From 51e7bb4fe1e9a9a2f090dc0abe591b87d4455bc5 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 22 Aug 2023 16:58:45 -0500 Subject: [PATCH 01/23] Update django-cms to v3.7.4 (#1067) * Update django-cms to v3.7.4 * don't show site messages on EF sites --------- Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg --- .../apps/cms_plugins/context_processors.py | 4 +- designsafe/middleware.py | 3 +- poetry.lock | 2504 +++++++++++------ pyproject.toml | 9 +- 4 files changed, 1590 insertions(+), 930 deletions(-) diff --git a/designsafe/apps/cms_plugins/context_processors.py b/designsafe/apps/cms_plugins/context_processors.py index 5589f441a4..04431bcd72 100644 --- a/designsafe/apps/cms_plugins/context_processors.py +++ b/designsafe/apps/cms_plugins/context_processors.py @@ -1,11 +1,11 @@ -from menus.menu_pool import menu_pool +from menus.menu_pool import MenuPool import logging logger = logging.getLogger(__name__) def cms_section(request): - nodes = menu_pool.get_nodes(request) + nodes = MenuPool().get_renderer(request).get_nodes() if nodes: menu_root = nodes[0] if 'soft_root' in menu_root.attr: diff --git a/designsafe/middleware.py b/designsafe/middleware.py index 2f77fcfac3..33fdd2f136 100644 --- a/designsafe/middleware.py +++ b/designsafe/middleware.py @@ -67,7 +67,8 @@ def process_request(self, request): class SiteMessageMiddleware: def process_request(self, request): for message in SiteMessage.objects.filter(display=True): - messages.warning(request, message.message) + if settings.SITE_ID == 1: + messages.warning(request, message.message) class RequestProfilingMiddleware(object): diff --git a/poetry.lock b/poetry.lock index dbe1501eb8..e44224bf8f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. + [[package]] name = "agavepy" version = "1.0.0a12" @@ -5,6 +7,10 @@ description = "SDK for TACC Tapis (formerly Agave)" category = "main" optional = false python-versions = "*" +files = [ + {file = "agavepy-1.0.0a12-py2.py3-none-any.whl", hash = "sha256:ad096612c07a05d7f16b0e0e49d75dacfbccd3681e82c1b5f92c2c1b733b4209"}, + {file = "agavepy-1.0.0a12.tar.gz", hash = "sha256:60717e2749d1e4116a10b0aed509f691f56ebea8a1321f29f621ff1ddd4a9d1e"}, +] [package.dependencies] arrow = ">=0.15.5" @@ -29,6 +35,10 @@ description = "Low-level AMQP client for Python (fork of amqplib)." category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "amqp-5.1.1-py3-none-any.whl", hash = "sha256:6f0956d2c23d8fa6e7691934d8c3930eadb44972cbbd1a7ae3a520f735d43359"}, + {file = "amqp-5.1.1.tar.gz", hash = "sha256:2c1b13fecc0893e946c65cbd5f36427861cffa4ea2201d8f6fca22e2a373b5e2"}, +] [package.dependencies] vine = ">=5.0.0" @@ -40,32 +50,65 @@ description = "Disable App Nap on macOS >= 10.9" category = "main" optional = false python-versions = "*" +files = [ + {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, + {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, +] [[package]] name = "arrow" -version = "1.2.2" +version = "1.2.3" description = "Better dates & times for Python" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, + {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, +] [package.dependencies] python-dateutil = ">=2.7.0" typing-extensions = {version = "*", markers = "python_version < \"3.8\""} +[[package]] +name = "asgiref" +version = "3.7.2" +description = "ASGI specs, helper code, and adapters" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "asgiref-3.7.2-py3-none-any.whl", hash = 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\"cpython\" and python_version < \"3.8\""} -typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} -wrapt = ">=1.11,<2" +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} +wrapt = [ + {version = ">=1.11,<2", markers = "python_version < \"3.11\""}, + {version = ">=1.14,<2", markers = "python_version >= \"3.11\""}, +] [[package]] name = "async-timeout" @@ -74,6 +117,10 @@ description = "Timeout context manager for asyncio programs" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"}, + {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"}, +] [package.dependencies] typing-extensions = {version = ">=3.6.5", markers = "python_version < \"3.8\""} @@ -85,6 +132,9 @@ description = "Atomic file writes." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, +] [[package]] name = "attrdict" @@ -93,23 +143,35 @@ description = "A dict with attribute-style access" category = "main" optional = false python-versions = "*" +files = [ + {file = "attrdict-2.0.1-py2.py3-none-any.whl", hash = "sha256:9432e3498c74ff7e1b20b3d93b45d766b71cbffa90923496f82c4ae38b92be34"}, + {file = "attrdict-2.0.1.tar.gz", hash = "sha256:35c90698b55c683946091177177a9e9c0713a0860f0e049febd72649ccd77b70"}, +] [package.dependencies] six = "*" [[package]] name = "attrs" -version = "21.4.0" +version = "23.1.0" description = "Classes Without Boilerplate" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.7" +files = [ + {file = "attrs-23.1.0-py3-none-any.whl", hash = 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"Django app to allow superusers to impersonate other users." category = "main" optional = false python-versions = "*" +files = [ + {file = "django-impersonate-1.5.1.tar.gz", hash = "sha256:7c786ffaa7a5dd430f9277b53a64676c470b684eee5aa52c3b483298860d09b4"}, +] [[package]] name = "django-ipware" @@ -528,6 +898,9 @@ description = "A Django utility application that returns client's real IP addres category = "main" optional = false python-versions = "*" +files = [ + {file = "django-ipware-1.2.0.tar.gz", hash = "sha256:0fdf2c7b44ea5ce443bb00e143fa3cfdfc7fbc3f105d7a80625a3609889db2d6"}, +] [[package]] name = "django-js-asset" @@ -536,14 +909,22 @@ description = "script tag with additional attributes for django.forms.Media" category = "main" optional = false python-versions = "*" +files = [ + {file = "django-js-asset-1.2.3.tar.gz", hash = "sha256:25811cd67428ebdc5298661a2223a66b39c11696746a06f87f0896b93e1c5423"}, + {file = "django_js_asset-1.2.3-py2.py3-none-any.whl", hash = "sha256:4675015a390fd1f3937e79f7f516d58ab77572b0339c6873807555d6443fa9f8"}, +] [[package]] name = "django-mptt" -version = "0.13.4" +version = "0.14.0" description = "Utilities for implementing Modified Preorder Tree Traversal with your Django Models and working with trees of Model instances." category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "django-mptt-0.14.0.tar.gz", hash = "sha256:2c92a2b1614c53086278795ccf50580cf1f9b8564f3ff03055dd62bab5987711"}, + {file = "django_mptt-0.14.0-py3-none-any.whl", hash = "sha256:d9a87433ab0e4f35247c6f6d5a93ace6990860a4ba8796f815d185f773b9acfc"}, +] [package.dependencies] django-js-asset = "*" @@ -558,6 +939,10 @@ description = "Seamless polymorphic inheritance for Django models" category = "main" optional = false python-versions = "*" +files = [ + {file = "django-polymorphic-2.1.2.tar.gz", hash = "sha256:6e08a76c91066635ccb7ef3ebbe9a0ad149febae6b30be2579716ec16d3c6461"}, + {file = 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+files = [ + {file = "django-treebeard-4.3.1.tar.gz", hash = "sha256:83aebc34a9f06de7daaec330d858d1c47887e81be3da77e3541fe7368196dd8a"}, +] [package.dependencies] Django = ">=1.8" @@ -616,11 +1029,15 @@ description = "Websocket support for Django using Redis as datastore" category = "main" optional = false python-versions = "*" +files = [ + {file = "django-websocket-redis-0.6.0.tar.gz", hash = "sha256:cda77d9b87110f9482a7056a0bc5cef179feaea4313394faa5b291d777b426b9"}, +] [package.dependencies] gevent = "*" greenlet = "*" redis = "*" +setuptools = "*" six = "*" [package.extras] @@ -630,22 +1047,30 @@ wsaccel = ["wsaccel (>=0.6.2)"] [[package]] name = "djangocms-admin-style" -version = "3.2.0" +version = "3.2.4" description = "Adds pretty CSS styles for the django CMS admin interface." category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "djangocms-admin-style-3.2.4.tar.gz", hash = "sha256:0d981ccedf4252113acfd812a48d3284eb38d6b610d83c92e85f6bb681bd8bca"}, + {file = "djangocms_admin_style-3.2.4-py3-none-any.whl", hash = "sha256:f540d32026108c22f4b9f69347780fe04c63b9d699902f41d763f44780bb9cbb"}, +] [[package]] name = "djangocms-attributes-field" -version = "1.2.0" +version = "3.0.0" description = "Adds attributes to Django models." category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-attributes-field-3.0.0.tar.gz", hash = "sha256:70cbcb8e826b5a6bceba348119ddc01fa5910af4cb4002eb9895d311950b0d9a"}, + {file = "djangocms_attributes_field-3.0.0-py3-none-any.whl", hash = "sha256:21a0e1642ffc3d9fbc9284b07024c4ca29f7fe9ffbd2c0aecd22585ff5275a86"}, +] [package.dependencies] -django-cms = ">=3.4.5" +django-cms = ">=3.7" [[package]] name = "djangocms-cascade" @@ -654,6 +1079,9 @@ description = "Collection of extendible plugins for django-CMS to create and edi category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-cascade-0.16.3.tar.gz", hash = "sha256:c0fa072243b5b711ff363566dc15b750377b5dd4a267b7972ac7b607031ec1db"}, +] [package.dependencies] django-classy-tags = ">=0.8" @@ -668,6 +1096,9 @@ description = "Adds file plugin to django CMS" category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-file-2.4.0.tar.gz", hash = "sha256:dd5051465d44fa9a3728bac7943c2efc1b806edb316a741b9dbc171a361f27bf"}, +] [package.dependencies] django-cms = ">=3.4.5" @@ -681,6 +1112,9 @@ description = "The easiest and most flexible Django CMS Form builder w/ ReCaptch category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-forms-0.2.5.tar.gz", hash = "sha256:83719b7bec66f935fc30698d81541d52cf35a45bef27089cd8899fa9d4d19d36"}, +] [package.dependencies] django-appconf = "*" @@ -699,6 +1133,9 @@ description = "Adds Google Maps plugins to django CMS." category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-googlemap-1.4.0.tar.gz", hash = "sha256:84c350c5c4ee0c6a773d611366d080b79236855033db2b21131652a874a8d155"}, +] [package.dependencies] django-cms = ">=3.4.5" @@ -711,6 +1148,9 @@ description = "Adds an image plugin to django CMS" category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-picture-2.4.0.tar.gz", hash = "sha256:91c99716e0d31fee3b4440a8ed55b6c66a015eafdea39a4b51dd0aa3f0576575"}, +] [package.dependencies] django-cms = ">=3.4.5" @@ -725,6 +1165,9 @@ description = "Adds snippet plugin to django CMS." category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-snippet-2.3.0.tar.gz", hash = "sha256:05f8fefac98ba3d4e8de83a863f42648d0ad752cae4edb0243a9a774ab8274c6"}, +] [package.dependencies] django-cms = ">=3.4.5" @@ -736,6 +1179,9 @@ description = "Adds style plugin to django CMS" category = "main" optional = false python-versions = "*" +files = [ + {file = "djangocms-style-2.3.0.tar.gz", hash = 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"^2.3.2" -opf-fido = "^1.4.1" +opf-fido = "1.4.1" +asgiref = "^3.6.0" +importlib-metadata = "2.1.3" +django-select2 = "6.3.1" [build-system] requires = ["poetry-core>=1.0.0"] From 2fcc8e1bae9e134e656333033ec4b28d643ed500 Mon Sep 17 00:00:00 2001 From: Sal Tijerina Date: Tue, 29 Aug 2023 11:27:56 -0500 Subject: [PATCH 02/23] task/DES-2561: create Scratch dir on login (#1081) * create myworkingfiles dir on login * add missing setting * Update designsafe/settings/common_settings.py * task/DES-2562: Add `Scratch (Frontera)` to listings (#1082) * Add My Data (Work) to listings * update name to My Working Data * update name to My Working Files * Apply suggestions from code review Co-authored-by: Sal Tijerina --------- Co-authored-by: Jake Rosenberg Co-authored-by: Sal Tijerina * update labels to Working Files (scratch Frontera) --------- Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg --- conf/env_files/designsafe.sample.env | 1 + designsafe/apps/accounts/views.py | 4 ++- designsafe/apps/auth/tasks.py | 12 +++---- designsafe/apps/auth/views.py | 15 ++++++--- designsafe/settings/common_settings.py | 1 + .../data-depot-nav.component.js | 6 ++++ .../data-depot-toolbar.component.js | 1 + designsafe/static/scripts/data-depot/index.js | 33 +++++++++++++++++++ .../services/file-operation-service.js | 2 +- .../workspace-data-browser.component.js | 12 +++++++ 10 files changed, 75 insertions(+), 12 deletions(-) diff --git a/conf/env_files/designsafe.sample.env b/conf/env_files/designsafe.sample.env index fb9ab0f744..8e02f3b6f2 100644 --- a/conf/env_files/designsafe.sample.env +++ b/conf/env_files/designsafe.sample.env @@ -74,6 +74,7 @@ AGAVE_CLIENT_SECRET= AGAVE_SUPER_TOKEN= AGAVE_STORAGE_SYSTEM= +AGAVE_WORKING_SYSTEM= AGAVE_JWT_PUBKEY= AGAVE_JWT_ISSUER= AGAVE_JWT_HEADER= diff --git a/designsafe/apps/accounts/views.py b/designsafe/apps/accounts/views.py index 66171f7dd4..6da9e56064 100644 --- a/designsafe/apps/accounts/views.py +++ b/designsafe/apps/accounts/views.py @@ -441,7 +441,9 @@ def email_confirmation(request, code=None): user = tas.get_user(username=username) if tas.verify_user(user['id'], code, password=password): logger.info('TAS Account activation succeeded.') - check_or_create_agave_home_dir.apply(args=(user["username"],)) + from django.conf import settings + check_or_create_agave_home_dir.apply_async(args=(user.username, settings.AGAVE_STORAGE_SYSTEM)) + check_or_create_agave_home_dir.apply_async(args=(user.username, settings.AGAVE_WORKING_SYSTEM)) return HttpResponseRedirect(reverse('designsafe_accounts:manage_profile')) else: messages.error(request, diff --git a/designsafe/apps/auth/tasks.py b/designsafe/apps/auth/tasks.py index 8c415c6475..ccdfdf8583 100644 --- a/designsafe/apps/auth/tasks.py +++ b/designsafe/apps/auth/tasks.py @@ -13,20 +13,20 @@ @shared_task(default_retry_delay=1*30, max_retries=3) -def check_or_create_agave_home_dir(username): +def check_or_create_agave_home_dir(username, systemId): try: # TODO should use OS calls to create directory. logger.info( "Checking home directory for user=%s on " "default storage systemId=%s", username, - settings.AGAVE_STORAGE_SYSTEM + systemId ) ag = Agave(api_server=settings.AGAVE_TENANT_BASEURL, token=settings.AGAVE_SUPER_TOKEN) try: listing_response = ag.files.list( - systemId=settings.AGAVE_STORAGE_SYSTEM, + systemId=systemId, filePath=username) logger.info('check home dir response: {}'.format(listing_response)) @@ -34,7 +34,7 @@ def check_or_create_agave_home_dir(username): if e.response.status_code == 404: logger.info("Creating the home directory for user=%s then going to run setfacl", username) body = {'action': 'mkdir', 'path': username} - fm_response = ag.files.manage(systemId=settings.AGAVE_STORAGE_SYSTEM, + fm_response = ag.files.manage(systemId=systemId, filePath='', body=body) logger.info('mkdir response: {}'.format(fm_response)) @@ -62,13 +62,13 @@ def check_or_create_agave_home_dir(username): # add dir to index logger.info("Indexing the home directory for user=%s", username) - agave_indexer.apply_async(kwargs={'username': username, 'systemId': settings.AGAVE_STORAGE_SYSTEM, 'filePath': username}, queue='indexing') + agave_indexer.apply_async(kwargs={'username': username, 'systemId': systemId, 'filePath': username}, queue='indexing') except(AgaveException): #except (HTTPError, AgaveException): logger.exception('Failed to create home directory.', extra={'user': username, - 'systemId': settings.AGAVE_STORAGE_SYSTEM}) + 'systemId': systemId}) @shared_task(default_retry_delay=1*30, max_retries=3) diff --git a/designsafe/apps/auth/views.py b/designsafe/apps/auth/views.py index dc94dd6db7..8785de42cc 100644 --- a/designsafe/apps/auth/views.py +++ b/designsafe/apps/auth/views.py @@ -110,7 +110,7 @@ def agave_oauth_callback(request): http://agaveapi.co/documentation/authorization-guide/#authorization_code_flow """ state = request.GET.get('state') - + if request.session['auth_state'] != state: msg = ( 'OAuth Authorization State mismatch!? auth_state=%s ' @@ -152,7 +152,7 @@ def agave_oauth_callback(request): token_data['created'] = int(time.time()) # log user in user = authenticate(backend='agave', token=token_data['access_token']) - + if user: try: token = user.agave_oauth @@ -172,8 +172,15 @@ def agave_oauth_callback(request): filePath=user.username) except HTTPError as e: if e.response.status_code == 404: - check_or_create_agave_home_dir.apply_async(args=(user.username,),queue='files') - + check_or_create_agave_home_dir.apply_async(args=(user.username, settings.AGAVE_STORAGE_SYSTEM),queue='files') + + try: + ag.files.list(systemId=settings.AGAVE_WORKING_SYSTEM, + filePath=user.username) + except HTTPError as e: + if e.response.status_code == 404: + check_or_create_agave_home_dir.apply_async(args=(user.username, settings.AGAVE_WORKING_SYSTEM),queue='files') + else: messages.error( request, diff --git a/designsafe/settings/common_settings.py b/designsafe/settings/common_settings.py index f57546db5e..825ffd826f 100644 --- a/designsafe/settings/common_settings.py +++ b/designsafe/settings/common_settings.py @@ -486,6 +486,7 @@ AGAVE_TOKEN_SESSION_ID = os.environ.get('AGAVE_TOKEN_SESSION_ID', 'agave_token') AGAVE_STORAGE_SYSTEM = os.environ.get('AGAVE_STORAGE_SYSTEM') +AGAVE_WORKING_SYSTEM = os.environ.get('AGAVE_WORKING_SYSTEM', 'designsafe.storage.frontera.scratch') AGAVE_JWT_PUBKEY = os.environ.get('AGAVE_JWT_PUBKEY') AGAVE_JWT_ISSUER = os.environ.get('AGAVE_JWT_ISSUER') diff --git a/designsafe/static/scripts/data-depot/components/data-depot-nav/data-depot-nav.component.js b/designsafe/static/scripts/data-depot/components/data-depot-nav/data-depot-nav.component.js index e541c66c9a..64b3430aec 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-nav/data-depot-nav.component.js +++ b/designsafe/static/scripts/data-depot/components/data-depot-nav/data-depot-nav.component.js @@ -45,6 +45,12 @@ class DataDepotNavCtrl { state: 'myData', description: 'Private directory for your data' }, + { + name: 'Working Files (scratch Frontera)', + collapsible: false, + state: 'myDataScratch', + description: 'Scratch directory on Frontera for use with JupyterHub' + }, { name: 'My Projects', collapsible: false, diff --git a/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js b/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js index 7b08279d93..cf6114c4db 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js +++ b/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js @@ -16,6 +16,7 @@ class DataDepotToolbarCtrl { placeholder() { var stateNames = { 'myData': 'My Data', + 'myDataScratch': 'Working Files (scratch Frontera)', 'projects.list': 'My Projects', 'sharedData': 'Shared Data', 'boxData': 'Box', diff --git a/designsafe/static/scripts/data-depot/index.js b/designsafe/static/scripts/data-depot/index.js index dec411eed7..30255a1516 100644 --- a/designsafe/static/scripts/data-depot/index.js +++ b/designsafe/static/scripts/data-depot/index.js @@ -83,6 +83,39 @@ function config( }, }, }) + .state('myDataScratch', { + url: '/agave/{systemId}/{filePath:any}/?query_string&offset&limit', + component: 'dataDepotBrowser', + params: { + systemId: 'designsafe.storage.frontera.scratch', + filePath: Django.user, + }, + resolve: { + apiParams: ()=> { + return { + fileMgr: 'agave', + }; + }, + path: ($stateParams, Django) => { + 'ngInject'; + if ($stateParams.filePath.replace(/^\/+/, '') === '') { + return Django.user; + } + return $stateParams.filePath; + }, + auth: ($q, Django) => { + 'ngInject'; + if (Django.context.authenticated) { + return true; + } + + return $q.reject({ + type: 'authn', + context: Django.context, + }); + }, + }, + }) .state('sharedData', { url: '/shared/{systemId}/{filePath:any}?query_string', component: 'dataDepotBrowser', diff --git a/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js b/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js index c0b54338f5..5f9863a40c 100644 --- a/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js +++ b/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js @@ -49,7 +49,7 @@ export class FileOperationService { getTests(files) { const externalDataStates = ['boxData', 'dropboxData', 'googledriveData']; - const agaveDataStates = ['myData', 'projects.view', 'projects.curation']; + const agaveDataStates = ['myData', 'myDataScratch', 'projects.view', 'projects.curation']; let isHazmapper = files.length > 0 ? files.some((e) => e.name.endsWith('hazmapper')) : false; const tests = { copy: this.Django.context.authenticated && !isHazmapper && files.length > 0, diff --git a/designsafe/static/scripts/workspace/components/workspace-data-browser/workspace-data-browser.component.js b/designsafe/static/scripts/workspace/components/workspace-data-browser/workspace-data-browser.component.js index 4a78117081..871329818f 100644 --- a/designsafe/static/scripts/workspace/components/workspace-data-browser/workspace-data-browser.component.js +++ b/designsafe/static/scripts/workspace/components/workspace-data-browser/workspace-data-browser.component.js @@ -17,6 +17,7 @@ class WorkspaceDataBrowserCtrl { this.options = [ { name: 'myData', label: 'My Data' }, + { name: 'myDataScratch', label: 'Working Files (scratch Frontera)' }, { name: 'myProjects', label: 'My Projects' }, { name: 'publications', label: 'Published' }, { name: 'nees', label: 'Published (NEES)' }, @@ -58,6 +59,17 @@ class WorkspaceDataBrowserCtrl { }); this.breadcrumbParams = this.FileListingService.fileMgrMappings.agave.breadcrumbParams; break; + case 'myDataScratch': + this.listingType = 'files'; + this.FileListingService.browse({ + section: 'main', + api: 'agave', + scheme: 'private', + system: 'designsafe.storage.frontera.scratch', + path: this.Django.user, + }); + this.breadcrumbParams = this.FileListingService.fileMgrMappings.agave.breadcrumbParams; + break; case 'myProjects': this.listingType = 'projects'; this.ProjectService.listProjects({ section: 'main' }); From 62aac9e23cfcd1dea774324d37d6d6bf329e26f0 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 29 Aug 2023 11:37:55 -0500 Subject: [PATCH 03/23] remove text indicating that users can search by DOI (#1092) Co-authored-by: Jake Rosenberg --- designsafe/apps/api/publications/search_utils.py | 2 +- .../data-depot-listing/publications-listing.template.html | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/designsafe/apps/api/publications/search_utils.py b/designsafe/apps/api/publications/search_utils.py index 8fff6ecd0b..9f0f12cbf3 100644 --- a/designsafe/apps/api/publications/search_utils.py +++ b/designsafe/apps/api/publications/search_utils.py @@ -177,4 +177,4 @@ def search_string_query(search_string): 'project.value.projectType', 'project.value.dataType']) q2 = Q({'term': {'projectId._exact': search_string}}) - return q1 | q2 | author_query(search_string) + return q1 | q2 | author_query(f"\"{search_string}\"") diff --git a/designsafe/static/scripts/data-depot/components/data-depot-listing/publications-listing.template.html b/designsafe/static/scripts/data-depot/components/data-depot-listing/publications-listing.template.html index ed854ebb4b..ceb17eca69 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-listing/publications-listing.template.html +++ b/designsafe/static/scripts/data-depot/components/data-depot-listing/publications-listing.template.html @@ -9,8 +9,8 @@ - From 823c4df2eacba7bcdcf377737848a5060be6e71e Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 29 Aug 2023 11:42:29 -0500 Subject: [PATCH 04/23] Log DOIs when a file operation is performed in a published project (#1085) Co-authored-by: Jake Rosenberg --- designsafe/apps/api/datafiles/views.py | 7 +++++- .../data-depot-listing.component.js | 4 +++- .../data-depot-toolbar.component.js | 4 ++-- ...ication-preview-field-recon.component.html | 3 ++- ...publication-preview-hyb-sim.component.html | 24 ++++++++++++------- .../publication-preview-other.component.html | 3 ++- .../publication-preview-sim.component.html | 15 ++++++++---- .../publication-preview.component.html | 15 ++++++++---- .../published/published-view.component.js | 7 +++--- designsafe/static/scripts/data-depot/index.js | 2 +- .../data-browser-service-preview.component.js | 3 ++- .../services/file-listing-service.js | 5 ++-- .../services/file-operation-service.js | 11 +++++---- 13 files changed, 67 insertions(+), 36 deletions(-) diff --git a/designsafe/apps/api/datafiles/views.py b/designsafe/apps/api/datafiles/views.py index c57d82c92f..9326896932 100644 --- a/designsafe/apps/api/datafiles/views.py +++ b/designsafe/apps/api/datafiles/views.py @@ -32,6 +32,8 @@ def get_client(user, api): class DataFilesView(BaseApiView): def get(self, request, api, operation=None, scheme='private', system=None, path=''): + + doi = request.GET.get('doi', None) metrics.info('Data Depot', extra={ @@ -44,6 +46,7 @@ def get(self, request, api, operation=None, scheme='private', system=None, path= 'api': api, 'systemId': system, 'filePath': path, + 'doi': doi, 'query': request.GET.dict()} }) @@ -69,6 +72,7 @@ def get(self, request, api, operation=None, scheme='private', system=None, path= def put(self, request, api, operation=None, scheme='private', system=None, path='/'): body = json.loads(request.body) + doi = request.GET.get('doi', None) metrics.info('Data Depot', extra={ @@ -82,7 +86,8 @@ def put(self, request, api, operation=None, scheme='private', system=None, path= 'scheme': scheme, 'system': system, 'path': path, - 'body': body + 'body': body, + 'doi': doi } }) diff --git a/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js b/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js index ce7ec4744e..449ee7d9a4 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js +++ b/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js @@ -249,6 +249,7 @@ class FilesListingCtrl { onSelect(idx) { this.FileListingService.select(this.listing.params.section, idx) + this.FileListingService.currentDOI = this.doi; } icon(name, type) { @@ -354,7 +355,8 @@ export const FilesListingComponent = { operation: '&', // Callback for move/copy operation. showTags: '<', editTags: '<', - published: '<' + published: '<', + doi: '<' }, }; diff --git a/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js b/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js index cf6114c4db..ac1b8aba71 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js +++ b/designsafe/static/scripts/data-depot/components/data-depot-toolbar/data-depot-toolbar.component.js @@ -50,12 +50,12 @@ class DataDepotToolbarCtrl { const projectId = this.PublicationService.current.projectId; this.FileOperationService.microsurvey({projectId}) } - this.FileOperationService.download({api, scheme, files}); + this.FileOperationService.download({api, scheme, files, doi: this.FileListingService.currentDOI}); } preview() { const { api, scheme } = this.FileListingService.listings.main.params; const file = this.getAllSelected()[0]; - this.FileOperationService.openPreviewModal({api, scheme, file}); + this.FileOperationService.openPreviewModal({api, scheme, file, doi: this.FileListingService.currentDOI}); } previewImages() { const { api, scheme, system } = this.FileListingService.listings.main.params; diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html index f26df5f989..af065e7715 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html @@ -235,7 +235,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[mission.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="mission.doi" + on-browse="$ctrl.onBrowse(file, mission.doi)">  diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html index 5014968f78..10d5806113 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html @@ -277,8 +277,9 @@

