/z8ylPCktj5Jn6KIQcfth/yaZjRQnx7Seks2EWgY8YGFM3BL5z/R+JJ06smZig== + version "1.1.18" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.18.tgz#29abc9d60e7787a2c683d0ba77db30f2d6c513ae" + integrity sha512-EPTXVXgCnKdvoNemWv+aY3Auo6ojDD0siWAnjOgJgkBeJdFilakL87qPxI5xMnZYC1ZTHkkcQPF6xM309yKTPQ== From 9bdc2503a53aa2ce58319baada8837e79d6f1bf2 Mon Sep 17 00:00:00 2001 From: Dave Falke Date: Wed, 2 Oct 2024 08:28:51 -0400 Subject: [PATCH 204/204] upgrade client code --- Site/yarn.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Site/yarn.lock b/Site/yarn.lock index 4cb1a4b82..438270075 100644 --- a/Site/yarn.lock +++ b/Site/yarn.lock @@ -3,6 +3,6 @@ "@veupathdb/genomics-site@^1.1.0": - version "1.1.18" - resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.18.tgz#29abc9d60e7787a2c683d0ba77db30f2d6c513ae" - integrity sha512-EPTXVXgCnKdvoNemWv+aY3Auo6ojDD0siWAnjOgJgkBeJdFilakL87qPxI5xMnZYC1ZTHkkcQPF6xM309yKTPQ== + version "1.1.19" + resolved "https://registry.yarnpkg.com/@veupathdb/genomics-site/-/genomics-site-1.1.19.tgz#2689e95e0d725bd66a27d56f8aaea43012c99883" + integrity sha512-OR328yG3J6Uu1JNzchfjzxxmVqorkIMsrnVKHDzM+wS1xxqjJzytfRdMnR/7TIkFKNLEd59mi7WAhZuwu/wSQQ==