Merge branch 'master' into jbrowse2

.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"

.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: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - name: Dependabot metadata
+        id: metadata
+        uses: dependabot/[email protected]
+        with:
+          github-token: "${{ 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}}

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 }}

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"

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') }}"

Model/lib/conifer/roles/conifer/vars/ApiCommon/production/default.yml

@@ -12,8 +12,35 @@ 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:
+  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_DATASETS_DIRECTORY: "/var/www/Common/userDatasets"
+  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',
   'attr=google_analytics_id xpath=sites/site[@hostname=\"{}\"] default='.format( hostname|swap_hostname(_host_frontends) )
   )

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<String, String> userProps = updateEvent.getNewProfile().getProperties();
-    Map<String, String> 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()));
   }
 }

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",

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

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<String, String> 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());
   }
 }

Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java

@@ -1,16 +1,18 @@
 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;
 import org.gusdb.fgputil.db.runner.BasicArgumentBatch;
 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.
  */

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:

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