show-tags="true" published="true" on-scroll="$ctrl.scrollToBottom()" + doi="hybsim.value.dois.toString()" listing="$ctrl.FileListingService.listings[report.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString()")">  @@ -343,8 +344,9 @@

show-tags="true" published="true" on-scroll="$ctrl.scrollToBottom()" + doi="hybsim.value.dois.toString()" listing="$ctrl.FileListingService.listings[coordinator.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -381,9 +383,10 @@

  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -427,9 +430,10 @@

  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -474,8 +478,9 @@

show-tags="true" published="true" on-scroll="$ctrl.scrollToBottom()" + doi="hybsim.value.dois.toString()" listing="$ctrl.FileListingService.listings[sout.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -523,8 +528,9 @@

show-tags="true" published="true" on-scroll="$ctrl.scrollToBottom()" + doi="hybsim.value.dois.toString()" listing="$ctrl.FileListingService.listings[expsub.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -569,8 +575,9 @@

show-tags="true" published="true" on-scroll="$ctrl.scrollToBottom()" + doi="hybsim.value.dois.toString()" listing="$ctrl.FileListingService.listings[eout.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  @@ -619,9 +626,10 @@

  + on-browse="$ctrl.onBrowse(file, hybsim.value.dois.toString())">  diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html index 3481b10b2b..d62587d908 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html @@ -46,7 +46,8 @@

skip-root="$ctrl.breadcrumbParams.skipRoot" > diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html index 0af5580a08..38520381fd 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html @@ -279,7 +279,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[report.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="simulation.doi" + on-browse="$ctrl.onBrowse(file, simulation.doi)">  @@ -307,7 +308,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[model.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="simulation.doi" + on-browse="$ctrl.onBrowse(file, simulation.doi)">  @@ -347,7 +349,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[input.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="simulation.doi" + on-browse="$ctrl.onBrowse(file, simulation.doi)">  @@ -389,7 +392,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[output.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="simulation.doi" + on-browse="$ctrl.onBrowse(file, simulation.doi)">  @@ -437,7 +441,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[analysis.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="simulation.doi" + on-browse="$ctrl.onBrowse(file, simulation.doi)">  diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html index 7bf71d8666..93e8789ec1 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html @@ -306,7 +306,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[report.uuid]" - on-browse="$ctrl.onBrowse(file)">  + on-browse="$ctrl.onBrowse(file, experiment.doi)" + doi="experiment.doi">  @@ -336,7 +337,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[modelConfig.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="experiment.doi" + on-browse="$ctrl.onBrowse(file, experiment.doi)">  @@ -377,7 +379,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[sensorList.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="experiment.doi" + on-browse="$ctrl.onBrowse(file, experiment.doi)">  @@ -419,7 +422,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[event.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="experiment.doi" + on-browse="$ctrl.onBrowse(file, experiment.doi)">  @@ -464,7 +468,8 @@

published="true" on-scroll="$ctrl.scrollToBottom()" listing="$ctrl.FileListingService.listings[analysis.uuid]" - on-browse="$ctrl.onBrowse(file)">  + doi="experiment.doi" + on-browse="$ctrl.onBrowse(file, experiment.doi)">  diff --git a/designsafe/static/scripts/data-depot/components/published/published-view.component.js b/designsafe/static/scripts/data-depot/components/published/published-view.component.js index 550ac934ac..4450804636 100644 --- a/designsafe/static/scripts/data-depot/components/published/published-view.component.js +++ b/designsafe/static/scripts/data-depot/components/published/published-view.component.js @@ -156,6 +156,7 @@ class PublishedViewCtrl { system: 'designsafe.storage.published', path: this.$stateParams.filePath, query_string: this.$stateParams.query_string, + doi: this.$stateParams.doi }); } else { this.getProjectListings(); @@ -622,11 +623,11 @@ class PublishedViewCtrl { return arr.filter(Boolean); } - onBrowse(file) { + onBrowse(file, doi) { if (file.type === 'dir') { - this.$state.go(this.$state.current.name, { filePath: file.path, query_string: null }); + this.$state.go(this.$state.current.name, { filePath: file.path, query_string: null, doi: doi }); } else { - this.FileOperationService.openPreviewModal({ api: 'agave', scheme: 'private', file }); + this.FileOperationService.openPreviewModal({ api: 'agave', scheme: 'private', file, doi: doi }); } } diff --git a/designsafe/static/scripts/data-depot/index.js b/designsafe/static/scripts/data-depot/index.js index 30255a1516..69a52d7991 100644 --- a/designsafe/static/scripts/data-depot/index.js +++ b/designsafe/static/scripts/data-depot/index.js @@ -1083,7 +1083,7 @@ function config( }, }) .state('publishedData', { - url: '/public/designsafe.storage.published/{filePath:any}?query_string', + url: '/public/designsafe.storage.published/{filePath:any}?query_string&doi', component: 'publishedParent', resolve: { version: ($stateParams) => { diff --git a/designsafe/static/scripts/ng-designsafe/components/modals/data-browser-service-preview/data-browser-service-preview.component.js b/designsafe/static/scripts/ng-designsafe/components/modals/data-browser-service-preview/data-browser-service-preview.component.js index 51b87260fc..e00d9846d5 100644 --- a/designsafe/static/scripts/ng-designsafe/components/modals/data-browser-service-preview/data-browser-service-preview.component.js +++ b/designsafe/static/scripts/ng-designsafe/components/modals/data-browser-service-preview/data-browser-service-preview.component.js @@ -33,6 +33,7 @@ class DataBrowserServicePreviewCtrl { file: this.resolve.file, api: this.resolve.api, scheme: this.resolve.scheme, + doi: this.resolve.doi }).then( (resp) => { this.fileType = resp.data.fileType; @@ -127,7 +128,7 @@ class DataBrowserServicePreviewCtrl { download() { const { api, scheme, system, path } = this.FileListingService.listings.main.params; const files = [this.resolve.file]; - this.FileOperationService.download({ api, scheme, files }); + this.FileOperationService.download({ api, scheme, files, doi: this.resolve.doi }); if (system === 'designsafe.storage.published') { const projectId = this.PublicationService.current.projectId; this.FileOperationService.microsurvey({projectId}) diff --git a/designsafe/static/scripts/ng-designsafe/services/file-listing-service.js b/designsafe/static/scripts/ng-designsafe/services/file-listing-service.js index 17a4697181..caae1d9dc4 100644 --- a/designsafe/static/scripts/ng-designsafe/services/file-listing-service.js +++ b/designsafe/static/scripts/ng-designsafe/services/file-listing-service.js @@ -25,6 +25,7 @@ export class FileListingService { this.ProjectService = ProjectService; this.FileOperationService = FileOperationService; this.from = from; // bind rxjs method for mocking + this.currentDOI = null; this.modalCloseSubject = new Subject(); this.listingStartSubject = new Subject(); @@ -277,8 +278,8 @@ export class FileListingService { * @param {number} params.limit Number of results to return. * @param {string} params.query_string Optional query string for search. */ - browse({ section, api, scheme, system, path, offset, limit, query_string }) { - const params = { section, api, scheme, system, path, offset: offset || 0, limit: limit || 100, query_string }; + browse({ section, api, scheme, system, path, offset, limit, query_string, doi }) { + const params = { section, api, scheme, system, path, offset: offset || 0, limit: limit || 100, query_string, doi }; this.updateParams(section, params); // Deselect any selected files and update permissions on operations. if (section === 'main') { diff --git a/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js b/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js index 5f9863a40c..28e5a7e191 100644 --- a/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js +++ b/designsafe/static/scripts/ng-designsafe/services/file-operation-service.js @@ -340,13 +340,14 @@ export class FileOperationService { * @param {string} params.scheme Scheme (private, published, community) of files to preview. * @param {Object} params.file File object {name, system, path} to preview. */ - openPreviewModal({ api, scheme, file }) { + openPreviewModal({ api, scheme, file, doi }) { var modal = this.$uibModal.open({ component: 'preview', resolve: { file: () => file, api: () => api, scheme: () => scheme, + doi: () => doi, }, size: 'lg', }); @@ -359,9 +360,9 @@ export class FileOperationService { * @param {string} params.api API of current listing. * @param {string} params.scheme Scheme (private, published, community) of files to preview. */ - getPreviewHref({ file, api, scheme }) { + getPreviewHref({ file, api, scheme, doi }) { const previewUrl = this.removeDuplicateSlashes( - `/api/datafiles/${api}/${scheme}/preview/${file.system}/${encodeURIComponent(file.path)}/` + `/api/datafiles/${api}/${scheme}/preview/${file.system}/${encodeURIComponent(file.path)}/?doi=${doi}` ); switch (api) { case 'shared': @@ -693,13 +694,13 @@ export class FileOperationService { * @param {string} params.scheme Scheme (private, published, community) of current listing. * @param {Object} params.files File objects ({name, system, path}) to download. */ - download({ api, scheme, files }) { + download({ api, scheme, files, doi }) { if (!Array.isArray(files)) { files = [files]; } if (api === 'agave') { const system = files[0].system; - const zipUrl = this.removeDuplicateSlashes(`/api/datafiles/${api}/${scheme}/download/${system}/`); + const zipUrl = this.removeDuplicateSlashes(`/api/datafiles/${api}/${scheme}/download/${system}/?doi=${doi}`); const request = this.$http .put(zipUrl, { paths: files.map((f) => f.path) }) .then((resp) => { From ea1da8cd1847b517ed0205fe7a2e6be944ef133d Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 29 Aug 2023 12:11:49 -0500 Subject: [PATCH 05/23] reduce Data Files sidebar size --- .../scripts/data-depot/components/main/main.template.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/designsafe/static/scripts/data-depot/components/main/main.template.html b/designsafe/static/scripts/data-depot/components/main/main.template.html index 6b21bd91bf..d0cf6dc69c 100644 --- a/designsafe/static/scripts/data-depot/components/main/main.template.html +++ b/designsafe/static/scripts/data-depot/components/main/main.template.html @@ -1,5 +1,5 @@
-
+

Data Depot

From 040e0d88eac6037703a6128d6f4644b5a99ea11b Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 29 Aug 2023 17:00:26 -0500 Subject: [PATCH 06/23] fix max-width on data depot sidebar --- .../scripts/data-depot/components/main/main.template.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/designsafe/static/scripts/data-depot/components/main/main.template.html b/designsafe/static/scripts/data-depot/components/main/main.template.html index d0cf6dc69c..75f5b1aadf 100644 --- a/designsafe/static/scripts/data-depot/components/main/main.template.html +++ b/designsafe/static/scripts/data-depot/components/main/main.template.html @@ -1,5 +1,5 @@
-
+

Data Depot

From a03e1df4707d444efcd4a9f2cfabed892ea32106 Mon Sep 17 00:00:00 2001 From: Van Go <35277477+van-go@users.noreply.github.com> Date: Wed, 13 Sep 2023 13:10:43 -0500 Subject: [PATCH 07/23] des-2579-fix-text-under-published-bullet-list (#1091) Co-authored-by: Jake Rosenberg --- .../projects/pipeline-start/pipeline-start.template.html | 2 -- 1 file changed, 2 deletions(-) diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.template.html index b0ee0be88e..ebdf6a6676 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.template.html @@ -37,8 +37,6 @@

Publishing

submit a ticket with your project number and the name of the dataset(s). -
  • The project will receive a new citation and DOI to include any new authors.
    • -
  • The updated project will display as a new version.
  • If you already published and would like to publish additional data in this same project, submit a ticket with the project ID, project title, what you want to publish, and the order of the authors. From 2817aa8fab90d220f3f4950ef30645b33a924069 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Wed, 13 Sep 2023 14:13:52 -0500 Subject: [PATCH 08/23] hide trash folder for Community Data and published projects (#1093) Co-authored-by: Jake Rosenberg --- .../data-depot-listing/data-depot-listing.component.js | 7 +++++++ .../data-depot-listing/files-listing.template.html | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js b/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js index 449ee7d9a4..85b77c9ae8 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js +++ b/designsafe/static/scripts/data-depot/components/data-depot-listing/data-depot-listing.component.js @@ -224,6 +224,7 @@ class FilesListingCtrl { this.FileOperationService = FileOperationService; this.PublicationService = PublicationService; this.handleScroll = this.handleScroll.bind(this); + this.filterTrash = this.filterTrash.bind(this); } $onInit() { @@ -236,6 +237,12 @@ class FilesListingCtrl { } } + filterTrash(f) { + // Don't display the trash folder in Community listings. + return !(['designsafe.storage.community', 'designsafe.storage.published'].includes(this.listing.params.system) + && f.name.toLowerCase() === '.trash') + } + browse($event, file) { $event.preventDefault(); $event.stopPropagation(); diff --git a/designsafe/static/scripts/data-depot/components/data-depot-listing/files-listing.template.html b/designsafe/static/scripts/data-depot/components/data-depot-listing/files-listing.template.html index 1a80b50042..547abd192b 100644 --- a/designsafe/static/scripts/data-depot/components/data-depot-listing/files-listing.template.html +++ b/designsafe/static/scripts/data-depot/components/data-depot-listing/files-listing.template.html @@ -26,7 +26,7 @@ From d29e8143def61980170cc83d3d62524de829a2b1 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Wed, 13 Sep 2023 14:19:38 -0500 Subject: [PATCH 09/23] Use Datacite metrics when displaying view/download counts (#1094) Co-authored-by: Jake Rosenberg --- ...publication-preview-field-recon.component.html | 12 ++++++------ .../publication-preview-hyb-sim.component.html | 6 +++--- .../publication-preview-sim.component.html | 6 +++--- .../publication-preview.component.html | 6 +++--- .../published/published-view.component.js | 15 ++++++++++++++- .../prj-pub-preview-metadata-template.html | 10 +++++----- 6 files changed, 34 insertions(+), 21 deletions(-) diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html index af065e7715..9248de1072 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html @@ -118,15 +118,15 @@

    - {{ $ctrl.cumDoiMetrics[mission.value.dois].fileDownloads || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[mission.value.dois]) }} Downloads    - {{ $ctrl.cumDoiMetrics[mission.value.dois].filePreviews || 0}} Views + {{ $ctrl.metricDisplay($ctrl.viewCounts[mission.value.dois]) }} Views    - {{ $ctrl.citationCounts[mission.value.dois] || 0}} Citations + {{ $ctrl.metricDisplay($ctrl.citationCounts[mission.value.dois]) }} Citations    @@ -310,15 +310,15 @@

    - {{ $ctrl.cumDoiMetrics[mission.value.dois].fileDownloads || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[mission.value.dois]) }} Downloads    - {{ $ctrl.cumDoiMetrics[mission.value.dois].filePreviews || 0}} Views + {{ $ctrl.metricDisplay($ctrl.viewCounts[mission.value.dois]) }} Views    - {{ $ctrl.citationCounts[mission.value.dois] || 0}} Citations + {{ $ctrl.metricDisplay($ctrl.citationCounts[mission.value.dois]) }} Citations    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html index 10d5806113..ccc609b85f 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html @@ -138,15 +138,15 @@

    - {{ $ctrl.cumDoiMetrics[hybsim.value.dois].fileDownloads || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[hybsim.value.dois])}} Downloads    - {{ $ctrl.cumDoiMetrics[hybsim.value.dois].filePreviews || 0}} Views + {{ $ctrl.metricDisplay($ctrl.viewCounts[hybsim.value.dois])}} Views    - {{ $ctrl.citationCounts[hybsim.value.dois] || 0}} Citations + {{ $ctrl.metricDisplay($ctrl.citationCounts[hybsim.value.dois])}} Citations    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html index 38520381fd..6bb30ad5e9 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html @@ -139,15 +139,15 @@

    - {{ $ctrl.cumDoiMetrics[simulation.value.dois].fileDownloads || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[simulation.value.dois]) }} Downloads    - {{ $ctrl.cumDoiMetrics[simulation.value.dois].filePreviews || 0}} Views + {{ $ctrl.metricDisplay($ctrl.viewCounts[simulation.value.dois])}} Views    - {{ $ctrl.citationCounts[simulation.value.dois] || 0}} Citations + {{ $ctrl.metricDisplay($ctrl.citationCounts[simulation.value.dois])}} Citations    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html index 93e8789ec1..8f2d1ee23e 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html @@ -135,15 +135,15 @@

    - {{ $ctrl.cumDoiMetrics[experiment.value.dois].fileDownloads || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[experiment.value.dois]) }} Downloads    - {{ $ctrl.cumDoiMetrics[experiment.value.dois].filePreviews || 0}} Views + {{ $ctrl.metricDisplay($ctrl.viewCounts[experiment.value.dois]) }} Views    - {{ $ctrl.citationCounts[experiment.value.dois] || 0}} Citations + {{ $ctrl.metricDisplay($ctrl.citationCounts[experiment.value.dois]) }} Citations    diff --git a/designsafe/static/scripts/data-depot/components/published/published-view.component.js b/designsafe/static/scripts/data-depot/components/published/published-view.component.js index 4450804636..5d02e7a74a 100644 --- a/designsafe/static/scripts/data-depot/components/published/published-view.component.js +++ b/designsafe/static/scripts/data-depot/components/published/published-view.component.js @@ -92,7 +92,9 @@ class PublishedViewCtrl { }); }); } - this.citationCounts = {} + this.citationCounts = {}; + this.viewCounts = {}; + this.downloadCounts = {}; this.projId = this.$stateParams.filePath.replace(/^\/+/, '').split('/')[0]; this.versions = this.prepVersions(this.publication); this.selectedVersion = this.publication.revision || 1; @@ -315,6 +317,9 @@ class PublishedViewCtrl { this.doi = this.doiList[ent.uuid]; }); } + if (this.project.value.projectType === 'other') { + this.doiList[this.project.uuid] = {doi: this.project.value.dois[0]}; + } if (this.doiList) { const dataciteRequests = Object.values(this.doiList).map(({ doi }) => { return this.$http.get(`/api/publications/data-cite/${doi}`); @@ -328,6 +333,8 @@ class PublishedViewCtrl { citations.forEach((cite) => { const doiObj = Object.values(this.doiList).find((x) => x.doi === cite.doi); this.citationCounts[cite.doi] = cite.citationCount; + this.downloadCounts[cite.doi] = cite.downloadCount; + this.viewCounts[cite.doi] = cite.viewCount; doiObj.created = cite.created; }); }); @@ -348,6 +355,12 @@ class PublishedViewCtrl { ); } + metricDisplay(metric) { + if (metric === 0) return 0; + if (metric) return metric; + return "--"; + } + prepVersions(publication) { // returns a list of publication versions if (publication.latestRevision) { diff --git a/designsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-preview-metadata-template.html b/designsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-preview-metadata-template.html index d1f321aae6..26189e3401 100644 --- a/designsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-preview-metadata-template.html +++ b/designsafe/static/scripts/ng-designsafe/directives/templates/prj-pub-preview-metadata-template.html @@ -81,15 +81,15 @@
    - {{ $ctrl.cumMetrics.otherTotal || 0 }} Downloads + {{ $ctrl.metricDisplay($ctrl.downloadCounts[$ctrl.project.value.dois[0]]) }} Downloads    - - {{ $ctrl.cumMetrics.filePreviews || 0}} Views + + {{ $ctrl.metricDisplay($ctrl.viewCounts[$ctrl.project.value.dois[0]]) }} Views    - - {{ $ctrl.citationCounts[experiment.value.dois] || 0}} Citations + + {{ $ctrl.metricDisplay($ctrl.citationCounts[$ctrl.project.value.dois[0]]) }} Citations    From f56ac5b777e591bcc25efc7bb5f4766dc66ada5e Mon Sep 17 00:00:00 2001 From: Van Go <35277477+van-go@users.noreply.github.com> Date: Mon, 18 Sep 2023 14:54:59 -0500 Subject: [PATCH 10/23] Hybrid Sim Amend/Revision (#1070) * changes for amends * version changes * Update pipeline-amend-citation.component.js fix typo * Update pipeline-amend.component.js * Update pipeline-version-changes.component.js * Update pipeline-version.component.js * Update pipeline-version-changes.component.js * add hybrid sim mapping and file tag support for Fedora * use new Fedora operations in the publication pipeline. * fix bug when constructing coordinator paths. --------- Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg --- designsafe/apps/api/tasks.py | 49 +- .../apps/projects/managers/publication.py | 5 +- designsafe/libs/fedora/fedora_operations.py | 32 +- designsafe/libs/fedora/fr_operations.py | 13 +- designsafe/libs/fedora/hyb_sim_operations.py | 421 ++++++++++++ designsafe/libs/fedora/sim_operations.py | 12 +- .../data-depot/components/projects/index.js | 10 +- .../amend-hybrid-sim.template.html | 610 ++++++++++++++++++ .../pipeline-amend-citation.component.js | 23 + .../pipeline-amend.component.js | 33 +- .../pipeline-start.component.js | 3 + .../pipeline-version-changes.component.js | 10 + .../pipeline-version.component.js | 45 +- .../version-hyb-sim-citation.template.html | 86 +++ .../version-hyb-sim-selection.template.html | 425 ++++++++++++ ...ication-preview-field-recon.component.html | 2 +- ...publication-preview-hyb-sim.component.html | 2 +- .../publication-preview-other.component.html | 2 +- .../publication-preview-sim.component.html | 2 +- .../publication-preview.component.html | 2 +- designsafe/static/scripts/data-depot/index.js | 36 ++ 21 files changed, 1764 insertions(+), 59 deletions(-) create mode 100644 designsafe/libs/fedora/hyb_sim_operations.py create mode 100644 designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html create mode 100644 designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html create mode 100644 designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html diff --git a/designsafe/apps/api/tasks.py b/designsafe/apps/api/tasks.py index 6247dcc571..7df8fa2bc1 100644 --- a/designsafe/apps/api/tasks.py +++ b/designsafe/apps/api/tasks.py @@ -670,6 +670,8 @@ def amend_publication_data(self, project_id, amendments=None, authors=None, revi from designsafe.apps.projects.managers import publication as PublicationManager from designsafe.libs.fedora.fedora_operations import amend_project_fedora, ingest_project_experimental from designsafe.libs.fedora.sim_operations import ingest_project_sim + from designsafe.libs.fedora.fr_operations import ingest_project_fr + from designsafe.libs.fedora.hyb_sim_operations import ingest_project_hyb_sim try: amended_pub = PublicationManager.amend_publication(project_id, amendments, authors, revision) PublicationManager.amend_datacite_doi(amended_pub) @@ -680,6 +682,10 @@ def amend_publication_data(self, project_id, amendments=None, authors=None, revi ingest_project_experimental(project_id, version=revision, amend=True) if amended_pub.project.value.projectType == 'simulation': ingest_project_sim(project_id, version=revision, amend=True) + if amended_pub.project.value.projectType == 'hybrid_simulation': + ingest_project_hyb_sim(project_id, version=revision, amend=True) + if amended_pub.project.value.projectType == 'field_recon': + ingest_project_fr(project_id, version=revision, amend=True) except Exception as exc: logger.error('Proj Id: %s. %s', project_id, exc, exc_info=True) raise self.retry(exc=exc) @@ -780,41 +786,14 @@ def save_to_fedora(self, project_id, revision=None): from designsafe.libs.fedora.sim_operations import ingest_project_sim ingest_project_sim(project_id, version=revision) return - - _root = os.path.join('/corral-repl/tacc/NHERI/published', project_id) - fedora_base = 'http://fedoraweb01.tacc.utexas.edu:8080/fcrepo/rest/publications_01' - res = requests.get(fedora_base) - if res.status_code == 404 or res.status_code == 410: - requests.put(fedora_base) - - fedora_project_base = ''.join([fedora_base, '/', project_id]) - res = requests.get(fedora_project_base) - if res.status_code == 404 or res.status_code == 410: - requests.put(fedora_project_base) - - headers = {'Content-Type': 'text/plain'} - #logger.debug('walking: %s', _root) - for root, dirs, files in os.walk(_root): - for name in files: - mime = magic.Magic(mime=True) - headers['Content-Type'] = mime.from_file(os.path.join(root, name)) - #files - full_path = os.path.join(root, name) - _path = full_path.replace(_root, '', 1) - _path = _path.replace('[', '-') - _path = _path.replace(']', '-') - url = ''.join([fedora_project_base, urllib.parse.quote(_path)]) - #logger.debug('uploading: %s', url) - with open(os.path.join(root, name), 'rb') as _file: - requests.put(url, data=_file, headers=headers) - - for name in dirs: - #dirs - full_path = os.path.join(root, name) - _path = full_path.replace(_root, '', 1) - url = ''.join([fedora_project_base, _path]) - #logger.debug('creating: %s', _path) - requests.put(url) + if pub.project.value.projectType == 'hybrid_simulation': + from designsafe.libs.fedora.hyb_sim_operations import ingest_project_hyb_sim + ingest_project_hyb_sim(project_id, version=revision) + return + if pub.project.value.projectType == 'field_recon': + from designsafe.libs.fedora.fr_operations import ingest_project_fr + ingest_project_fr(project_id, version=revision) + return except Exception as exc: logger.error('Proj Id: %s. %s', project_id, exc) diff --git a/designsafe/apps/projects/managers/publication.py b/designsafe/apps/projects/managers/publication.py index 11d716d0cc..88d6476a83 100644 --- a/designsafe/apps/projects/managers/publication.py +++ b/designsafe/apps/projects/managers/publication.py @@ -252,10 +252,9 @@ def draft_publication( def amend_publication(project_id, amendments=None, authors=None, revision=None): """Amend a Publication - Update Amendable fields on a publication and the corrosponding DataCite + Update Amendable fields on a publication and the corresponding DataCite records. These changes do not produce a new version of a publication, but - they do allow for limited changes to a published project. This is currently - configured to support "Other" publications only. + they do allow for limited changes to a published project. :param str project_id: Project uuid to amend :param int revision: Revision number to amend diff --git a/designsafe/libs/fedora/fedora_operations.py b/designsafe/libs/fedora/fedora_operations.py index 0320e85825..ee5bf40280 100644 --- a/designsafe/libs/fedora/fedora_operations.py +++ b/designsafe/libs/fedora/fedora_operations.py @@ -114,6 +114,9 @@ }, "influenced": { "@id": "https://www.w3.org/TR/2013/REC-prov-o-20130430/#influenced" + }, + "Influence": { + "@id": "https://www.w3.org/TR/2013/REC-prov-o-20130430/#Influence" } } @@ -297,8 +300,10 @@ def format_metadata_for_fedora(project_id, version=None): def generate_manifest_other(project_id, version=None): + fido_client = Fido() doc = IndexedPublication.from_id(project_id, revision=version) uuid = doc.project.uuid + file_tags = getattr(doc.project.value, 'fileTags', []) if version: project_id = '{}v{}'.format(project_id, str(version)) @@ -306,10 +311,15 @@ def generate_manifest_other(project_id, version=None): archive_path = os.path.join(PUBLICATIONS_MOUNT_ROOT, project_id) for path in get_child_paths(archive_path): + rel_path = os.path.relpath(path, archive_path) + + tags = filter(lambda t: t['path'].strip('/') == rel_path.strip('/'), file_tags) manifest.append({ 'parent_entity': uuid, 'corral_path': path, - 'checksum': get_sha1_hash(path) + 'checksum': get_sha1_hash(path), + 'tags': [t['tagName'] for t in tags], + 'ffi': get_fido_output(fido_client, path) }) return manifest @@ -411,7 +421,8 @@ def walk_experimental(project_id, version=None): 'uuid': doc.project.uuid, 'container_path': project_id, 'fedora_mapping': {**project_meta, 'generated': [], 'license': None}, - 'fileObjs': [] + 'fileObjs': [], + 'fileTags': [] } experiments_list = doc.experimentsList @@ -426,7 +437,8 @@ def walk_experimental(project_id, version=None): 'uuid': expt.uuid, 'container_path': expt_container_path, 'fedora_mapping': {**format_experiment(expt), 'license': license, 'wasGeneratedBy': project_id, 'generated': []}, - 'fileObjs': expt.fileObjs + 'fileObjs': expt.fileObjs, + 'fileTags': getattr(expt.value, 'fileTags', []), } full_author_list += experiment_map['fedora_mapping']['creator'] @@ -443,6 +455,7 @@ def walk_experimental(project_id, version=None): report_map = { 'uuid': report.uuid, 'fileObjs': report.fileObjs, + 'fileTags': getattr(report.value, 'fileTags', []), 'container_path': report_container_path, 'fedora_mapping': {**format_report(report), 'wasGeneratedBy': 'Experiment: {}'.format(exp_doi)} } @@ -460,6 +473,7 @@ def walk_experimental(project_id, version=None): analysis_map = { 'uuid': analysis.uuid, 'fileObjs': analysis.fileObjs, + 'fileTags': getattr(analysis.value, 'fileTags', []), 'container_path': analysis_container_path, 'fedora_mapping': {**format_analysis(analysis), 'wasGeneratedBy': 'Experiment: {}'.format(exp_doi)} @@ -478,6 +492,7 @@ def walk_experimental(project_id, version=None): mc_map = { 'uuid': mc.uuid, 'fileObjs': mc.fileObjs, + 'fileTags': getattr(mc.value, 'fileTags', []), 'container_path': configs_container_path, 'fedora_mapping': {**format_model_config(mc), 'wasGeneratedBy': exp_doi} } @@ -494,6 +509,7 @@ def walk_experimental(project_id, version=None): sl_map = { 'uuid': sl.uuid, 'fileObjs': sl.fileObjs, + 'fileTags': getattr(sl.value, 'fileTags', []), 'container_path': sl_container_path, 'fedora_mapping': {**format_sensor_info(sl), 'wasGeneratedBy': 'Experiment: {}'.format(exp_doi), @@ -514,6 +530,7 @@ def walk_experimental(project_id, version=None): event_map = { 'uuid': event.uuid, 'fileObjs': event.fileObjs, + 'fileTags': getattr(event.value, 'fileTags', []), 'container_path': evt_container_path, 'fedora_mapping': {**format_event(event), 'wasGeneratedBy': 'Experiment: {}'.format(exp_doi), @@ -667,27 +684,36 @@ def generate_manifest(walk_result, project_id, version=None): archive_path = os.path.join(PUBLICATIONS_MOUNT_ROOT, project_id) for entity in walk_result: file_objs = entity['fileObjs'] + file_tags = entity.get('fileTags', []) for file in file_objs: + + file_path = os.path.join(archive_path, file['path'].strip('/')) rel_path = os.path.join(parse.unquote(entity['container_path']), file['path'].strip('/')) if file['type'] == 'dir': for path in get_child_paths(file_path): + tag_path = os.path.relpath(path, archive_path) + tags = filter(lambda t: t['path'].strip('/') == tag_path.strip('/'), file_tags) + manifest.append({ 'parent_entity': entity['uuid'], 'corral_path': path, 'project_path': path.replace(file_path, rel_path, 1), 'checksum': get_sha1_hash(path), + 'tags': [t['tagName'] for t in tags], 'ffi': get_fido_output(fido_client, path) }) else: + tags = filter(lambda t: t['path'] == file['path'], file_tags) manifest.append({ 'parent_entity': entity['uuid'], 'corral_path': file_path, 'project_path': rel_path, 'checksum': get_sha1_hash(file_path), + 'tags': [t['tagName'] for t in tags], 'ffi': get_fido_output(fido_client, file_path) }) diff --git a/designsafe/libs/fedora/fr_operations.py b/designsafe/libs/fedora/fr_operations.py index 8149959b49..111e495775 100644 --- a/designsafe/libs/fedora/fr_operations.py +++ b/designsafe/libs/fedora/fr_operations.py @@ -45,7 +45,8 @@ def walk_fr(project_id, version=None): 'uuid': doc.project.uuid, 'container_path': project_id, 'fedora_mapping': {**project_meta, 'generated': [], 'license': None}, - 'fileObjs': [] + 'fileObjs': [], + 'fileTags': [] } docs_list = getattr(doc, 'reports', []) @@ -60,7 +61,8 @@ def walk_fr(project_id, version=None): 'uuid': document.uuid, 'container_path': doc_container_path, 'fedora_mapping': {**format_docs(document), 'license': license, 'wasGeneratedBy': project_id, 'generated': [], 'hasVersion': version}, - 'fileObjs': document.fileObjs + 'fileObjs': document.fileObjs, + 'fileTags': getattr(document.value, 'fileTags', []), } relation_map.append(doc_map) @@ -77,7 +79,8 @@ def walk_fr(project_id, version=None): 'uuid': mission.uuid, 'container_path': mission_container_path, 'fedora_mapping': {**format_mission(mission), 'license': license, 'wasGeneratedBy': project_id, 'generated': [], 'hasVersion': version}, - 'fileObjs': [] + 'fileObjs': [], + 'fileTags': getattr(mission.value, 'fileTags', []), } @@ -93,6 +96,7 @@ def walk_fr(project_id, version=None): collection_map = { 'uuid': collection.uuid, 'fileObjs': collection.fileObjs, + 'fileTags': getattr(collection.value, 'fileTags', []), 'container_path': collection_container_path, 'fedora_mapping': {**format_geo(collection), 'wasGeneratedBy': 'Mission: {}'.format(mission_doi)} } @@ -110,6 +114,7 @@ def walk_fr(project_id, version=None): collection_map = { 'uuid': geo_collection.uuid, 'fileObjs': geo_collection.fileObjs, + 'fileTags': getattr(geo_collection.value, 'fileTags', []), 'container_path': geo_container_path, 'fedora_mapping': {**format_geo(geo_collection), 'wasGeneratedBy': 'Mission: {}'.format(mission_doi)} } @@ -127,6 +132,7 @@ def walk_fr(project_id, version=None): collection_map = { 'uuid': soc_collection.uuid, 'fileObjs': soc_collection.fileObjs, + 'fileTags': getattr(soc_collection.value, 'fileTags', []), 'container_path': soc_container_path, 'fedora_mapping': {**format_soc(soc_collection), 'wasGeneratedBy': 'Mission: {}'.format(mission_doi)} } @@ -144,6 +150,7 @@ def walk_fr(project_id, version=None): collection_map = { 'uuid': planning_coll.uuid, 'fileObjs': planning_coll.fileObjs, + 'fileTags': getattr(planning_coll.value, 'fileTags', []), 'container_path': planning_container_path, 'fedora_mapping': {**format_planning(planning_coll), 'wasGeneratedBy': 'Mission: {}'.format(mission_doi)} } diff --git a/designsafe/libs/fedora/hyb_sim_operations.py b/designsafe/libs/fedora/hyb_sim_operations.py new file mode 100644 index 0000000000..3775e454d0 --- /dev/null +++ b/designsafe/libs/fedora/hyb_sim_operations.py @@ -0,0 +1,421 @@ +import requests +from requests import HTTPError +from django.conf import settings +import json +import magic +import os +import hashlib +from urllib import parse +from io import StringIO +from requests.adapters import HTTPAdapter +from requests.packages.urllib3.util.retry import Retry +from designsafe.apps.data.models.elasticsearch import IndexedPublication +from django.contrib.auth import get_user_model +from designsafe.apps.api.publications.operations import _get_user_by_username +from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest +import logging +logger = logging.getLogger(__name__) + +def walk_hyb_sim(project_id, version=None): + """ + Walk an experimental project and reconstruct parent/child relationships + + Params + ------ + project_id: Project ID to look up (e.g. PRJ-1234) + + Returns + ------- + dict: dict in form {'uuid-ex-1': + {'children': ['title of child 1', ...], + 'parent': 'title of parent', + 'container_path': 'path/relative/to/fcroot', + 'fedora_mapping': {}}} + """ + from urllib import parse + doc = IndexedPublication.from_id(project_id, revision=version) + + relation_map = [] + + project_meta = format_metadata_for_fedora(project_id, version=version) + if version: + project_id = '{}v{}'.format(project_id, str(version)) + license = project_meta.get('license', None) + + project_map = { + 'uuid': doc.project.uuid, + 'container_path': project_id, + 'fedora_mapping': {**project_meta, 'generated': [], 'license': None}, + 'fileObjs': [], + 'fileTags': [] + } + + + + hybrid_sim_list = getattr(doc, 'hybrid_simulations', []) + for hyb_sim in hybrid_sim_list: + # Do stuff with hyb sim. + hyb_sim_container_path = "{}/{}".format(project_id, parse.quote(hyb_sim.value.title)) + print('hybrid sim ' + hyb_sim.value.title) + hyb_sim_doi = hyb_sim.doi + project_map['fedora_mapping']['generated'].append('Hybrid Simulation: {}'.format(hyb_sim_doi)) + + hyb_sim_map = { + 'uuid': hyb_sim.uuid, + 'container_path': hyb_sim_container_path, + 'fedora_mapping': {**format_hyb_sim(hyb_sim), 'license': license, 'wasGeneratedBy': project_id, 'generated': [], 'hasVersion': version}, + 'fileObjs': [], + 'fileTags': [] + } + + reports_list = filter( + lambda report: hyb_sim.uuid in report.value.hybridSimulations, + getattr(doc, 'reports', [])) + for report in reports_list: + # Do stuff with report. + report_container_path = "{}/{}".format(project_id, parse.quote(report.value.title)) + print('\treport ' + report.value.title) + project_map['fedora_mapping']['generated'].append('Report: {}'.format(report.value.title)) + + report_map = { + 'uuid': report.uuid, + 'container_path': report_container_path, + 'fedora_mapping': {**format_report(report), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi)}, + 'fileObjs': report.fileObjs, + 'fileTags': getattr(report.value, 'fileTags', []) + } + + relation_map.append(report_map) + + + analysis_list = filter( + lambda analysis: hyb_sim.uuid in analysis.value.hybridSimulations, + getattr(doc, 'analysiss', [])) + for analysis in analysis_list: + # Do stuff with analysis. + analysis_container_path = "{}/{}".format(project_id, parse.quote(analysis.value.title)) + print('analysis ' + analysis.value.title) + project_map['fedora_mapping']['generated'].append('Analysis: {}'.format(analysis.value.title)) + + analysis_map = { + 'uuid': report.uuid, + 'container_path': analysis_container_path, + 'fedora_mapping': {**format_report(analysis), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi)}, + 'fileObjs': analysis.fileObjs, + 'fileTags': getattr(analysis.value, 'fileTags', []) + } + + relation_map.append(analysis_map) + + + global_model_list = filter( + lambda global_model: hyb_sim.uuid in global_model.value.hybridSimulations, + getattr(doc, 'global_models', [])) + for global_model in global_model_list: + # Do stuff with global model. + global_model_container_path = "{}/{}".format(hyb_sim_container_path, parse.quote(global_model.value.title)) + print('\tGlobal Model ' + global_model.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Global Model: {}'.format(global_model.value.title)) + + global_model_map = { + 'uuid': global_model.uuid, + 'fileObjs': global_model.fileObjs, + 'fileTags': getattr(global_model.value, 'fileTags', []), + 'container_path': global_model_container_path, + 'fedora_mapping': {**format_global_modal(global_model), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi)} + } + + + coordinator_list = filter( + lambda coordinator: global_model.uuid in coordinator.value.globalModels, + getattr(doc, 'coordinators', [])) + for coordinator in coordinator_list: + # Do stuff with coordinator. + coordinator_container_path = "{}/{}".format(global_model_container_path, parse.quote(coordinator.value.title)) + print('\t\tCoordinator ' + coordinator.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Coordinator: {}'.format(coordinator.value.title)) + + coordinator_map = { + 'uuid': coordinator.uuid, + 'fileObjs': coordinator.fileObjs, + 'fileTags': getattr(coordinator.value, 'fileTags', []), + 'container_path': coordinator_container_path, + 'fedora_mapping': {**format_coordinator(coordinator), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi), + 'wasInfluencedBy': 'Global Model: {}'.format(global_model.value.title)} + } + + coordinator_output_list = filter( + lambda coordinator_output: coordinator.uuid in coordinator_output.value.coordinators, + getattr(doc, 'coordinator_outputs', [])) + for coordinator_output in coordinator_output_list: + # Do stuff with coordinator output. + coordinator_output_container_path = "{}/{}".format(coordinator_container_path, parse.quote(coordinator_output.value.title)) + print('\t\t\tCoordinator Output ' + coordinator_output.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Coordinator Output: {}'.format(coordinator_output.value.title)) + + coordinator_output_map = { + 'uuid': coordinator_output.uuid, + 'fileObjs': coordinator_output.fileObjs, + 'fileTags': getattr(coordinator_output.value, 'fileTags', []), + 'container_path': coordinator_output_container_path, + 'fedora_mapping': {**format_coordinator_output(coordinator_output), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi), + 'wasInfluencedBy': 'Global Model: {}'.format(global_model.value.title), + 'wasDerivedFrom': 'Coordinator: {}'.format(coordinator.value.title)} + } + relation_map.append(coordinator_output_map) + + + sim_sub_list = filter( + lambda sim_sub: coordinator.uuid in sim_sub.value.coordinators, + getattr(doc, 'sim_substructures', [])) + for sim_sub in sim_sub_list: + # Do stuff with sim substructure. + sim_sub_container_path = "{}/{}".format(coordinator_container_path, parse.quote(sim_sub.value.title)) + print('\t\t\tSimulation Substructure ' + sim_sub.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Simulation Substructure: {}'.format(sim_sub.value.title)) + + sim_sub_map = { + 'uuid': sim_sub.uuid, + 'fileObjs': sim_sub.fileObjs, + 'fileTags': getattr(sim_sub.value, 'fileTags', []), + 'container_path': sim_sub_container_path, + 'fedora_mapping': {**format_sim_substructure(sim_sub), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi), + 'wasInfluencedBy': 'Global Model: {}'.format(global_model.value.title), + 'wasInfluencedBy': 'Coordinator: {}'.format(coordinator.value.title)} + } + + sim_out_list = filter( + lambda sim_out: sim_sub.uuid in sim_out.value.simSubstructures, + getattr(doc, 'sim_outputs', [])) + for sim_out in sim_out_list: + # Do stuff with sim output. + sim_out_container_path = "{}/{}".format(sim_sub_container_path, parse.quote(sim_out.value.title)) + print('\t\t\t\tSimulation Output ' + sim_out.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Simulation Output: {}'.format(sim_sub.value.title)) + + sim_out_map = { + 'uuid': sim_out.uuid, + 'fileObjs': sim_out.fileObjs, + 'fileTags': getattr(sim_out.value, 'fileTags', []), + 'container_path': sim_out_container_path, + 'fedora_mapping': {**format_sim_output(sim_out), 'wasDerivedFrom': 'Simulation Substructure: {}'.format(sim_sub.value.title)} + } + relation_map.append(sim_out_map) + + relation_map.append(sim_sub_map) + + exp_sub_list = filter( + lambda exp_sub: coordinator.uuid in exp_sub.value.coordinators, + getattr(doc, 'exp_substructures', [])) + for exp_sub in exp_sub_list: + # Do stuff with experimental substructure. + exp_sub_container_path = "{}/{}".format(coordinator_container_path, parse.quote(exp_sub.value.title)) + print('\t\t\tExperimental Substructure ' + exp_sub.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Experimental Substructure: {}'.format(exp_sub.value.title)) + + exp_sub_map = { + 'uuid': exp_sub.uuid, + 'fileObjs': exp_sub.fileObjs, + 'fileTags': getattr(exp_sub.value, 'fileTags', []), + 'container_path': exp_sub_container_path, + 'fedora_mapping': {**format_exp_substructure(exp_sub), 'wasGeneratedBy': 'Hybrid Simulation: {}'.format(hyb_sim_doi), + 'wasInfluencedBy': 'Global Model: {}'.format(global_model.value.title), + 'wasInfluencedBy': 'Coordinator: {}'.format(coordinator.value.title)} + } + + exp_out_list = filter( + lambda exp_out: exp_sub.uuid in exp_out.value.expSubstructures, + getattr(doc, 'exp_outputs', [])) + for exp_out in exp_out_list: + # Do stuff with experimental output. + exp_out_container_path = "{}/{}".format(exp_sub_container_path, parse.quote(exp_out.value.title)) + print('\t\t\t\tExperimental Output ' + exp_out.value.title) + hyb_sim_map['fedora_mapping']['generated'].append('Experimental Output: {}'.format(exp_sub.value.title)) + + exp_out_map = { + 'uuid': exp_out.uuid, + 'fileObjs': exp_out.fileObjs, + 'fileTags': getattr(exp_out.value, 'fileTags', []), + 'container_path': exp_out_container_path, + 'fedora_mapping': {**format_exp_output(exp_out), 'wasDerivedFrom': 'Experimental Substructure: {}'.format(exp_sub.value.title)} + } + relation_map.append(exp_out_map) + + relation_map.append(exp_sub_map) + + relation_map.append(coordinator_map) + relation_map.append(global_model_map) + + relation_map.append(hyb_sim_map) + # project_map['fedora_mapping']['creator'] = list(set(full_author_list)) + relation_map.append(project_map) + + return relation_map[::-1] + + + +def format_hyb_sim(hyb_sim): + meta = hyb_sim.value + + try: + authors = hyb_sim.authors + creator = list(map(lambda author: "{lname}, {fname}".format(**author.to_dict()), authors)) + except AttributeError: + creator = list(map(lambda username: _get_user_by_username(hyb_sim, username), meta.authors)) + + try: + dois = list(hyb_sim.dois) + except AttributeError: + dois = [hyb_sim.doi] + + publication_date = str(hyb_sim.created) + + referenced_by = [] + part_of = [] + references = [] + + refs = getattr(meta, 'referencedData', []) + for ref in refs: + if ref['hrefType'] == 'URL': + ref_val = f"{ref['title']} ({ref['doi']})" + elif ref['hrefType'] == 'DOI': + ref_val = ref['doi'] + references.append(ref_val) + + related_work = getattr(meta, 'relatedWork', []) + for work in related_work: + if work['hrefType'] == 'URL': + work_val = f"{work['title']} ({work['href']})" + elif work['hrefType'] == 'DOI': + work_val = work['href'] + + if work['type'] == 'Linked Project': + part_of.append(work_val) + + if work['type'] == 'Linked Dataset': + part_of.append(work_val) + + if work['type'] == 'Context': + references.append(work_val) + + if work['type'] == 'Cited By': + referenced_by.append(work_val) + + return { + "title": meta.title, + "type": meta.simulationType, + "creator": creator, + "identifier": dois, + "available": publication_date, + "publisher": "DesignSafe", + "description": meta.description, + 'isReferencedBy': referenced_by, + 'isPartOf': part_of, + 'references': references + + } + +def format_global_modal(global_model): + return { + "type": "global model", + "title": global_model.value.title, + "abstract": global_model.value.description, + } + +def format_coordinator(coordinator): + return { + "type": "simulation coordinator", + "title": coordinator.value.title, + "description": coordinator.value.description + } + +def format_sim_substructure(sim_sub): + return { + "type": "simulation substructure", + "title": sim_sub.value.title, + "abstract": sim_sub.value.description + } + +def format_sim_output(sim_out): + return { + "type": "simulation output", + "title": sim_out.value.title, + "abstract": sim_out.value.description + } + +def format_exp_substructure(exp_sub): + return { + "type": "experimental substructure", + "title": exp_sub.value.title, + "description": exp_sub.value.description + } + +def format_exp_output(exp_out): + return { + "type": "experimental output", + "title": exp_out.value.title, + "description": exp_out.value.description + } + +def format_coordinator_output(coord_out): + return { + "type": "coordinator output", + "title": coord_out.value.title, + "abstract": coord_out.value.description + } + +def format_analysis(analysis): + return { + "type": "analysis", + "title": analysis.value.title, + "description": analysis.value.description + } + + +def format_report(report): + return { + "type": "report", + "title": report.value.title, + "description": report.value.description + } + + +def format_member(member): + try: + return f'{member.lname}, {member.fname}' + except AttributeError: + user_obj = get_user_model().objects.get(username=member.name) + return "{}, {}".format(user_obj.last_name, user_obj.first_name) + + + + + +def generate_manifest_hyb_sim(project_id, version=None): + walk_result = walk_hyb_sim(project_id, version=version) + return generate_manifest(walk_result, project_id, version) + + +def upload_manifest_hyb_sim(project_id, version=None): + manifest_dict = generate_manifest_hyb_sim(project_id, version=version) + return upload_manifest(manifest_dict, project_id, version) + + +def ingest_project_hyb_sim(project_id, version=None, amend=False): + """ + Ingest a project into Fedora by creating a record in the repo, updating it + with the published metadata, and uploading its files. + """ + container_path = project_id + if version: + container_path = '{}v{}'.format(container_path, str(version)) + + walk_result = walk_hyb_sim(project_id, version=version) + for entity in walk_result: + if amend: + create_fc_version(entity['container_path']) + fedora_post(entity['container_path']) + fedora_update(entity['container_path'], entity['fedora_mapping']) + + if not amend: + upload_manifest_hyb_sim(project_id, version=version) \ No newline at end of file diff --git a/designsafe/libs/fedora/sim_operations.py b/designsafe/libs/fedora/sim_operations.py index 353e58f427..2900cd6e2f 100644 --- a/designsafe/libs/fedora/sim_operations.py +++ b/designsafe/libs/fedora/sim_operations.py @@ -49,7 +49,8 @@ def walk_sim(project_id, version=None): 'uuid': sim.uuid, 'container_path': sim_container_path, 'fedora_mapping': {**format_sim(sim), 'license': license, 'wasGeneratedBy': project_id, 'generated': []}, - 'fileObjs': getattr(sim, 'fileObjs', []) + 'fileObjs': getattr(sim, 'fileObjs', []), + 'fileTags': getattr(sim.value, 'fileTags', []) } full_author_list += sim_map['fedora_mapping']['creator'] @@ -67,6 +68,7 @@ def walk_sim(project_id, version=None): report_map = { 'uuid': report.uuid, 'fileObjs': report.fileObjs, + 'fileTags': getattr(report.value, 'fileTags', []), 'container_path': report_container_path, 'fedora_mapping': {**format_report(report), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)} } @@ -85,6 +87,7 @@ def walk_sim(project_id, version=None): analysis_map = { 'uuid': analysis.uuid, 'fileObjs': analysis.fileObjs, + 'fileTags': getattr(analysis.value, 'fileTags', []), 'container_path': analysis_container_path, 'fedora_mapping': {**format_analysis(analysis), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)} } @@ -104,6 +107,7 @@ def walk_sim(project_id, version=None): model_map = { 'uuid': model.uuid, 'fileObjs': model.fileObjs, + 'fileTags': getattr(model.value, 'fileTags', []), 'container_path': model_container_path, 'fedora_mapping': {**format_model(model), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi)} } @@ -120,11 +124,12 @@ def walk_sim(project_id, version=None): input_map = { 'uuid': input.uuid, 'fileObjs': input.fileObjs, + 'fileTags': getattr(input.value, 'fileTags', []), 'container_path': input_container_path, 'fedora_mapping': {**format_input(input), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi), 'wasDerivedFrom': 'Simulation Model: {}'.format(model.value.title), - 'wasInfluencedBy': []} + 'Influence': []} } outputs = filter( @@ -136,10 +141,11 @@ def walk_sim(project_id, version=None): output_container_path = "{}/{}".format(input_container_path, parse.quote(output.value.title)) print('\t\t\toutput ' + output.value.title) sim_map['fedora_mapping']['generated'].append('Simulation Input: {}'.format(output.value.title)) - input_map['fedora_mapping']['wasInfluencedBy'].append('Simulation Output: {}'.format(output.value.title)) + input_map['fedora_mapping']['Influence'].append('Simulation Output: {}'.format(output.value.title)) output_map = { 'uuid': output.uuid, 'fileObjs': output.fileObjs, + 'fileTags': getattr(output.value, 'fileTags', []), 'container_path': output_container_path, 'fedora_mapping': {**format_output(output), 'wasGeneratedBy': 'Simulation: {}'.format(sim_doi), diff --git a/designsafe/static/scripts/data-depot/components/projects/index.js b/designsafe/static/scripts/data-depot/components/projects/index.js index 422aef73fb..d1959398ff 100644 --- a/designsafe/static/scripts/data-depot/components/projects/index.js +++ b/designsafe/static/scripts/data-depot/components/projects/index.js @@ -17,10 +17,16 @@ import { VersionExperimentSelectionComponent, VersionFieldReconSelectionComponent, VersionSimulationSelectionComponent, + VersionHybSimSelectionComponent, VersionCitationComponent } from './pipeline-version/pipeline-version.component'; import { VersionChangesComponent } from './pipeline-version/pipeline-version-changes.component'; -import { AmendExperimentComponent, AmendFieldReconComponent, AmendSimulationComponent } from './pipeline-amend/pipeline-amend.component'; +import { + AmendExperimentComponent, + AmendFieldReconComponent, + AmendSimulationComponent, + AmendHybSimComponent +} from './pipeline-amend/pipeline-amend.component'; import { AmendOtherComponent } from './pipeline-amend/pipeline-amend-other.component'; import { AmendCitationComponent } from './pipeline-amend/pipeline-amend-citation.component'; import { @@ -93,12 +99,14 @@ ddProjectsComponents.component('amendOther', AmendOtherComponent); ddProjectsComponents.component('amendExperiment', AmendExperimentComponent); ddProjectsComponents.component('amendFieldRecon', AmendFieldReconComponent); ddProjectsComponents.component('amendSimulation', AmendSimulationComponent); +ddProjectsComponents.component('amendHybSim', AmendHybSimComponent); ddProjectsComponents.component('amendCitation', AmendCitationComponent); ddProjectsComponents.component('versionOtherSelection', VersionOtherSelectionComponent); ddProjectsComponents.component('versionOtherCitation', VersionOtherCitationComponent); ddProjectsComponents.component('versionExperimentSelection', VersionExperimentSelectionComponent); ddProjectsComponents.component('versionFieldReconSelection', VersionFieldReconSelectionComponent); ddProjectsComponents.component('versionSimulationSelection', VersionSimulationSelectionComponent); +ddProjectsComponents.component('versionHybSimSelection', VersionHybSimSelectionComponent); ddProjectsComponents.component('versionCitation', VersionCitationComponent); ddProjectsComponents.component('versionChanges', VersionChangesComponent); ddProjectsComponents.component('pipelineSelectExp', PipelineSelectionExpComponent); diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html new file mode 100644 index 0000000000..c1b6dd2015 --- /dev/null +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html @@ -0,0 +1,610 @@ +
    + + Back + + +
    +
    +
    +

    Amend Metadata

    + If you need help, attend curation office hours. +
    +

    + Loading... +

    +
    +
    + +
    +
    + +
    + Some of your project's amendments were not able to be imported. Please review and amend + the the highlighted categories below. + + IMPORTANT: None of the changes made during this process will save to the project. + Changes made here will only amend the publication once submitted. + +
    +
    +
  • {{entity.title}}
    • +
    +
    +
    +
    +
    +
    +
      +
    • Please review the preview of your amended publication carefully.
      • +
    • Any acceptable changes you make from the project workspace are automatically imported to this preview.
      • +
    • This preview shows what your publication will look like once it is amended.
      • +
    • Categories may not be added or removed.
      • +
    • Files related to any categories may not be modified.
      • +
    • When you have finished proofreading your amended publication, click continue to move onto the next step.
      • +
    +
    + +
    +
    + + {{$ctrl.amendment.project.value.projectId}} | {{ $ctrl.amendment.project.value.title }} + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PI + +
    Co-PIs + +
    Project Type + {{ $ctrl.amendment.project.value.projectType.replace('_', ' ') }} + + Field Research + + | + + {{ frType }}, + {{ frType }} + + +
    Data Type{{ $ctrl.amendment.project.value.dataType }}
    Natural Hazard Type + + {{ nhtype }}, + {{ nhtype }} + +
    Awards{{ award.name }} - {{ award.number }}
    Related Work + +
    Keywords{{ $ctrl.amendment.project.value.keywords }}
    Hazmapper Maps + +
    +
    +

    {{ $ctrl.amendment.project.value.description }}

    +
    + +
    + +
    +
    + +
    + +
    +
    +
    +
    diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend-citation.component.js b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend-citation.component.js index 2bc5b7008e..e72adb7473 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend-citation.component.js +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend-citation.component.js @@ -101,6 +101,29 @@ class PipelineAmendCitationCtrl { this.ui.savedStatus[simulation.uuid] = false; } }); + } + else if (prj_type == 'hybrid_simulation'){ + this.amendComp = 'projects.amendHybSim'; + this.ui.placeholder = 'HybSim'; + this.amendFields = [ + 'hybrid_simulations', + 'global_models', + 'coordinators', + 'sim_substructures', + 'exp_substructures', + 'coordinator_outputs', + 'sim_outputs', + 'exp_outputs', + 'analysiss', + 'reports' + ] + this.amendment.hybrid_simulations.forEach((hybsim) => { + if (hybsim.value.dois.length) { + this.publishedEntities.push(hybsim); + this.authors[hybsim.uuid] = hybsim.authors; + this.ui.savedStatus[hybsim.uuid] = false; + } + }); } else { this.goStart(); } diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend.component.js b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend.component.js index a7e6e3b5c9..bfca8deb22 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend.component.js +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/pipeline-amend.component.js @@ -1,6 +1,7 @@ import AmendExperimentTemplate from './amend-experimental.template.html'; import AmendFieldReconTemplate from './amend-field-recon.template.html'; -import AmendSimulationTemplate from './amend-simulation.template.html' +import AmendSimulationTemplate from './amend-simulation.template.html'; +import AmendHybridSimTemplate from './amend-hybrid-sim.template.html'; import experimentalData from '../../../../projects/components/manage-experiments/experimental-data.json'; class PipelineAmendCtrl { @@ -62,6 +63,7 @@ class PipelineAmendCtrl { 'reportEntity': ['project','files','authors','dois'], 'missionEntity': ['project','files','authors','dois'], 'simulationEntity': ['project','files','authors','dois'], + 'hybsimEntity': ['project','files','authors','dois'], } let prjEnts = this.project.getAllRelatedObjects(); @@ -96,7 +98,21 @@ class PipelineAmendCtrl { 'reports' ] } - + else if (prj_type == 'hybrid_simulation') { + primaryEntNames = ['hybidsimulations'] + secondaryEntNames = [ + 'hybrid_simulations', + 'global_models', + 'coordinators', + 'sim_substructures', + 'exp_substructures', + 'coordinator_outputs', + 'sim_outputs', + 'exp_outputs', + 'analysiss', + 'reports' + ] + } if (update === 'all') { this.amendment = JSON.parse(JSON.stringify(this.publication)); } @@ -405,4 +421,15 @@ export const AmendSimulationComponent = { close: '&', dismiss: '&' }, -}; \ No newline at end of file +}; + +export const AmendHybSimComponent = { + template: AmendHybridSimTemplate, + controller: PipelineAmendCtrl, + controllerAs: '$ctrl', + bindings: { + resolve: '<', + close: '&', + dismiss: '&' + }, +}; diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.component.js b/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.component.js index 7708ab53d7..6285b3d728 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.component.js +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-start/pipeline-start.component.js @@ -53,7 +53,10 @@ class PipelineStartCtrl { } case 'hybrid_simulation': { this.ui.publicationComp = 'projects.pipelineSelectHybSim' + this.ui.amendComp = 'projects.amendHybSim' + this.ui.versionComp = 'projects.versionHybSimSelection' this.ui.previewComp = 'projects.previewHybSim' + this.ui.showAmendVersion = true; break; } case 'field_recon': { diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version-changes.component.js b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version-changes.component.js index 493bbd2255..78fa9b65b1 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version-changes.component.js +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version-changes.component.js @@ -103,6 +103,16 @@ class PipelineVersionChangesCtrl { this.mainEntityUuids.push(entity.uuid); }); } + if (this.prjType === 'hybrid_simulation') { + this.ui.selectionComp = 'projects.versionHybSimSelection' + this.ui.citationComp = 'projects.versionCitation' + + this.pubData['hybrid_simulations'] = []; + this.selectedEnts.forEach((entity) => { + this.pubData['hybrid_simulations'].push({uuid: entity.uuid}); + this.mainEntityUuids.push(entity.uuid); + }); + } } else { this.revisionAuthors = this.publication.project.value.teamOrder this.ui.selectionComp = 'projects.versionOtherSelection' diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version.component.js b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version.component.js index 3c7fb764b2..5fac22ef84 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version.component.js +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/pipeline-version.component.js @@ -1,6 +1,7 @@ import VersionExperimentSelectionTemplate from './version-experiment-selection.template.html'; import VersionFieldReconSelectionTemplate from './version-field-recon-selection.template.html'; import VersionSimulationSelectionTemplate from './version-simulation-selection.template.html'; +import VersionHybSimSelectionTemplate from './version-hyb-sim-selection.template.html'; import VersionCitationTemplate from './version-citation.template.html'; import experimentalData from '../../../../projects/components/manage-experiments/experimental-data.json'; @@ -62,21 +63,48 @@ class PipelineVersionCtrl { this.ui.placeholder = 'Experiment'; this.matchingGroupKey = 'experiments'; this.publishedKeyNames = ['experimentsList']; - this.subEntities = ['modelconfig_set', 'sensorlist_set', 'event_set', 'report_set', 'analysis_set']; + this.subEntities = ['modelconfig_set', + 'sensorlist_set', + 'event_set', + 'report_set', + 'analysis_set']; } else if (prjType === 'simulation') { this.ui.selectionComp = 'projects.versionSimulationSelection'; this.ui.citationComp = 'projects.versionCitation'; this.ui.placeholder = 'Simulation'; this.matchingGroupKey = 'simulations'; this.publishedKeyNames = ['simulation']; - this.subEntities = ['simulation_set', 'model_set', 'input_set', 'output_set', 'analysis_set', 'report_set']; + this.subEntities = ['simulation_set', + 'model_set', + 'input_set', + 'output_set', + 'analysis_set', + 'report_set']; + } else if (prjType === 'hybrid_simulation') { + this.ui.selectionComp = 'projects.versionHybSimSelection'; + this.ui.citationComp = 'projects.versionCitation'; + this.ui.placeholder = 'HybSim'; + this.matchingGroupKey = 'hybrid_simulations'; + this.publishedKeyNames = ['hybrid_simulation']; + this.subEntities = ['hybridsimulation_set', + 'globalmodel_set', + 'coordinator_set', + 'simsubstructure_set', + 'expsubstructure_set', + 'coordinatoroutput_set', + 'simoutput_set', + 'expoutput_set', + 'analysis_set', + 'report_set']; } else if (prjType === 'field_recon') { this.ui.selectionComp = 'projects.versionFieldReconSelection'; this.ui.citationComp = 'projects.versionCitation'; this.ui.placeholder = 'Mission'; this.matchingGroupKey = 'missions'; this.publishedKeyNames = ['missions', 'reports']; - this.subEntities = ['planning_set', 'socialscience_set', 'geoscience_set']; + this.subEntities = ['planning_set', + 'socialscience_set', + 'geoscience_set']; this.primaryEnts = [].concat( this.project.mission_set || [], @@ -403,6 +431,17 @@ export const VersionSimulationSelectionComponent = { }, }; +export const VersionHybSimSelectionComponent = { + template: VersionHybSimSelectionTemplate, + controller: PipelineVersionCtrl, + controllerAs: '$ctrl', + bindings: { + resolve: '<', + close: '&', + dismiss: '&' + }, +}; + export const VersionCitationComponent = { template: VersionCitationTemplate, controller: PipelineVersionCtrl, diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html new file mode 100644 index 0000000000..bea6273b82 --- /dev/null +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html @@ -0,0 +1,86 @@ +
    + + Back + + +
    +
    +
    +

    Confirm Author Order

    + You are required to confirm the list of Authors on your Citation(s) before continuing. + Your citation(s) will be updated to match what is shown in the preview. +
    +

    + Loading... +

    +
    +
    +
    +
    + +
    +
    + {{$ctrl.ui.placeholder}} | {{ primEnt.value.title }} +
    + +
    +

    Success

    + The author order for this {{$ctrl.ui.placeholder}} has been saved. +
    +
    + Your authors need to be updated. Edit your {{$ctrl.ui.placeholder}} and select which users are authors for the {{$ctrl.ui.placeholder}}. +
    +
    +

    + Loading... +

    +
    + +
    Citation Preview
    +
    +
    + + + + ({{ $ctrl.curDate }}) “{{ primEnt.value.title }}”, in {{ $ctrl.project.value.title }}. DesignSafe-CI. https://doi.org/10.12345/ABCDEF. + +
    +
    + + + + + + + +
    +
    + + + + {{ author.name }} + + + + {{ author.lname }}, {{ author.fname }} + +
    +
    + + + Save +
    +
    +
    +
    +
    \ No newline at end of file diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html new file mode 100644 index 0000000000..610ba8dd96 --- /dev/null +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html @@ -0,0 +1,425 @@ +
    + + Back + + +
    +
    + +
    +

    Your Selection is Incomplete!

    +

    + Your selection has missing data or incomplete requirements. + Please review the following fields: +

    +
    +
    + In the {{entity.type}} {{entity.title}}, the following requirements are missing or incomplete: +
  • {{ err }}
    • +
    +
    +
    +
    +

    Version Selection

    +
      +
    • A new version of your publication will be created with the information shown below.
      • +
    • The selected Hybrid Simulations will be included the the new version.
      • +
    • You may select additional Hybrid Simulations to publish with the new version.
      • +
    • Previously published Hybrid Simulations cannot be excluded.
      • + +
    • If you need help, attend curation office hours.
      • +
    +
    +
    +

    + Loading... +

    +
    +
    + +
    + + +
    + +
    + +
    \ No newline at end of file diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html index 9248de1072..2ac669628c 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-field-recon.component.html @@ -16,7 +16,7 @@
    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html index ccc609b85f..84e9c8afa4 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-hyb-sim.component.html @@ -16,7 +16,7 @@
    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html index d62587d908..67e6e7d346 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-other.component.html @@ -16,7 +16,7 @@
    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html index 6bb30ad5e9..a2994d213d 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview-sim.component.html @@ -16,7 +16,7 @@
    diff --git a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html index 8f2d1ee23e..fcf54b012f 100644 --- a/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html +++ b/designsafe/static/scripts/data-depot/components/projects/publication-preview/publication-preview.component.html @@ -16,7 +16,7 @@

    diff --git a/designsafe/static/scripts/data-depot/index.js b/designsafe/static/scripts/data-depot/index.js index 69a52d7991..1906a51622 100644 --- a/designsafe/static/scripts/data-depot/index.js +++ b/designsafe/static/scripts/data-depot/index.js @@ -405,6 +405,23 @@ function config( }] } }) + .state('projects.amendHybSim', { + url: '/projects/{projectId}/curation/amend/hybsim', + component: 'amendHybSim', + params: { + project: null, + publication: null, + amendment: null + }, + resolve: { + projectId: ['$stateParams', 'ProjectService', ($stateParams, ProjectService) => { + ProjectService.resolveParams.projectId = $stateParams.projectId; + ProjectService.resolveParams.project = $stateParams.project; + ProjectService.resolveParams.publication = $stateParams.publication; + ProjectService.resolveParams.amendment = $stateParams.amendment; + }] + } + }) .state('projects.amendCitation', { url: '/projects/{projectId}/curation/amend/citation', component: 'amendCitation', @@ -515,6 +532,25 @@ function config( }] } }) + .state('projects.versionHybSimSelection', { + url: '/projects/{projectId}/curation/version/{filePath:any}', + component: 'versionHybSimSelection', + params: { + project: null, + publication: null, + selectedEnts: [], + selectedListings: null + }, + resolve: { + projectId: ['$stateParams', 'ProjectService', ($stateParams, ProjectService) => { + ProjectService.resolveParams.projectId = $stateParams.projectId; + ProjectService.resolveParams.project = $stateParams.project; + ProjectService.resolveParams.publication = $stateParams.publication; + ProjectService.resolveParams.selectedEnts = $stateParams.selectedEnts; + ProjectService.resolveParams.selectedListings = $stateParams.selectedListings; + }] + } + }) .state('projects.versionCitation', { url: '/projects/{projectId}/curation/citation', component: 'versionCitation', From c9b6ae260cd38e3edd5645fb45bbaf3de07f0c11 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 19 Sep 2023 09:03:37 -0500 Subject: [PATCH 11/23] Add message to registration page dealing with countries of concern (#1095) Co-authored-by: Jake Rosenberg --- .../templates/designsafe/apps/accounts/register.html | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/designsafe/apps/accounts/templates/designsafe/apps/accounts/register.html b/designsafe/apps/accounts/templates/designsafe/apps/accounts/register.html index f2c12c77ed..7b5b29e6e5 100644 --- a/designsafe/apps/accounts/templates/designsafe/apps/accounts/register.html +++ b/designsafe/apps/accounts/templates/designsafe/apps/accounts/register.html @@ -26,6 +26,12 @@

    to request an account. Once your account has been approved, you will then be able to log into DesignSafe.

    +

    + For citizens of countries designated as “countries of concern” by United States government + regulations, additional documentation in the form of a currently valid visa and passport will + be requested after the account registration form has been submitted. Citizens of these countries + are only eligible to have accounts while legally residing in the United States. +

    From 761c9e42f3ef29214d1764c0fe1f44e6edd06fc2 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 19 Sep 2023 10:44:23 -0500 Subject: [PATCH 12/23] hardcode URLs in the CMS indexer to fix deprecated page.site variable (#1096) Co-authored-by: Jake Rosenberg --- designsafe/apps/search/search_indexes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/designsafe/apps/search/search_indexes.py b/designsafe/apps/search/search_indexes.py index 70c7811441..dbc5e99647 100644 --- a/designsafe/apps/search/search_indexes.py +++ b/designsafe/apps/search/search_indexes.py @@ -79,7 +79,7 @@ def prepare(self, obj): self.prepared_data['text'] = text self.prepared_data["body"] = text self.prepared_data["slug"] = obj.slug - self.prepared_data["url"] = "https://" + obj.page.site.domain + '/' + obj.path + self.prepared_data["url"] = "https://designsafe-ci.org" + '/' + obj.path self.prepared_data["title"] = obj.title # self.prepared_data['language'] = self._language From 85ab2d9f4d7a491c7962932106b15e1b304d3217 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Mon, 2 Oct 2023 09:39:27 -0500 Subject: [PATCH 13/23] prevent entities from being double-counted if their parents are reused (#1099) Co-authored-by: Jake Rosenberg --- designsafe/libs/fedora/fedora_operations.py | 7 +++++++ designsafe/libs/fedora/fr_operations.py | 2 +- designsafe/libs/fedora/hyb_sim_operations.py | 15 ++++++++------- designsafe/libs/fedora/sim_operations.py | 6 +++--- 4 files changed, 19 insertions(+), 11 deletions(-) diff --git a/designsafe/libs/fedora/fedora_operations.py b/designsafe/libs/fedora/fedora_operations.py index ee5bf40280..874f9d6ce5 100644 --- a/designsafe/libs/fedora/fedora_operations.py +++ b/designsafe/libs/fedora/fedora_operations.py @@ -392,6 +392,13 @@ def amend_project_fedora(project_id, version=None): return res +def has_associations(child, parents): + for parent in parents: + if parent.uuid not in child.associationIds: + return False + return True + + def walk_experimental(project_id, version=None): """ Walk an experimental project and reconstruct parent/child relationships diff --git a/designsafe/libs/fedora/fr_operations.py b/designsafe/libs/fedora/fr_operations.py index 111e495775..9800bbad84 100644 --- a/designsafe/libs/fedora/fr_operations.py +++ b/designsafe/libs/fedora/fr_operations.py @@ -11,7 +11,7 @@ from requests.packages.urllib3.util.retry import Retry from designsafe.apps.data.models.elasticsearch import IndexedPublication from django.contrib.auth import get_user_model -from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest +from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest, has_associations import logging logger = logging.getLogger(__name__) diff --git a/designsafe/libs/fedora/hyb_sim_operations.py b/designsafe/libs/fedora/hyb_sim_operations.py index 3775e454d0..26c6f8704c 100644 --- a/designsafe/libs/fedora/hyb_sim_operations.py +++ b/designsafe/libs/fedora/hyb_sim_operations.py @@ -12,10 +12,11 @@ from designsafe.apps.data.models.elasticsearch import IndexedPublication from django.contrib.auth import get_user_model from designsafe.apps.api.publications.operations import _get_user_by_username -from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest +from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest, has_associations import logging logger = logging.getLogger(__name__) + def walk_hyb_sim(project_id, version=None): """ Walk an experimental project and reconstruct parent/child relationships @@ -127,7 +128,7 @@ def walk_hyb_sim(project_id, version=None): coordinator_list = filter( - lambda coordinator: global_model.uuid in coordinator.value.globalModels, + lambda coordinator: global_model.uuid in coordinator.value.globalModels and has_associations(coordinator, [global_model, hyb_sim]), getattr(doc, 'coordinators', [])) for coordinator in coordinator_list: # Do stuff with coordinator. @@ -145,7 +146,7 @@ def walk_hyb_sim(project_id, version=None): } coordinator_output_list = filter( - lambda coordinator_output: coordinator.uuid in coordinator_output.value.coordinators, + lambda coordinator_output: coordinator.uuid in coordinator_output.value.coordinators and has_associations(coordinator_output, [hyb_sim, global_model, coordinator]), getattr(doc, 'coordinator_outputs', [])) for coordinator_output in coordinator_output_list: # Do stuff with coordinator output. @@ -166,7 +167,7 @@ def walk_hyb_sim(project_id, version=None): sim_sub_list = filter( - lambda sim_sub: coordinator.uuid in sim_sub.value.coordinators, + lambda sim_sub: coordinator.uuid in sim_sub.value.coordinators and has_associations(sim_sub, [hyb_sim, global_model, coordinator]), getattr(doc, 'sim_substructures', [])) for sim_sub in sim_sub_list: # Do stuff with sim substructure. @@ -185,7 +186,7 @@ def walk_hyb_sim(project_id, version=None): } sim_out_list = filter( - lambda sim_out: sim_sub.uuid in sim_out.value.simSubstructures, + lambda sim_out: sim_sub.uuid in sim_out.value.simSubstructures and has_associations(sim_out, [hyb_sim, global_model]), getattr(doc, 'sim_outputs', [])) for sim_out in sim_out_list: # Do stuff with sim output. @@ -205,7 +206,7 @@ def walk_hyb_sim(project_id, version=None): relation_map.append(sim_sub_map) exp_sub_list = filter( - lambda exp_sub: coordinator.uuid in exp_sub.value.coordinators, + lambda exp_sub: coordinator.uuid in exp_sub.value.coordinators and has_associations(exp_sub, [hyb_sim, global_model]), getattr(doc, 'exp_substructures', [])) for exp_sub in exp_sub_list: # Do stuff with experimental substructure. @@ -224,7 +225,7 @@ def walk_hyb_sim(project_id, version=None): } exp_out_list = filter( - lambda exp_out: exp_sub.uuid in exp_out.value.expSubstructures, + lambda exp_out: exp_sub.uuid in exp_out.value.expSubstructures and has_associations(exp_out, [hyb_sim, global_model]), getattr(doc, 'exp_outputs', [])) for exp_out in exp_out_list: # Do stuff with experimental output. diff --git a/designsafe/libs/fedora/sim_operations.py b/designsafe/libs/fedora/sim_operations.py index 2900cd6e2f..1f1e663f50 100644 --- a/designsafe/libs/fedora/sim_operations.py +++ b/designsafe/libs/fedora/sim_operations.py @@ -12,7 +12,7 @@ from designsafe.apps.data.models.elasticsearch import IndexedPublication from django.contrib.auth import get_user_model from designsafe.apps.api.publications.operations import _get_user_by_username -from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest, generate_report_experimental +from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest, generate_report_experimental, has_associations import logging logger = logging.getLogger(__name__) @@ -113,7 +113,7 @@ def walk_sim(project_id, version=None): } inputs = filter( - lambda input: model.uuid in input.value.modelConfigs, + lambda input: model.uuid in input.value.modelConfigs and has_associations(input, [model, sim]), getattr(doc, 'inputs', []) ) @@ -133,7 +133,7 @@ def walk_sim(project_id, version=None): } outputs = filter( - lambda output: input.uuid in output.value.simInputs, + lambda output: input.uuid in output.value.simInputs and has_associations(output, [input, model, sim]), getattr(doc, 'outputs', []) ) From a0a3762091940f95498cb6b265c9dd418d7072d9 Mon Sep 17 00:00:00 2001 From: Van Go <35277477+van-go@users.noreply.github.com> Date: Mon, 2 Oct 2023 13:30:06 -0500 Subject: [PATCH 14/23] des/2506-changes-to-simulation-project-type (#1097) * des/2506-changes-to-simulation-project-type * Update manage-simulations.template.html --------- Co-authored-by: Jake Rosenberg --- .../pipeline-selection-sim.template.html | 7 ++++--- .../publication-preview-sim.component.html | 5 +++-- .../ng-designsafe/services/project-service.js | 14 ++++++++++---- .../manage-categories.component.html | 16 +++++++++------- .../manage-simulations.template.html | 8 ++++++++ 5 files changed, 34 insertions(+), 16 deletions(-) diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-selection/pipeline-selection-sim.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-selection/pipeline-selection-sim.template.html index c9c7f44a4f..384043fe2e 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-selection/pipeline-selection-sim.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-selection/pipeline-selection-sim.template.html @@ -88,8 +88,8 @@

    Loading...

    - -
    + +
    -
    +
    --> +
    diff --git a/designsafe/static/scripts/projects/components/manage-simulations/manage-simulations.template.html b/designsafe/static/scripts/projects/components/manage-simulations/manage-simulations.template.html index c76d82b8ca..d4910c06ce 100644 --- a/designsafe/static/scripts/projects/components/manage-simulations/manage-simulations.template.html +++ b/designsafe/static/scripts/projects/components/manage-simulations/manage-simulations.template.html @@ -7,6 +7,14 @@

    +
    + + Simulation: + + A stand-alone dataset published under a unique citation and DOI. + One or more can be published under a project and each can be published progressively. + +
    {{$ctrl.ui.error}}
    From 0ac7f0b7220f05db53cae22fde7da959945379fc Mon Sep 17 00:00:00 2001 From: Van Go <35277477+van-go@users.noreply.github.com> Date: Mon, 2 Oct 2023 13:33:11 -0500 Subject: [PATCH 15/23] des-2512-more-text-changes--mostly-hyb-sim (#1098) * des-2512-more-text-changes--mostly-hyb-sim * Update pipeline-start.template.html --------- Co-authored-by: Jake Rosenberg --- .../pipeline-amend/amend-hybrid-sim.template.html | 15 +++++++++------ .../version-experiment-selection.template.html | 2 +- .../version-field-recon-selection.template.html | 2 +- .../version-hyb-sim-citation.template.html | 3 +-- .../version-hyb-sim-selection.template.html | 2 +- .../version-simulation-selection.template.html | 2 +- 6 files changed, 14 insertions(+), 12 deletions(-) diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html index c1b6dd2015..dded7946c5 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-hybrid-sim.template.html @@ -42,12 +42,15 @@

      -
    • Please review the preview of your amended publication carefully.
      • -
    • Any acceptable changes you make from the project workspace are automatically imported to this preview.
      • -
    • This preview shows what your publication will look like once it is amended.
      • -
    • Categories may not be added or removed.
      • -
    • Files related to any categories may not be modified.
      • -
    • When you have finished proofreading your amended publication, click continue to move onto the next step.
      • +
    • Please review the amendable metadata carefully and make changes if necessary.
      • +
    • Any changes made in the project workspace are reflected in this preview.
      • +
    • Categories may not be added or removed and files related to any categories may not be modified.
      • +
    • When you have finished proofreading your amended publication, click "Continue to Authors".
      • +
    • If you need help, attend + + curation office hours + . +
    diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-experiment-selection.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-experiment-selection.template.html index 40aab54a62..de612e4e44 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-experiment-selection.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-experiment-selection.template.html @@ -26,7 +26,7 @@

    Version Selection

      -
    • A new version of your publication will be created with the information shown below.
      • +
    • A new version of your project will be created with the information shown below.
    • The selected datasets will be included the the new version.
    • You may select additional datasets to publish with the new version.
    • Previously published datasets cannot be excluded.
      • diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-field-recon-selection.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-field-recon-selection.template.html index 3e560af3fb..c2db6b15a0 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-field-recon-selection.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-field-recon-selection.template.html @@ -26,7 +26,7 @@

      Version Selection

        -
      • A new version of your publication will be created with the information shown below.
        • +
      • A new version of your project will be created with the information shown below.
      • The selected datasets will be included the the new version.
      • You may select additional datasets to publish with the new version.
      • Previously published datasets can not be excluded.
        • diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html index bea6273b82..5a23217c9e 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-citation.template.html @@ -11,8 +11,7 @@

        Confirm Author Order

        - You are required to confirm the list of Authors on your Citation(s) before continuing. - Your citation(s) will be updated to match what is shown in the preview. + Before proceeding, please review the list of authors and their order on your citation(s) and click "Save" to confirm. Your citation(s) will be updated accordingly.

        Loading... diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html index 610ba8dd96..cfcfc5b8cf 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-hyb-sim-selection.template.html @@ -26,7 +26,7 @@

        Version Selection

          -
        • A new version of your publication will be created with the information shown below.
          • +
        • A new version of your project will be created with the information shown below.
        • The selected Hybrid Simulations will be included the the new version.
        • You may select additional Hybrid Simulations to publish with the new version.
        • Previously published Hybrid Simulations cannot be excluded.
          • diff --git a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-simulation-selection.template.html b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-simulation-selection.template.html index 45f95c9ebe..198b25f87e 100644 --- a/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-simulation-selection.template.html +++ b/designsafe/static/scripts/data-depot/components/projects/pipeline-version/version-simulation-selection.template.html @@ -26,7 +26,7 @@

          Version Selection

            -
          • A new version of your publication will be created with the information shown below.
            • +
          • A new version of your project will be created with the information shown below.
          • The selected datasets will be included the the new version.
          • You may select additional datasets to publish with the new version.
          • Previously published datasets can not be excluded.
            • From 837fa77d567a43459e67c259bc56b244ebad0351 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Mon, 2 Oct 2023 13:38:19 -0500 Subject: [PATCH 16/23] Django/1to2 (#1066) * django 1to2 with working tests * Bug fixes and requirements export * re-add context processor * update packages to LTS versions * re-enable broken test * increment major version in pyproject.toml * pin django-treebeard version * specify poetry version * revert Fido to working version * use vendored djangocms-cascade plugin * move to django-cms 3.7 * Update dependencies and middleware --------- Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg --- designsafe/LoginTest.py | 2 +- designsafe/apps/accounts/forms.py | 2 +- .../apps/accounts/migrations/0001_initial.py | 2 +- .../0002_notificationpreferences.py | 2 +- designsafe/apps/accounts/models.py | 6 +- designsafe/apps/accounts/tests.py | 2 +- designsafe/apps/accounts/urls.py | 2 +- designsafe/apps/accounts/views.py | 3 +- designsafe/apps/api/datafiles/handlers.py | 2 +- designsafe/apps/api/decorators.py | 3 +- designsafe/apps/api/notifications/tests.py | 2 +- .../apps/api/notifications/views/api.py | 2 +- .../apps/api/notifications/views/webhooks.py | 2 +- designsafe/apps/api/projects/tests.py | 3 + designsafe/apps/api/projects/views.py | 2 +- designsafe/apps/api/search/tests.py | 2 +- designsafe/apps/api/tasks.py | 2 +- designsafe/apps/api/urls.py | 4 +- designsafe/apps/applications/urls.py | 2 +- designsafe/apps/applications/views.py | 2 +- designsafe/apps/auth/middleware.py | 3 +- .../apps/auth/migrations/0001_initial.py | 2 +- designsafe/apps/auth/models.py | 2 +- designsafe/apps/auth/urls.py | 2 +- designsafe/apps/auth/views.py | 2 +- .../apps/box_integration/integrations.py | 2 +- .../migrations/0001_initial.py | 2 +- .../migrations/0003_auto_20160328_2215.py | 2 +- designsafe/apps/box_integration/models.py | 2 +- .../apps/box_integration/tests/test_views.py | 2 +- designsafe/apps/box_integration/views.py | 2 +- .../cms_plugins/migrations/0001_initial.py | 2 +- designsafe/apps/dashboard/tests.py | 2 +- designsafe/apps/dashboard/urls.py | 2 +- .../apps/data/management/commands/tests.py | 1 + designsafe/apps/data/urls.py | 2 +- designsafe/apps/data/views/base.py | 2 +- designsafe/apps/djangoRT/tests.py | 2 +- designsafe/apps/djangoRT/views.py | 2 +- .../apps/dropbox_integration/integrations.py | 2 +- .../migrations/0001_initial.py | 2 +- designsafe/apps/dropbox_integration/models.py | 4 +- designsafe/apps/dropbox_integration/views.py | 2 +- designsafe/apps/geo/urls.py | 2 +- .../googledrive_integration/integrations.py | 2 +- .../migrations/0001_initial.py | 2 +- .../migrations/0002_auto_20180215_2239.py | 2 +- .../migrations/0003_auto_20230211_2158.py | 21 + .../apps/googledrive_integration/models.py | 67 +- .../apps/googledrive_integration/views.py | 2 +- .../apps/licenses/migrations/0001_initial.py | 2 +- designsafe/apps/licenses/models.py | 2 +- designsafe/apps/nco/apps.py | 2 +- designsafe/apps/notifications/urls.py | 2 +- designsafe/apps/projects/apps.py | 2 +- designsafe/apps/rapid/tests.py | 2 +- designsafe/apps/rapid/urls.py | 2 +- designsafe/apps/rapid/views.py | 2 +- designsafe/apps/search/urls.py | 2 +- designsafe/apps/token_access/middleware.py | 3 +- .../token_access/migrations/0001_initial.py | 2 +- designsafe/apps/token_access/models.py | 2 +- designsafe/apps/workspace/tasks.py | 2 +- designsafe/apps/workspace/tests.py | 2 +- designsafe/apps/workspace/urls.py | 2 +- designsafe/apps/workspace/views.py | 2 +- designsafe/conftest.py | 5 + designsafe/middleware.py | 10 +- designsafe/settings/common_settings.py | 22 +- designsafe/settings/test_settings.py | 36 +- designsafe/storage.py | 6 +- designsafe/urls.py | 40 +- poetry.lock | 674 +++++++++++------- pyproject.toml | 8 +- requirements.txt | 212 +++--- 75 files changed, 755 insertions(+), 486 deletions(-) create mode 100644 designsafe/apps/googledrive_integration/migrations/0003_auto_20230211_2158.py diff --git a/designsafe/LoginTest.py b/designsafe/LoginTest.py index 1d754efe01..05f648a313 100644 --- a/designsafe/LoginTest.py +++ b/designsafe/LoginTest.py @@ -1,7 +1,7 @@ #python manage.py test designsafe.LoginTest --settings=designsafe.settings.test_settings from django.test import TestCase, RequestFactory from django.contrib.auth import get_user_model -from django.core.urlresolvers import reverse +from django.urls import reverse import mock from designsafe.apps.auth.models import AgaveOAuthToken from designsafe.apps.auth.tasks import check_or_create_agave_home_dir diff --git a/designsafe/apps/accounts/forms.py b/designsafe/apps/accounts/forms.py index d2f81cb6ff..85feca7a7e 100644 --- a/designsafe/apps/accounts/forms.py +++ b/designsafe/apps/accounts/forms.py @@ -2,7 +2,7 @@ import logging from django import forms from django.contrib.auth import get_user_model -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext as _ from django.utils.safestring import mark_safe from django.utils.html import escape diff --git a/designsafe/apps/accounts/migrations/0001_initial.py b/designsafe/apps/accounts/migrations/0001_initial.py index 78ba51bd4c..ba2fabb336 100644 --- a/designsafe/apps/accounts/migrations/0001_initial.py +++ b/designsafe/apps/accounts/migrations/0001_initial.py @@ -18,7 +18,7 @@ class Migration(migrations.Migration): ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('ethnicity', models.CharField(max_length=255)), ('gender', models.CharField(max_length=255)), - ('user', models.OneToOneField(related_name='profile', to=settings.AUTH_USER_MODEL)), + ('user', models.OneToOneField(related_name='profile', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/accounts/migrations/0002_notificationpreferences.py b/designsafe/apps/accounts/migrations/0002_notificationpreferences.py index 1323ef6e51..34ee985908 100644 --- a/designsafe/apps/accounts/migrations/0002_notificationpreferences.py +++ b/designsafe/apps/accounts/migrations/0002_notificationpreferences.py @@ -18,7 +18,7 @@ class Migration(migrations.Migration): fields=[ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('announcements', models.BooleanField(default=True, help_text='Receive occasional announcements from DesignSafe')), - ('user', models.OneToOneField(related_name='notification_preferences', to=settings.AUTH_USER_MODEL)), + ('user', models.OneToOneField(related_name='notification_preferences', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/accounts/models.py b/designsafe/apps/accounts/models.py index edae4a6dc2..aedc88990d 100644 --- a/designsafe/apps/accounts/models.py +++ b/designsafe/apps/accounts/models.py @@ -61,7 +61,7 @@ def __str__(self): class DesignSafeProfile(models.Model): - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='profile') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='profile', on_delete=models.CASCADE) ethnicity = models.CharField(max_length=255) gender = models.CharField(max_length=255) agree_to_account_limit = models.DateTimeField(auto_now_add=True, null=True) @@ -69,7 +69,7 @@ class DesignSafeProfile(models.Model): website = models.CharField(max_length=256, default=None, null=True, blank=True) orcid_id = models.CharField(max_length=256, default=None, null=True, blank=True) nh_interests = models.ManyToManyField(DesignSafeProfileNHInterests) - nh_interests_primary = models.ForeignKey(DesignSafeProfileNHInterests, related_name='nh_interests_primary', null=True) + nh_interests_primary = models.ForeignKey(DesignSafeProfileNHInterests, related_name='nh_interests_primary', null=True, on_delete=models.CASCADE) nh_technical_domains = models.ManyToManyField(DesignSafeProfileNHTechnicalDomains) professional_level = models.CharField(max_length=256, default=None, null=True) research_activities = models.ManyToManyField(DesignSafeProfileResearchActivities) @@ -86,7 +86,7 @@ def send_mail(self, subject, body=None): class NotificationPreferences(models.Model): user = models.OneToOneField(settings.AUTH_USER_MODEL, - related_name='notification_preferences') + related_name='notification_preferences', on_delete=models.CASCADE) announcements = models.BooleanField( default=True, verbose_name=_('Announcements: to communicate EF Workshops, NHERI Newsletter, Student Opportunities, etc.')) diff --git a/designsafe/apps/accounts/tests.py b/designsafe/apps/accounts/tests.py index f529c87f81..be9084feec 100644 --- a/designsafe/apps/accounts/tests.py +++ b/designsafe/apps/accounts/tests.py @@ -1,7 +1,7 @@ from django.test import TestCase from django.contrib.auth import get_user_model, signals from django.contrib.auth.models import Permission -from django.core.urlresolvers import reverse +from django.urls import reverse from unittest import skip from mock import patch import pytest diff --git a/designsafe/apps/accounts/urls.py b/designsafe/apps/accounts/urls.py index 79ccab49ba..70e0caf3a2 100644 --- a/designsafe/apps/accounts/urls.py +++ b/designsafe/apps/accounts/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.accounts import views diff --git a/designsafe/apps/accounts/views.py b/designsafe/apps/accounts/views.py index 6da9e56064..2385c8ff01 100644 --- a/designsafe/apps/accounts/views.py +++ b/designsafe/apps/accounts/views.py @@ -3,10 +3,9 @@ from django.contrib.auth import get_user_model, logout from django.contrib.auth.decorators import login_required, permission_required from django.core.exceptions import ObjectDoesNotExist -from django.core.urlresolvers import reverse +from django.urls import reverse from django.db.models import Q from django.http import HttpResponse, HttpResponseRedirect -from django.shortcuts import render_to_response from django.utils.translation import ugettext_lazy as _ from designsafe.apps.accounts import forms, integrations from designsafe.apps.accounts.models import (NEESUser, DesignSafeProfile, diff --git a/designsafe/apps/api/datafiles/handlers.py b/designsafe/apps/api/datafiles/handlers.py index 921174df37..31a98a8c0c 100644 --- a/designsafe/apps/api/datafiles/handlers.py +++ b/designsafe/apps/api/datafiles/handlers.py @@ -7,7 +7,7 @@ from designsafe.apps.api.datafiles.operations import shared_operations from designsafe.apps.api.exceptions import ApiException from django.core.exceptions import PermissionDenied -from django.core.urlresolvers import reverse +from django.urls import reverse logger = logging.getLogger(__name__) diff --git a/designsafe/apps/api/decorators.py b/designsafe/apps/api/decorators.py index f0db5df718..8681b5b450 100644 --- a/designsafe/apps/api/decorators.py +++ b/designsafe/apps/api/decorators.py @@ -4,7 +4,6 @@ import logging from functools import wraps from base64 import b64decode -from django.utils.six import text_type from django.conf import settings from django.contrib.auth import get_user_model from django.contrib.auth import login @@ -52,7 +51,7 @@ def _get_jwt_payload(request): :rtype: str """ payload = request.META.get(settings.AGAVE_JWT_HEADER) - if payload and isinstance(payload, text_type): + if payload and isinstance(payload, str): # Header encoding (see RFC5987) payload = payload.encode('iso-8859-1') diff --git a/designsafe/apps/api/notifications/tests.py b/designsafe/apps/api/notifications/tests.py index 2a01bf638a..cf93dfc8fc 100644 --- a/designsafe/apps/api/notifications/tests.py +++ b/designsafe/apps/api/notifications/tests.py @@ -10,7 +10,7 @@ from urllib.parse import urlencode from unittest import skip from django.dispatch import receiver -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.api.notifications.models import Notification from .receivers import send_notification_ws diff --git a/designsafe/apps/api/notifications/views/api.py b/designsafe/apps/api/notifications/views/api.py index 2e96abc9ae..85546e0bf9 100644 --- a/designsafe/apps/api/notifications/views/api.py +++ b/designsafe/apps/api/notifications/views/api.py @@ -1,7 +1,7 @@ import logging from django.http.response import HttpResponseBadRequest from django.http import HttpResponse -from django.core.urlresolvers import reverse +from django.urls import reverse from django.shortcuts import render from designsafe.apps.api.notifications.models import Notification diff --git a/designsafe/apps/api/notifications/views/webhooks.py b/designsafe/apps/api/notifications/views/webhooks.py index 65fe8142d9..3dd9470757 100644 --- a/designsafe/apps/api/notifications/views/webhooks.py +++ b/designsafe/apps/api/notifications/views/webhooks.py @@ -1,7 +1,7 @@ from django.http.response import HttpResponseBadRequest from django.core.exceptions import ObjectDoesNotExist from django.contrib.auth import get_user_model -from django.core.urlresolvers import reverse +from django.urls import reverse from django.views.decorators.csrf import csrf_exempt from django.utils.decorators import method_decorator from django.shortcuts import render diff --git a/designsafe/apps/api/projects/tests.py b/designsafe/apps/api/projects/tests.py index 9895ffc946..c2c63069e7 100644 --- a/designsafe/apps/api/projects/tests.py +++ b/designsafe/apps/api/projects/tests.py @@ -1,5 +1,7 @@ from designsafe.apps.api.projects.fixtures import exp_instance_meta, exp_instance_resp, exp_entity_meta, exp_entity_json +import pytest +@pytest.mark.django_db def test_project_instance_get(client, mock_agave_client, authenticated_user): mock_agave_client.meta.getMetadata.return_value = exp_instance_meta resp = client.get('/api/projects/1052668239654088215-242ac119-0001-012/') @@ -7,6 +9,7 @@ def test_project_instance_get(client, mock_agave_client, authenticated_user): expected = exp_instance_resp assert actual == expected +@pytest.mark.django_db def test_project_meta_all(client, mock_agave_client, authenticated_user): mock_agave_client.meta.getMetadata.return_value = exp_instance_meta mock_agave_client.meta.listMetadata.return_value = exp_entity_meta diff --git a/designsafe/apps/api/projects/views.py b/designsafe/apps/api/projects/views.py index a2827eda5f..8ace83d5ec 100644 --- a/designsafe/apps/api/projects/views.py +++ b/designsafe/apps/api/projects/views.py @@ -3,7 +3,7 @@ import logging import json from celery import group, chain -from django.core.urlresolvers import reverse +from django.urls import reverse from django.conf import settings from django.http.response import HttpResponseForbidden from django.http import JsonResponse, HttpResponseBadRequest diff --git a/designsafe/apps/api/search/tests.py b/designsafe/apps/api/search/tests.py index 06a41e6697..44062c47a3 100644 --- a/designsafe/apps/api/search/tests.py +++ b/designsafe/apps/api/search/tests.py @@ -2,7 +2,7 @@ from django.test import TestCase from django.contrib.auth import get_user_model from django.conf import settings -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.api.search.views import SearchView import json diff --git a/designsafe/apps/api/tasks.py b/designsafe/apps/api/tasks.py index 7df8fa2bc1..1a30649564 100644 --- a/designsafe/apps/api/tasks.py +++ b/designsafe/apps/api/tasks.py @@ -7,7 +7,7 @@ import urllib.request, urllib.parse, urllib.error from datetime import datetime from celery import shared_task -from django.core.urlresolvers import reverse +from django.urls import reverse from django.contrib.auth import get_user_model from pytas.models import User as TASUser from django.conf import settings diff --git a/designsafe/apps/api/urls.py b/designsafe/apps/api/urls.py index 64e5a7a540..409a8ecd81 100644 --- a/designsafe/apps/api/urls.py +++ b/designsafe/apps/api/urls.py @@ -4,7 +4,7 @@ from django.http import JsonResponse urlpatterns = [ - url(r'^projects/', include('designsafe.apps.api.projects.urls', + url(r'^projects/', include(('designsafe.apps.api.projects.urls', 'designsafe.apps.api.projects'), namespace='ds_projects_api')), url(r'^datafiles/', include('designsafe.apps.api.datafiles.urls')), @@ -13,6 +13,6 @@ url(r'^logger/$', LoggerApi.as_view(), name='logger'), url(r'^notifications/', include('designsafe.apps.api.notifications.urls')), url(r'^users/', include('designsafe.apps.api.users.urls')), - url(r'^search/', include('designsafe.apps.api.search.urls', namespace="ds_search_api")), + url(r'^search/', include(('designsafe.apps.api.search.urls', 'designsafe.apps.api.search'), namespace="ds_search_api")), url(r'^licenses/', include('designsafe.apps.api.licenses.urls')) ] diff --git a/designsafe/apps/applications/urls.py b/designsafe/apps/applications/urls.py index 4e69a3616b..0d41a3d129 100644 --- a/designsafe/apps/applications/urls.py +++ b/designsafe/apps/applications/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.applications import views diff --git a/designsafe/apps/applications/views.py b/designsafe/apps/applications/views.py index fad5a2c4b0..c82237bf6b 100644 --- a/designsafe/apps/applications/views.py +++ b/designsafe/apps/applications/views.py @@ -47,7 +47,7 @@ def call_api(request, service): :param request: http request from angular service :returns: JSON response for agave call """ - if request.user.is_authenticated(): + if request.user.is_authenticated: try: token = request.user.agave_oauth agave = Agave(api_server=settings.AGAVE_TENANT_BASEURL, diff --git a/designsafe/apps/auth/middleware.py b/designsafe/apps/auth/middleware.py index 8310a70eb7..acfc8174a5 100644 --- a/designsafe/apps/auth/middleware.py +++ b/designsafe/apps/auth/middleware.py @@ -2,11 +2,12 @@ from django.core.exceptions import ObjectDoesNotExist from requests.exceptions import RequestException, HTTPError import logging +from django.utils.deprecation import MiddlewareMixin logger = logging.getLogger(__name__) -class AgaveTokenRefreshMiddleware(object): +class AgaveTokenRefreshMiddleware(MiddlewareMixin): def process_request(self, request): if request.path != '/logout/' and request.user.is_authenticated: diff --git a/designsafe/apps/auth/migrations/0001_initial.py b/designsafe/apps/auth/migrations/0001_initial.py index 505d5f075f..0742af39aa 100644 --- a/designsafe/apps/auth/migrations/0001_initial.py +++ b/designsafe/apps/auth/migrations/0001_initial.py @@ -20,7 +20,7 @@ class Migration(migrations.Migration): ('refresh_token', models.CharField(max_length=255)), ('expires_in', models.BigIntegerField()), ('created', models.BigIntegerField()), - ('user', models.OneToOneField(related_name='agave_oauth', to=settings.AUTH_USER_MODEL)), + ('user', models.OneToOneField(related_name='agave_oauth', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/auth/models.py b/designsafe/apps/auth/models.py index 3aa45b0dcd..9f57bc9fb8 100644 --- a/designsafe/apps/auth/models.py +++ b/designsafe/apps/auth/models.py @@ -18,7 +18,7 @@ AGAVE_RESOURCES = agave.load_resource(getattr(settings, 'AGAVE_TENANT_BASEURL')) class AgaveOAuthToken(models.Model): - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='agave_oauth') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='agave_oauth', on_delete=models.CASCADE) token_type = models.CharField(max_length=255) scope = models.CharField(max_length=255) access_token = models.CharField(max_length=255) diff --git a/designsafe/apps/auth/urls.py b/designsafe/apps/auth/urls.py index 9c34a2c06b..c36604c5ca 100644 --- a/designsafe/apps/auth/urls.py +++ b/designsafe/apps/auth/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.auth import views diff --git a/designsafe/apps/auth/views.py b/designsafe/apps/auth/views.py index 8785de42cc..92e0813d53 100644 --- a/designsafe/apps/auth/views.py +++ b/designsafe/apps/auth/views.py @@ -1,7 +1,7 @@ from django.conf import settings from django.contrib import messages from django.contrib.auth import authenticate, login -from django.core.urlresolvers import reverse +from django.urls import reverse from django.core.exceptions import ObjectDoesNotExist from django.http import HttpResponseRedirect, HttpResponseBadRequest from django.shortcuts import render diff --git a/designsafe/apps/box_integration/integrations.py b/designsafe/apps/box_integration/integrations.py index eae3e5dc3c..1875a3dbcd 100644 --- a/designsafe/apps/box_integration/integrations.py +++ b/designsafe/apps/box_integration/integrations.py @@ -1,4 +1,4 @@ -from django.core.urlresolvers import reverse +from django.urls import reverse def provide_integrations(): diff --git a/designsafe/apps/box_integration/migrations/0001_initial.py b/designsafe/apps/box_integration/migrations/0001_initial.py index 2dc618d2ab..841e835f19 100644 --- a/designsafe/apps/box_integration/migrations/0001_initial.py +++ b/designsafe/apps/box_integration/migrations/0001_initial.py @@ -18,7 +18,7 @@ class Migration(migrations.Migration): ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('access_token', models.CharField(max_length=255)), ('refresh_token', models.CharField(max_length=255)), - ('user', models.ForeignKey(to=settings.AUTH_USER_MODEL)), + ('user', models.ForeignKey(to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/box_integration/migrations/0003_auto_20160328_2215.py b/designsafe/apps/box_integration/migrations/0003_auto_20160328_2215.py index bb4de9771d..01f4963c6b 100644 --- a/designsafe/apps/box_integration/migrations/0003_auto_20160328_2215.py +++ b/designsafe/apps/box_integration/migrations/0003_auto_20160328_2215.py @@ -16,6 +16,6 @@ class Migration(migrations.Migration): migrations.AlterField( model_name='boxusertoken', name='user', - field=models.OneToOneField(related_name='box_user_token', to=settings.AUTH_USER_MODEL), + field=models.OneToOneField(related_name='box_user_token', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE), ), ] diff --git a/designsafe/apps/box_integration/models.py b/designsafe/apps/box_integration/models.py index e56461d18a..4b4d2360b8 100644 --- a/designsafe/apps/box_integration/models.py +++ b/designsafe/apps/box_integration/models.py @@ -8,7 +8,7 @@ class BoxUserToken(models.Model): """ Represents an OAuth Token for a Box.com user """ - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='box_user_token') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='box_user_token', on_delete=models.CASCADE) box_user_id = models.CharField(max_length=48) access_token = models.CharField(max_length=255) refresh_token = models.CharField(max_length=255) diff --git a/designsafe/apps/box_integration/tests/test_views.py b/designsafe/apps/box_integration/tests/test_views.py index 15ebaaa080..eac35a7de6 100644 --- a/designsafe/apps/box_integration/tests/test_views.py +++ b/designsafe/apps/box_integration/tests/test_views.py @@ -1,6 +1,6 @@ from django.test import TestCase from django.contrib.auth import get_user_model, signals -from django.core.urlresolvers import reverse +from django.urls import reverse from boxsdk.object.user import User from designsafe.apps.box_integration.models import BoxUserToken from designsafe.apps.auth.signals import on_user_logged_in diff --git a/designsafe/apps/box_integration/views.py b/designsafe/apps/box_integration/views.py index 0a14786878..259257bda5 100644 --- a/designsafe/apps/box_integration/views.py +++ b/designsafe/apps/box_integration/views.py @@ -3,7 +3,7 @@ from django.conf import settings from django.contrib.auth.decorators import login_required from django.contrib import messages -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import (HttpResponseRedirect, HttpResponseBadRequest) from django.shortcuts import render from designsafe.apps.box_integration.models import BoxUserToken diff --git a/designsafe/apps/cms_plugins/migrations/0001_initial.py b/designsafe/apps/cms_plugins/migrations/0001_initial.py index 8d59904f18..eee22a75d5 100644 --- a/designsafe/apps/cms_plugins/migrations/0001_initial.py +++ b/designsafe/apps/cms_plugins/migrations/0001_initial.py @@ -14,7 +14,7 @@ class Migration(migrations.Migration): migrations.CreateModel( name='ResponsiveEmbedPlugin', fields=[ - ('cmsplugin_ptr', models.OneToOneField(parent_link=True, auto_created=True, primary_key=True, serialize=False, to='cms.CMSPlugin')), + ('cmsplugin_ptr', models.OneToOneField(parent_link=True, auto_created=True, primary_key=True, serialize=False, to='cms.CMSPlugin', on_delete=models.CASCADE)), ('url', models.CharField(max_length=255)), ('aspect', models.CharField(max_length=255, choices=[(b'16by9', b'16by9'), (b'4by3', b'4by3'), (b'podcast', b'podcast')])), ], diff --git a/designsafe/apps/dashboard/tests.py b/designsafe/apps/dashboard/tests.py index 91dbf5a149..8bfab4afd1 100644 --- a/designsafe/apps/dashboard/tests.py +++ b/designsafe/apps/dashboard/tests.py @@ -5,7 +5,7 @@ from django.test import TestCase from django.contrib.auth import get_user_model, signals from django.contrib.auth.models import Permission -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.data.models.elasticsearch import IndexedFile logger = logging.getLogger(__name__) diff --git a/designsafe/apps/dashboard/urls.py b/designsafe/apps/dashboard/urls.py index 27d0521d55..e60aaf92c4 100644 --- a/designsafe/apps/dashboard/urls.py +++ b/designsafe/apps/dashboard/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.dashboard import views diff --git a/designsafe/apps/data/management/commands/tests.py b/designsafe/apps/data/management/commands/tests.py index 4b4d7cfeb2..69e37b5a05 100644 --- a/designsafe/apps/data/management/commands/tests.py +++ b/designsafe/apps/data/management/commands/tests.py @@ -23,6 +23,7 @@ def setUp(self): @patch('designsafe.apps.data.management.commands.swap_reindex.Command.handle') def test_working(self, mock_handle): + mock_handle.return_value='OK' opts = {'index': 'files'} call_command('swap_reindex', **opts) self.assertEqual(mock_handle.call_count, 1) diff --git a/designsafe/apps/data/urls.py b/designsafe/apps/data/urls.py index c9a203f6a4..c3448fa347 100644 --- a/designsafe/apps/data/urls.py +++ b/designsafe/apps/data/urls.py @@ -5,7 +5,7 @@ DataDepotPublishedView, DataDepotLegacyPublishedView ) -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ urlpatterns = [ diff --git a/designsafe/apps/data/views/base.py b/designsafe/apps/data/views/base.py index 5299c46d68..69c66e5cf9 100644 --- a/designsafe/apps/data/views/base.py +++ b/designsafe/apps/data/views/base.py @@ -5,7 +5,7 @@ from designsafe.apps.notifications.views import get_number_unread_notifications from django.conf import settings from django.core.exceptions import PermissionDenied -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import Http404, HttpResponse from django.shortcuts import resolve_url from django.utils.decorators import method_decorator diff --git a/designsafe/apps/djangoRT/tests.py b/designsafe/apps/djangoRT/tests.py index 4ad07f0cc9..000162171b 100755 --- a/designsafe/apps/djangoRT/tests.py +++ b/designsafe/apps/djangoRT/tests.py @@ -1,5 +1,5 @@ from django.test import TestCase -from django.core.urlresolvers import reverse +from django.urls import reverse from django.contrib.auth import get_user_model, signals from unittest import skip import mock diff --git a/designsafe/apps/djangoRT/views.py b/designsafe/apps/djangoRT/views.py index c419cd05ab..9ecbe785c7 100755 --- a/designsafe/apps/djangoRT/views.py +++ b/designsafe/apps/djangoRT/views.py @@ -1,7 +1,7 @@ from django.shortcuts import render from django.http import HttpResponse, HttpResponseRedirect, JsonResponse, HttpResponseBadRequest from django.core.exceptions import PermissionDenied -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.djangoRT import rtUtil, forms, rtModels from django.contrib.auth.decorators import login_required from django.contrib import messages diff --git a/designsafe/apps/dropbox_integration/integrations.py b/designsafe/apps/dropbox_integration/integrations.py index eae14b9384..4c0b2cc0d0 100644 --- a/designsafe/apps/dropbox_integration/integrations.py +++ b/designsafe/apps/dropbox_integration/integrations.py @@ -1,4 +1,4 @@ -from django.core.urlresolvers import reverse +from django.urls import reverse def provide_integrations(): diff --git a/designsafe/apps/dropbox_integration/migrations/0001_initial.py b/designsafe/apps/dropbox_integration/migrations/0001_initial.py index 71b45594e6..edccf1fc65 100644 --- a/designsafe/apps/dropbox_integration/migrations/0001_initial.py +++ b/designsafe/apps/dropbox_integration/migrations/0001_initial.py @@ -19,7 +19,7 @@ class Migration(migrations.Migration): ('dropbox_user_id', models.CharField(max_length=48)), ('access_token', models.CharField(max_length=255)), ('refresh_token', models.CharField(max_length=255)), - ('user', models.OneToOneField(related_name='dropbox_user_token', to=settings.AUTH_USER_MODEL)), + ('user', models.OneToOneField(related_name='dropbox_user_token', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/dropbox_integration/models.py b/designsafe/apps/dropbox_integration/models.py index 5d2e04c765..11dca2eb53 100644 --- a/designsafe/apps/dropbox_integration/models.py +++ b/designsafe/apps/dropbox_integration/models.py @@ -1,6 +1,6 @@ from dropbox import DropboxOAuth2Flow, Dropbox from django.conf import settings -from django.core.urlresolvers import reverse +from django.urls import reverse from django.db import models import json @@ -9,7 +9,7 @@ class DropboxUserToken(models.Model): """ Represents an OAuth Token for a dropbox.com user """ - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='dropbox_user_token') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='dropbox_user_token', on_delete=models.CASCADE) dropbox_user_id = models.CharField(max_length=48) access_token = models.CharField(max_length=255) account_id = models.CharField(max_length=255) diff --git a/designsafe/apps/dropbox_integration/views.py b/designsafe/apps/dropbox_integration/views.py index 65c516d531..403cd36db1 100644 --- a/designsafe/apps/dropbox_integration/views.py +++ b/designsafe/apps/dropbox_integration/views.py @@ -6,7 +6,7 @@ from django.contrib.auth.decorators import login_required from django.utils.decorators import method_decorator from django.contrib import messages -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import (HttpResponse, HttpResponseRedirect, HttpResponseBadRequest, Http404) from django.views.decorators.csrf import csrf_exempt diff --git a/designsafe/apps/geo/urls.py b/designsafe/apps/geo/urls.py index 051ca6c613..0a36890c52 100644 --- a/designsafe/apps/geo/urls.py +++ b/designsafe/apps/geo/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.geo import views urlpatterns = [ diff --git a/designsafe/apps/googledrive_integration/integrations.py b/designsafe/apps/googledrive_integration/integrations.py index c13b258f8a..692b6abdc9 100644 --- a/designsafe/apps/googledrive_integration/integrations.py +++ b/designsafe/apps/googledrive_integration/integrations.py @@ -1,4 +1,4 @@ -from django.core.urlresolvers import reverse +from django.urls import reverse def provide_integrations(): diff --git a/designsafe/apps/googledrive_integration/migrations/0001_initial.py b/designsafe/apps/googledrive_integration/migrations/0001_initial.py index de5175d576..a0affd84cf 100644 --- a/designsafe/apps/googledrive_integration/migrations/0001_initial.py +++ b/designsafe/apps/googledrive_integration/migrations/0001_initial.py @@ -20,7 +20,7 @@ class Migration(migrations.Migration): ('refresh_token', models.CharField(max_length=255)), ('token_uri', models.CharField(max_length=255)), ('scopes', models.CharField(max_length=255)), - ('user', models.OneToOneField(related_name='googledrive_user_token', to=settings.AUTH_USER_MODEL)), + ('user', models.OneToOneField(related_name='googledrive_user_token', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/googledrive_integration/migrations/0002_auto_20180215_2239.py b/designsafe/apps/googledrive_integration/migrations/0002_auto_20180215_2239.py index dcddeb7257..5599ea5250 100644 --- a/designsafe/apps/googledrive_integration/migrations/0002_auto_20180215_2239.py +++ b/designsafe/apps/googledrive_integration/migrations/0002_auto_20180215_2239.py @@ -5,7 +5,7 @@ from django.db import migrations from django.conf import settings from google.oauth2.credentials import Credentials -from oauth2client.contrib.django_util.models import CredentialsField +from designsafe.apps.googledrive_integration.models import CredentialsField import os import json diff --git a/designsafe/apps/googledrive_integration/migrations/0003_auto_20230211_2158.py b/designsafe/apps/googledrive_integration/migrations/0003_auto_20230211_2158.py new file mode 100644 index 0000000000..ec0d7565e8 --- /dev/null +++ b/designsafe/apps/googledrive_integration/migrations/0003_auto_20230211_2158.py @@ -0,0 +1,21 @@ +# -*- coding: utf-8 -*- +# Generated by Django 1.11.29 on 2023-02-11 21:58 +from __future__ import unicode_literals + +import designsafe.apps.googledrive_integration.models +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('googledrive_integration', '0002_auto_20180215_2239'), + ] + + operations = [ + migrations.AlterField( + model_name='googledriveusertoken', + name='credential', + field=designsafe.apps.googledrive_integration.models.CredentialsField(null=True), + ), + ] diff --git a/designsafe/apps/googledrive_integration/models.py b/designsafe/apps/googledrive_integration/models.py index 802fc71bf8..4dc48e436e 100644 --- a/designsafe/apps/googledrive_integration/models.py +++ b/designsafe/apps/googledrive_integration/models.py @@ -1,20 +1,83 @@ -from oauth2client.contrib.django_util.models import CredentialsField from google.auth.transport.requests import Request from googleapiclient import discovery +import google.oauth2.credentials from django.conf import settings from django.db import models import logging import os +import base64 +import pickle + +from django.utils import encoding +import jsonpickle + logger = logging.getLogger(__name__) CLIENT_SECRETS_FILE = os.path.join(settings.SITE_DIR, 'client_secrets.json') +class CredentialsField(models.Field): + """Django ORM field for storing OAuth2 Credentials.""" + + def __init__(self, *args, **kwargs): + if 'null' not in kwargs: + kwargs['null'] = True + super(CredentialsField, self).__init__(*args, **kwargs) + + def get_internal_type(self): + return 'BinaryField' + + def from_db_value(self, value, expression, connection): + """Overrides ``models.Field`` method. This converts the value + returned from the database to an instance of this class. + """ + return self.to_python(value) + + def to_python(self, value): + """Overrides ``models.Field`` method. This is used to convert + bytes (from serialization etc) to an instance of this class""" + if value is None: + return None + elif isinstance(value, google.oauth2.credentials.Credentials): + return value + else: + try: + return jsonpickle.decode( + base64.b64decode(encoding.smart_bytes(value)).decode()) + except ValueError: + return pickle.loads( + base64.b64decode(encoding.smart_bytes(value))) + + def get_prep_value(self, value): + """Overrides ``models.Field`` method. This is used to convert + the value from an instance of this class to bytes that can be + inserted into the database. + """ + if value is None: + return None + else: + return encoding.smart_text( + base64.b64encode(jsonpickle.encode(value).encode())) + + def value_to_string(self, obj): + """Convert the field value from the provided model to a string. + + Used during model serialization. + + Args: + obj: db.Model, model object + + Returns: + string, the serialized field value + """ + value = self.value_from_object(obj) + return self.get_prep_value(value) + class GoogleDriveUserToken(models.Model): """ Represents an OAuth Token for a Google Drive user """ - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='googledrive_user_token') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='googledrive_user_token', on_delete=models.CASCADE) credential = CredentialsField() diff --git a/designsafe/apps/googledrive_integration/views.py b/designsafe/apps/googledrive_integration/views.py index 671db41257..266b3ddd16 100644 --- a/designsafe/apps/googledrive_integration/views.py +++ b/designsafe/apps/googledrive_integration/views.py @@ -6,7 +6,7 @@ from django.contrib.auth.decorators import login_required from django.utils.decorators import method_decorator from django.contrib import messages -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import (HttpResponse, HttpResponseRedirect, HttpResponseBadRequest, Http404) from django.views.decorators.csrf import csrf_exempt diff --git a/designsafe/apps/licenses/migrations/0001_initial.py b/designsafe/apps/licenses/migrations/0001_initial.py index 7955eebc89..900887826b 100644 --- a/designsafe/apps/licenses/migrations/0001_initial.py +++ b/designsafe/apps/licenses/migrations/0001_initial.py @@ -18,7 +18,7 @@ class Migration(migrations.Migration): ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)), ('license_type', models.CharField(max_length=255, choices=[(b'MATLAB', b'Matlab')])), ('license_file_content', models.TextField(help_text=b"This should be entire contents ofthe user's MATLAB license file. Please ensure you paste the license exactly as it is in the license file.")), - ('user', models.ForeignKey(related_name='licenses', to=settings.AUTH_USER_MODEL)), + ('user', models.ForeignKey(related_name='licenses', to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], options={ 'abstract': False, diff --git a/designsafe/apps/licenses/models.py b/designsafe/apps/licenses/models.py index d0ed033c32..a9eb23099c 100644 --- a/designsafe/apps/licenses/models.py +++ b/designsafe/apps/licenses/models.py @@ -26,7 +26,7 @@ def get_license_info(): class BaseLicense(models.Model): - user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='%(class)s') + user = models.OneToOneField(settings.AUTH_USER_MODEL, related_name='%(class)s', on_delete=models.CASCADE) class Meta: abstract = True diff --git a/designsafe/apps/nco/apps.py b/designsafe/apps/nco/apps.py index 9b195213fd..8946a0ecd1 100644 --- a/designsafe/apps/nco/apps.py +++ b/designsafe/apps/nco/apps.py @@ -4,4 +4,4 @@ class ProjectsConfig(AppConfig): - name = 'nco' + name = 'designsafe.apps.nco' diff --git a/designsafe/apps/notifications/urls.py b/designsafe/apps/notifications/urls.py index 827cdf072e..f03525b224 100644 --- a/designsafe/apps/notifications/urls.py +++ b/designsafe/apps/notifications/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.notifications import views diff --git a/designsafe/apps/projects/apps.py b/designsafe/apps/projects/apps.py index 2cad6ea1f6..9f39670609 100644 --- a/designsafe/apps/projects/apps.py +++ b/designsafe/apps/projects/apps.py @@ -4,4 +4,4 @@ class ProjectsConfig(AppConfig): - name = 'projects' + name = 'designsafe.apps.projects' diff --git a/designsafe/apps/rapid/tests.py b/designsafe/apps/rapid/tests.py index 42b549b621..e64aab9c35 100644 --- a/designsafe/apps/rapid/tests.py +++ b/designsafe/apps/rapid/tests.py @@ -1,5 +1,5 @@ from django.test import TestCase -from django.core.urlresolvers import reverse +from django.urls import reverse from django.contrib.auth import get_user_model, models, signals from designsafe.apps.rapid.models import RapidNHEvent from unittest import skip diff --git a/designsafe/apps/rapid/urls.py b/designsafe/apps/rapid/urls.py index 5299ac2dd6..777407c61f 100644 --- a/designsafe/apps/rapid/urls.py +++ b/designsafe/apps/rapid/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.rapid import views urlpatterns = [ diff --git a/designsafe/apps/rapid/views.py b/designsafe/apps/rapid/views.py index 00dabb9ea0..faf5638c14 100644 --- a/designsafe/apps/rapid/views.py +++ b/designsafe/apps/rapid/views.py @@ -5,7 +5,7 @@ from datetime import datetime from PIL import Image from elasticsearch import TransportError, ConnectionTimeout -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import JsonResponse, HttpResponseRedirect, HttpResponseNotFound, HttpResponseBadRequest from django.shortcuts import render from django.contrib.auth.decorators import login_required, user_passes_test diff --git a/designsafe/apps/search/urls.py b/designsafe/apps/search/urls.py index 57b103d06d..61c22d4073 100644 --- a/designsafe/apps/search/urls.py +++ b/designsafe/apps/search/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import include, url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.search import views diff --git a/designsafe/apps/token_access/middleware.py b/designsafe/apps/token_access/middleware.py index 4441160dbe..afb738c68f 100644 --- a/designsafe/apps/token_access/middleware.py +++ b/designsafe/apps/token_access/middleware.py @@ -1,8 +1,9 @@ from django.http import HttpResponseForbidden from .models import Token +from django.utils.deprecation import MiddlewareMixin -class TokenAuthenticationMiddleware(object): +class TokenAuthenticationMiddleware(MiddlewareMixin): """ Middleware that checks the HTTP Authorization Header for Token authorization. If the Authorization header exists and the authorization type is 'Token', looks up the token diff --git a/designsafe/apps/token_access/migrations/0001_initial.py b/designsafe/apps/token_access/migrations/0001_initial.py index 66c2b93b06..c4c641ec5b 100644 --- a/designsafe/apps/token_access/migrations/0001_initial.py +++ b/designsafe/apps/token_access/migrations/0001_initial.py @@ -18,7 +18,7 @@ class Migration(migrations.Migration): ('token', models.CharField(max_length=40, serialize=False, primary_key=True)), ('nickname', models.CharField(max_length=255)), ('created', models.DateTimeField(auto_now_add=True)), - ('user', models.ForeignKey(to=settings.AUTH_USER_MODEL)), + ('user', models.ForeignKey(to=settings.AUTH_USER_MODEL, on_delete=models.CASCADE)), ], ), ] diff --git a/designsafe/apps/token_access/models.py b/designsafe/apps/token_access/models.py index 84437703a6..68534af297 100644 --- a/designsafe/apps/token_access/models.py +++ b/designsafe/apps/token_access/models.py @@ -11,7 +11,7 @@ class Token(models.Model): """ token = models.CharField(max_length=40, primary_key=True) nickname = models.CharField(max_length=255) - user = models.ForeignKey(settings.AUTH_USER_MODEL) + user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.CASCADE) created = models.DateTimeField(auto_now_add=True) def save(self, *args, **kwargs): diff --git a/designsafe/apps/workspace/tasks.py b/designsafe/apps/workspace/tasks.py index 9fbbf47b2c..29cfa9f887 100644 --- a/designsafe/apps/workspace/tasks.py +++ b/designsafe/apps/workspace/tasks.py @@ -5,7 +5,7 @@ from django.conf import settings from django.contrib.auth import get_user_model from django.core.exceptions import ObjectDoesNotExist -from django.core.urlresolvers import reverse +from django.urls import reverse from designsafe.apps.api.agave import impersonate_service_account from designsafe.apps.api.notifications.models import Notification from django.db import transaction diff --git a/designsafe/apps/workspace/tests.py b/designsafe/apps/workspace/tests.py index a558fc13ed..fd700895b8 100644 --- a/designsafe/apps/workspace/tests.py +++ b/designsafe/apps/workspace/tests.py @@ -3,7 +3,7 @@ from mock import patch from django.test import TestCase from .models.app_descriptions import AppDescription -from django.core.urlresolvers import reverse +from django.urls import reverse from django.contrib.auth import get_user_model diff --git a/designsafe/apps/workspace/urls.py b/designsafe/apps/workspace/urls.py index 2270f3dfd8..091c286fa3 100644 --- a/designsafe/apps/workspace/urls.py +++ b/designsafe/apps/workspace/urls.py @@ -1,5 +1,5 @@ from django.conf.urls import url -from django.core.urlresolvers import reverse +from django.urls import reverse from django.utils.translation import ugettext_lazy as _ from designsafe.apps.workspace import views diff --git a/designsafe/apps/workspace/views.py b/designsafe/apps/workspace/views.py index 030dfe3c30..86bf3cae4f 100644 --- a/designsafe/apps/workspace/views.py +++ b/designsafe/apps/workspace/views.py @@ -3,7 +3,7 @@ from django.conf import settings from django.contrib.auth.decorators import login_required from django.core.serializers.json import DjangoJSONEncoder -from django.core.urlresolvers import reverse +from django.urls import reverse from django.core.exceptions import ObjectDoesNotExist from django.http import HttpResponse from designsafe.apps.api.notifications.models import Notification diff --git a/designsafe/conftest.py b/designsafe/conftest.py index b103ae4884..22fbd2ec3f 100644 --- a/designsafe/conftest.py +++ b/designsafe/conftest.py @@ -14,6 +14,11 @@ def regular_user(django_user_model, django_db_reset_sequences, mock_agave_client first_name="Firstname", last_name="Lastname", email="user@user.com") + django_user_model.objects.create_user(username="username2", + password="password2", + first_name="Firstname2", + last_name="Lastname2", + email="user@user.com2") user = django_user_model.objects.get(username="username") token = AgaveOAuthToken.objects.create( user=user, diff --git a/designsafe/middleware.py b/designsafe/middleware.py index 33fdd2f136..d9deca554f 100644 --- a/designsafe/middleware.py +++ b/designsafe/middleware.py @@ -13,12 +13,14 @@ from termsandconditions.middleware import (TermsAndConditionsRedirectMiddleware, is_path_protected) from termsandconditions.models import TermsAndConditions -from django.shortcuts import redirect, reverse +from django.shortcuts import redirect +from django.urls import reverse +from django.utils.deprecation import MiddlewareMixin from designsafe.apps.notifications.models import SiteMessage logger = logging.getLogger(__name__) -class DesignsafeProfileUpdateMiddleware: +class DesignsafeProfileUpdateMiddleware(MiddlewareMixin): """ Middleware to check if a user's profile has the update_required flag set to @@ -64,14 +66,14 @@ def process_request(self, request): return None -class SiteMessageMiddleware: +class SiteMessageMiddleware(MiddlewareMixin): def process_request(self, request): for message in SiteMessage.objects.filter(display=True): if settings.SITE_ID == 1: messages.warning(request, message.message) -class RequestProfilingMiddleware(object): +class RequestProfilingMiddleware(MiddlewareMixin): """Middleware to run cProfiler on each request""" def __init__(self, get_response=None): diff --git a/designsafe/settings/common_settings.py b/designsafe/settings/common_settings.py index 825ffd826f..583048f105 100644 --- a/designsafe/settings/common_settings.py +++ b/designsafe/settings/common_settings.py @@ -14,6 +14,8 @@ # Build paths inside the project like this: os.path.join(BASE_DIR, ...) import os import json +from django.urls import reverse_lazy +from django.utils.text import format_lazy gettext = lambda s: s @@ -38,11 +40,9 @@ # Application definition INSTALLED_APPS = ( - 'djangocms_admin_style', - 'djangocms_text_ckeditor', - 'cmsplugin_cascade', - 'cmsplugin_cascade.extra_fields', + # + 'djangocms_admin_style', 'django.contrib.admin', 'django.contrib.auth', 'django.contrib.contenttypes', @@ -52,6 +52,12 @@ 'django.contrib.sites', 'django.contrib.sitemaps', 'django.contrib.staticfiles', + + 'cmsplugin_cascade', + 'cmsplugin_cascade.extra_fields', + + 'djangocms_text_ckeditor', + 'django_select2', 'cms', 'treebeard', @@ -70,8 +76,8 @@ 'bootstrap3', 'termsandconditions', 'impersonate', + 'captcha', - 'oauth2client.contrib.django_util', #websockets 'ws4redis', @@ -124,13 +130,12 @@ }, } -MIDDLEWARE_CLASSES = ( +MIDDLEWARE = ( 'designsafe.middleware.RequestProfilingMiddleware', 'django.contrib.sessions.middleware.SessionMiddleware', 'django.middleware.common.CommonMiddleware', 'django.middleware.csrf.CsrfViewMiddleware', 'django.contrib.auth.middleware.AuthenticationMiddleware', - 'django.contrib.auth.middleware.SessionAuthenticationMiddleware', 'designsafe.apps.token_access.middleware.TokenAuthenticationMiddleware', 'django.contrib.messages.middleware.MessageMiddleware', 'designsafe.apps.auth.middleware.AgaveTokenRefreshMiddleware', @@ -158,6 +163,7 @@ 'APP_DIRS': True, 'OPTIONS': { 'context_processors': [ + 'django.contrib.messages.context_processors.messages', 'django.contrib.auth.context_processors.auth', 'django.template.context_processors.debug', 'django.template.context_processors.request', @@ -311,6 +317,7 @@ 'easy_thumbnails.processors.filters', ) + CKEDITOR_SETTINGS = { 'allowedContent': True } @@ -330,6 +337,7 @@ DJANGOCMS_FORMS_TEMPLATES = ( ('djangocms_forms/form_template/default.html', 'Default'), ) +DJANGOCMS_FORMS_FORMAT_CHOICES = () DJANGOCMS_FORMS_USE_HTML5_REQUIRED = False DJANGOCMS_FORMS_WIDGET_CSS_CLASSES = { 'text': ('form-control', ), diff --git a/designsafe/settings/test_settings.py b/designsafe/settings/test_settings.py index ed9b1c109a..be29059f0d 100644 --- a/designsafe/settings/test_settings.py +++ b/designsafe/settings/test_settings.py @@ -14,6 +14,8 @@ # Build paths inside the project like this: os.path.join(BASE_DIR, ...) import os import json +from django.urls import reverse_lazy +from django.utils.text import format_lazy gettext = lambda s: s @@ -39,10 +41,7 @@ # Application definition INSTALLED_APPS = ( - 'djangocms_admin_style', - 'djangocms_text_ckeditor', - 'cmsplugin_cascade', - 'cmsplugin_cascade.extra_fields', + 'django.contrib.admin', 'django.contrib.auth', @@ -53,6 +52,11 @@ 'django.contrib.sites', 'django.contrib.sitemaps', 'django.contrib.staticfiles', + 'djangocms_admin_style', + 'djangocms_text_ckeditor', + 'django_select2', + 'cmsplugin_cascade', + 'cmsplugin_cascade.extra_fields', 'cms', 'treebeard', @@ -74,8 +78,6 @@ 'termsandconditions', 'impersonate', - 'oauth2client.contrib.django_util', - #websockets 'ws4redis', @@ -108,7 +110,7 @@ 'designsafe.apps.rapid', #haystack integration - 'haystack' + # 'haystack' ) AUTHENTICATION_BACKENDS = ('django.contrib.auth.backends.ModelBackend',) @@ -121,13 +123,12 @@ }, } -MIDDLEWARE_CLASSES = ( - 'designsafe.middleware.RequestProfilingMiddleware', +MIDDLEWARE = ( 'django.contrib.sessions.middleware.SessionMiddleware', 'django.middleware.common.CommonMiddleware', 'django.middleware.csrf.CsrfViewMiddleware', 'django.contrib.auth.middleware.AuthenticationMiddleware', - 'django.contrib.auth.middleware.SessionAuthenticationMiddleware', + 'django.contrib.sessions.middleware.SessionMiddleware', 'designsafe.apps.token_access.middleware.TokenAuthenticationMiddleware', 'django.contrib.messages.middleware.MessageMiddleware', 'designsafe.apps.auth.middleware.AgaveTokenRefreshMiddleware', @@ -260,7 +261,7 @@ ) } CMSPLUGIN_CASCADE_PLUGINS = ( - 'cmsplugin_cascade.bootstrap3', + # 'cmsplugin_cascade.bootstrap3', 'cmsplugin_cascade.link', ) CMSPLUGIN_CASCADE_ALIEN_PLUGINS = ( @@ -285,7 +286,10 @@ ) CKEDITOR_SETTINGS = { - 'allowedContent': True +'language': '{{ language }}', +'skin': 'moono-lisa', +'toolbar': 'CMS', +'stylesSet': format_lazy('default:{}', reverse_lazy('admin:cascade_texteditor_config')), } MIGRATION_MODULES = { @@ -319,6 +323,8 @@ } DJANGOCMS_FORMS_DATETIME_FORMAT = '%d-%b-%Y %H:%M' +DJANGOCMS_FORMS_FORMAT_CHOICES = () + ##### # # Bootstrap3 Settings @@ -483,8 +489,8 @@ # RECAPTCHA SETTINGS FOR LESS SPAMMO DJANGOCMS_FORMS_RECAPTCHA_PUBLIC_KEY = os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_PUBLIC_KEY') DJANGOCMS_FORMS_RECAPTCHA_SECRET_KEY = os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_SECRET_KEY') -RECAPTCHA_PUBLIC_KEY = os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_PUBLIC_KEY') -RECAPTCHA_PRIVATE_KEY= os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_SECRET_KEY') +RECAPTCHA_PUBLIC_KEY = os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_PUBLIC_KEY', '') +RECAPTCHA_PRIVATE_KEY= os.environ.get('DJANGOCMS_FORMS_RECAPTCHA_SECRET_KEY', '') NOCAPTCHA = True #FOR RAPID UPLOADS @@ -529,7 +535,7 @@ BROKER_BACKEND = 'memory' # No token refreshes during testing -MIDDLEWARE_CLASSES = [c for c in MIDDLEWARE_CLASSES if c != +MIDDLEWARE= [c for c in MIDDLEWARE if c != 'designsafe.apps.auth.middleware.AgaveTokenRefreshMiddleware'] STATIC_ROOT = os.path.join(BASE_DIR, 'static') diff --git a/designsafe/storage.py b/designsafe/storage.py index 5b633dbe30..3b3af72665 100644 --- a/designsafe/storage.py +++ b/designsafe/storage.py @@ -1,7 +1,7 @@ -from django.contrib.staticfiles.storage import CachedStaticFilesStorage, StaticFilesStorage +from django.contrib.staticfiles.storage import StaticFilesStorage from django.core.files.storage import FileSystemStorage -class CustomPipelineCachedStorage(CachedStaticFilesStorage): +class CustomPipelineCachedStorage(StaticFilesStorage): def url(self, name, force=False): """ Return the non-hashed URL when detecting cms paths in order to work @@ -10,4 +10,4 @@ def url(self, name, force=False): if name.startswith('cms/'): return FileSystemStorage.url(self, name) - return super(CustomPipelineCachedStorage, self).url(name, force) + return super(CustomPipelineCachedStorage, self).url(name) diff --git a/designsafe/urls.py b/designsafe/urls.py index 11c22052c3..47fdba6768 100644 --- a/designsafe/urls.py +++ b/designsafe/urls.py @@ -27,10 +27,10 @@ from django.conf.urls.static import static from django.contrib import admin from django.views.generic import RedirectView, TemplateView -from django.core.urlresolvers import reverse +from django.urls import reverse from django.http import HttpResponse, HttpResponseRedirect from designsafe.apps.auth.views import login_options as des_login_options -from django.contrib.auth.views import logout as des_logout +from django.contrib.auth.views import LogoutView as des_logout from designsafe.views import project_version as des_version, redirect_old_nees # sitemap - classes must be imported and added to sitemap dictionary @@ -49,7 +49,7 @@ urlpatterns = [ # admin - url(r'^admin/', include(admin.site.urls)), + url(r'^admin/', admin.site.urls), url(r'^admin/impersonate/', include('impersonate.urls')), # sitemap @@ -62,37 +62,37 @@ url(r'{}.html$'.format(settings.RAMP_VERIFICATION_ID), TemplateView.as_view(template_name='ramp_verification.html')), # api urls, just for the samples. - url(r'^applications/', include('designsafe.apps.applications.urls', + url(r'^applications/', include(('designsafe.apps.applications.urls', 'desigsnafe.apps.applications'), namespace='designsafe_applications')), - url(r'^data/', include('designsafe.apps.data.urls', namespace='designsafe_data')), - url(r'^rw/workspace/', include('designsafe.apps.workspace.urls', + url(r'^data/', include(('designsafe.apps.data.urls', 'designsafe.apps.data'), namespace='designsafe_data')), + url(r'^rw/workspace/', include(('designsafe.apps.workspace.urls', 'designsafe.apps.workspace'), namespace='designsafe_workspace')), - url(r'^notifications/', include('designsafe.apps.notifications.urls', + url(r'^notifications/', include(('designsafe.apps.notifications.urls', 'designsafe.apps.notifications'), namespace='designsafe_notifications')), - url(r'^search/', include('designsafe.apps.search.urls', + url(r'^search/', include(('designsafe.apps.search.urls', 'designsafe.apps.search'), namespace='designsafe_search')), - url(r'^geo/', include('designsafe.apps.geo.urls', + url(r'^geo/', include(('designsafe.apps.geo.urls', 'designsafe.apps.geo'), namespace='designsafe_geo')), - url(r'^recon-portal/', include('designsafe.apps.rapid.urls', + url(r'^recon-portal/', include(('designsafe.apps.rapid.urls', 'designsafe.apps.rapid'), namespace='designsafe_rapid')), - url(r'^nco/api/', include('designsafe.apps.nco.api_urls', namespace='nco_api')), + url(r'^nco/api/', include(('designsafe.apps.nco.api_urls', 'designsafe.apps.nco'), namespace='nco_api')), - url(r'^nco/', include('designsafe.apps.nco.urls', + url(r'^nco/', include(('designsafe.apps.nco.urls', 'designsafe.apps.nco'), namespace='nco')), - url(r'^api/', include('designsafe.apps.api.urls', namespace='designsafe_api')), + url(r'^api/', include(('designsafe.apps.api.urls', 'designsafe.apps.api'), namespace='designsafe_api')), # auth - url(r'^account/', include('designsafe.apps.accounts.urls', + url(r'^account/', include(('designsafe.apps.accounts.urls', 'designsafe.apps.accounts'), namespace='designsafe_accounts')), url(r'^register/$', RedirectView.as_view( pattern_name='designsafe_accounts:register', permanent=True), name='register'), # dashboard - url(r'^dashboard/', include('designsafe.apps.dashboard.urls', + url(r'^dashboard/', include(('designsafe.apps.dashboard.urls', 'designsafe.apps.dashboard'), namespace='designsafe_dashboard')), # need a fancier redirect here to pass the code param along @@ -108,29 +108,29 @@ )), # box - url(r'^account/applications/box/', include('designsafe.apps.box_integration.urls', + url(r'^account/applications/box/', include(('designsafe.apps.box_integration.urls', 'designsafe.apps.box_integration'), namespace='box_integration')), # dropbox - url(r'^account/applications/dropbox/', include('designsafe.apps.dropbox_integration.urls', + url(r'^account/applications/dropbox/', include(('designsafe.apps.dropbox_integration.urls', 'designsafe.apps.dropbox_integration'), namespace='dropbox_integration')), # googledrive - url(r'^account/applications/googledrive/', include('designsafe.apps.googledrive_integration.urls', + url(r'^account/applications/googledrive/', include(('designsafe.apps.googledrive_integration.urls', 'designsafe.apps.googledrive_integration'), namespace='googledrive_integration')), # google site verification url(r'{}.html$'.format(settings.GOOGLE_SITE_VERIFICATION_ID), TemplateView.as_view(template_name='google_verification.html')), # auth - url(r'^auth/', include('designsafe.apps.auth.urls', namespace='designsafe_auth')), + url(r'^auth/', include(('designsafe.apps.auth.urls', 'designsafe.apps.auth'), namespace='designsafe_auth')), url(r'^login/$', des_login_options, name='login'), url(r'^logout/$', des_logout, {'next_page': '/auth/logged-out/'}, name='logout'), # help - url(r'^help/', include('designsafe.apps.djangoRT.urls', namespace='djangoRT')), + url(r'^help/', include(('designsafe.apps.djangoRT.urls', 'designsafe.apps.djangoRT'), namespace='djangoRT')), # webhooks url(r'^webhooks/', include('designsafe.webhooks')), diff --git a/poetry.lock b/poetry.lock index e44224bf8f..54ce95234a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -91,14 +91,14 @@ tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"] [[package]] name = "astroid" -version = "2.15.5" +version = "2.15.6" description = "An abstract syntax tree for Python with inference support." category = "main" optional = false python-versions = ">=3.7.2" files = [ - {file = "astroid-2.15.5-py3-none-any.whl", hash = "sha256:078e5212f9885fa85fbb0cf0101978a336190aadea6e13305409d099f71b2324"}, - {file = "astroid-2.15.5.tar.gz", hash = "sha256:1039262575027b441137ab4a62a793a9b43defb42c32d5670f38686207cd780f"}, + {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"}, + {file = "astroid-2.15.6.tar.gz", hash = "sha256:903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd"}, ] [package.dependencies] @@ -112,14 +112,14 @@ wrapt = [ [[package]] name = "async-timeout" -version = "4.0.2" +version = "4.0.3" description = "Timeout context manager for asyncio programs" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"}, - {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"}, + {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, + {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"}, ] [package.dependencies] @@ -335,14 +335,14 @@ zstd = ["zstandard"] [[package]] name = "certifi" -version = "2023.5.7" +version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"}, - {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"}, + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, ] [[package]] @@ -424,99 +424,99 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.2.0" description = "The Real First Universal Charset Detector. 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-version = "5.2.12" +version = "6.0" description = "" authors = ["DesignSafe-CI "] [tool.poetry.dependencies] python = "^3.7.12" agavepy = "1.0.0a12" -Django = "^1.11" +Django = "^2.2.28" cryptography = "^2.3.1" django-cms = "3.7.4" importlib-resources = "^5.4.0" @@ -39,12 +39,12 @@ django-recaptcha2 = "1.4.1" djangocms-snippet = "^2.3.0" django-bootstrap3 = "^11.1.0" djangocms-text-ckeditor = "^3.5.0" -djangocms-cascade = "^0.16.3" +djangocms-cascade = { git = "https://github.com/DesignSafe-CI/djangocms-cascade", rev = "04d52dca46312b24ded3aa1d4cf3955a88ebc147" } djangocms-style = "^2.3.0" djangocms-video = "^2.3.0" djangocms-picture = "^2.4.0" djangocms-file = "^2.4.0" -djangocms-forms = "^0.2.5" +djangocms-forms-maintained = { git = "https://github.com/avryhof/djangocms-forms", rev = "d8a69efd2f447ee2f940c7b6f5b8b088c9cb79ed" } djangocms-googlemap = "^1.4.0" oauth2client = "^4.1.2" mysqlclient = "^1.4.6" diff --git a/requirements.txt b/requirements.txt index 5fc434c45e..fea69f2701 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,158 +1,168 @@ agavepy==1.0.0a12 -amqp==5.0.7; python_version >= "3.6" -appnope==0.1.2; sys_platform == "darwin" and python_version >= "3.4" -arrow==1.2.2; python_version >= "3.6" -astroid==2.9.0; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.2" -atomicwrites==1.4.0; python_version >= "3.5" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") or sys_platform == "win32" and python_version >= "3.5" and python_full_version >= "3.4.0" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") +amqp==5.1.1; python_version >= "3.7" +appnope==0.1.3; sys_platform == "darwin" and python_version >= "3.4" +arrow==1.2.3; python_version >= "3.6" +asgiref==3.6.0; python_version >= "3.7" +astroid==2.14.2; python_full_version >= "3.7.2" +async-timeout==4.0.2; python_version >= "3.7" +atomicwrites==1.4.1; python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5") or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.4.0" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5") attrdict==2.0.1 -attrs==21.2.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5" +attrs==22.2.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" backcall==0.2.0; python_version >= "3.4" -billiard==3.6.4.0; python_version >= "3.6" +billiard==3.6.4.0; python_version >= "3.7" black==21.12b0; python_full_version >= "3.6.2" boxsdk==2.14.0 -cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6" -cachetools==4.2.4; python_version >= "3.5" and python_version < "4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6") -celery==5.1.2; python_version >= "3.6" -certifi==2021.10.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" -cffi==1.15.0; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5") or platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5") and python_full_version >= "3.5.0" -charset-normalizer==2.0.9; python_full_version >= "3.6.0" and python_version >= "3" -click-didyoumean==0.3.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.6" -click-plugins==1.1.1; python_version >= "3.6" -click-repl==0.2.0; python_version >= "3.6" -click==7.1.2; python_full_version >= "3.6.2" and python_version >= "3.6" and python_full_version < "4.0.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") -cloudpickle==2.0.0; python_version >= "3.6" -colorama==0.4.4; sys_platform == "win32" and python_version >= "3.5" and python_full_version >= "3.6.2" and (python_version >= "3.4" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.4" and python_full_version >= "3.5.0") and (python_version >= "3.5" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") or sys_platform == "win32" and python_version >= "3.5" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and python_full_version >= "3.5.0") -coverage==6.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6" +cached-property==1.5.2; python_version < "3.8" and python_version >= "3.7" +cachetools==5.3.0; python_version >= "3.7" and python_version < "4.0" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7") +celery==5.2.7; python_version >= "3.7" +certifi==2022.12.7; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.7" +cffi==1.15.1; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5") or platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5") and python_full_version >= "3.5.0" +charset-normalizer==3.0.1; python_version >= "3.7" and python_version < "4" +click-didyoumean==0.3.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.7" +click-plugins==1.1.1; python_version >= "3.7" +click-repl==0.2.0; python_version >= "3.7" +click==8.1.3; python_version >= "3.7" and python_full_version >= "3.6.2" and python_full_version < "4.0.0" +cloudpickle==2.2.1; python_version >= "3.6" +colorama==0.4.6; sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.7.2" and platform_system == "Windows" and (python_version >= "3.4" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.4" and python_full_version >= "3.7.0") and (python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5") or sys_platform == "win32" and python_version >= "3.7" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5") and python_full_version >= "3.7.0") +coverage==7.1.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" cryptography==2.9.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") curlify==2.2.1 -dataclasses==0.8; python_version >= "3.6" and python_version < "3.7" and python_full_version >= "3.6.2" -decorator==5.1.0; python_version >= "3.5" -deprecated==1.2.13; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +decorator==5.1.1; python_version >= "3.5" +dill==0.3.6 django-appconf==1.0.5; python_version >= "3.6" django-bootstrap3==11.1.0 -django-classy-tags==1.0.0 -django-cms==3.4.7 +django-classy-tags==3.0.1; python_version >= "3.7" +django-cms==3.8.0 +django-entangled==0.5.3 django-filer==1.7.1 django-formtools==2.2 django-haystack==2.8.1 django-impersonate==1.5.1 django-ipware==1.2.0 -django-js-asset==1.2.2; python_version >= "3.6" -django-mptt==0.13.4; python_version >= "3.6" +django-js-asset==2.0.0; python_version >= "3.6" +django-mptt==0.14.0; python_version >= "3.6" django-polymorphic==2.1.2 django-recaptcha2==1.4.1 +django-recaptcha==3.0.0 django-sekizai==1.1.0 +django-select2==6.3.1 django-termsandconditions==1.2.15 -django-treebeard==4.3.1 +django-treebeard==4.5.1; python_version >= "3.6" django-websocket-redis==0.6.0 -django==1.11.29 -djangocms-admin-style==2.0.2 -djangocms-attributes-field==1.2.0 -djangocms-cascade==0.16.3 +django==2.2.28; python_version >= "3.5" +djangocms-admin-style==3.2.3; python_version >= "3.7" +djangocms-attributes-field==2.0.0 +djangocms-cascade==1.3.7 djangocms-file==2.4.0 -djangocms-forms==0.2.5 +djangocms-forms-maintained @ git+https://github.com/avryhof/djangocms-forms@d8a69efd2f447ee2f940c7b6f5b8b088c9cb79ed djangocms-googlemap==1.4.0 djangocms-picture==2.4.0 djangocms-snippet==2.3.0 djangocms-style==2.3.0 -djangocms-text-ckeditor==3.10.0 +djangocms-text-ckeditor==4.0.0 djangocms-video==2.3.0 dropbox==10.6.0 -easy-thumbnails==2.7.2; python_version >= "3.5" +easy-thumbnails==2.8.5; python_version >= "3.6" elasticsearch-dsl==7.4.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") -elasticsearch==7.16.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4") +elasticsearch==7.17.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4") +et-xmlfile==1.1.0; python_version >= "3.7" exifread==2.3.2 -future==0.18.2; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" -gevent==21.12.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" -google-api-core==2.3.0; python_version >= "3.6" -google-api-python-client==2.33.0; python_version >= "3.6" +future==0.18.3; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" +gevent==22.10.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" +google-api-core==2.11.0; python_version >= "3.7" +google-api-python-client==2.77.0; python_version >= "3.7" google-auth-httplib2==0.1.0 google-auth-oauthlib==0.4.6; python_version >= "3.6" -google-auth==2.3.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" -googleapis-common-protos==1.54.0; python_version >= "3.6" -greenlet==1.1.2; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" or python_version > "3.5" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" or python_version > "3.5" and platform_python_implementation == "CPython" and python_full_version >= "3.5.0" +google-auth==2.16.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7" +googleapis-common-protos==1.58.0; python_version >= "3.7" +greenlet==2.0.2; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" or python_version > "3.5" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" or python_version > "3.5" and platform_python_implementation == "CPython" and python_full_version >= "3.5.0" hashids==1.3.1; python_version >= "2.7" html5lib==1.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" -httplib2==0.20.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" -idna==3.3; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.5" -importlib-metadata==4.8.2; python_version < "3.8" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") -importlib-resources==5.4.0; python_version >= "3.6" +httplib2==0.21.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7" +idna==3.4; python_version >= "3.7" and python_version < "4" +importlib-metadata==2.1.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +importlib-resources==5.10.2; python_version >= "3.7" ipdb==0.12.3; python_version >= "2.7" -ipython-genutils==0.2.0; python_version >= "3.3" ipython==6.5.0; python_version >= "3.3" -isort==5.10.1; python_full_version >= "3.6.2" and python_version < "4.0" -jedi==0.18.1; python_version >= "3.6" -jinja2==3.0.3; python_version >= "3.6" -jsonfield==2.1.1 +isort==5.11.5; python_full_version >= "3.7.2" +jedi==0.18.2; python_version >= "3.6" +jinja2==3.1.2; python_version >= "3.7" +jsonfield==3.1.0; python_version >= "3.6" jsonpickle==0.9.6 -kombu==5.1.0; python_version >= "3.6" -lazy-object-proxy==1.7.0; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.2" -markupsafe==2.0.1; python_version >= "3.6" -mccabe==0.6.1; python_full_version >= "3.6.2" +kombu==5.2.4; python_version >= "3.7" +lazy-object-proxy==1.9.0; python_version >= "3.7" and python_full_version >= "3.7.2" +markupsafe==2.1.2; python_version >= "3.7" +mccabe==0.7.0; python_version >= "3.6" and python_full_version >= "3.7.2" mock==4.0.3; python_version >= "3.6" -more-itertools==8.12.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" -mypy-extensions==0.4.3; python_full_version >= "3.6.2" +more-itertools==9.0.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" +mypy-extensions==1.0.0; python_version >= "3.5" and python_full_version >= "3.6.2" mysqlclient==1.4.6 oauth2client==4.1.3 -oauthlib==3.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" -packaging==21.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +oauthlib==3.2.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +olefile==0.46; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" +openpyxl==3.1.1; python_version >= "3.7" +opf-fido==1.6.1 +packaging==23.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" parso==0.8.3; python_version >= "3.6" -pathspec==0.9.0; python_full_version >= "3.6.2" +pathspec==0.11.0; python_version >= "3.7" and python_full_version >= "3.6.2" petname==2.6 pexpect==4.8.0; sys_platform != "win32" and python_version >= "3.4" pickleshare==0.7.5; python_version >= "3.4" -pillow==8.4.0; python_version >= "3.6" -platformdirs==2.4.0; python_version >= "3.6" and python_full_version >= "3.6.2" -pluggy==0.13.1; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" +pillow==9.4.0; python_version >= "3.7" +platformdirs==3.0.0; python_version >= "3.7" and python_full_version >= "3.7.2" +pluggy==0.13.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" ply==3.11 -prompt-toolkit==1.0.18; python_version >= "3.6" -protobuf==3.19.1; python_version >= "3.6" +prompt-toolkit==1.0.18; python_version >= "3.7" +protobuf==4.21.12; python_version >= "3.7" ptyprocess==0.7.0; sys_platform != "win32" and python_version >= "3.3" -py==1.11.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5" -pyasn1-modules==0.2.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" -pyasn1==0.4.8; python_version >= "3.6" and python_version < "4" +py==1.11.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" +pyasn1-modules==0.2.8; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7" +pyasn1==0.4.8; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7") or python_full_version >= "3.6.0" and python_version >= "3.7" and python_version < "4" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7") pycparser==2.21; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" -pygments==2.10.0; python_version >= "3.5" +pygments==2.14.0; python_version >= "3.6" pyjwt==1.7.1 -pylint==2.12.2; python_full_version >= "3.6.2" -pymongo==3.12.3 -pyparsing==3.0.6; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pylint==2.16.2; python_full_version >= "3.7.2" +pymongo==3.13.0 +pyparsing==3.0.9; python_full_version >= "3.6.8" and python_version >= "3.7" pytest-asyncio==0.14.0; python_version >= "3.5" pytest-cov==2.12.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") pytest-django==3.10.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") -pytest-mock==3.6.1; python_version >= "3.6" +pytest-mock==3.10.0; python_version >= "3.7" pytest==5.4.3; python_version >= "3.5" python-dateutil==2.8.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" -python-dotenv==0.19.2; python_version >= "3.5" -python-magic==0.4.24; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +python-dotenv==0.21.1; python_version >= "3.7" +python-magic==0.4.27; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") python-memcached==1.59 -pytz==2021.3; python_version >= "3.6" -redis==4.0.2; python_version >= "3.6" -requests-mock==1.9.3 -requests-oauthlib==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" -requests-toolbelt==0.9.1 -requests==2.26.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" -rsa==4.8; python_version >= "3.6" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6") +pytz==2022.7.1; python_version >= "3.7" +pyyaml==6.0; python_version >= "3.7" +redis==4.5.1; python_version >= "3.7" +requests-mock==1.10.0 +requests-oauthlib==1.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +requests-toolbelt==0.10.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" +requests==2.28.2; python_version >= "3.7" and python_version < "4" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") +rsa==4.9; python_version >= "3.6" and python_version < "4" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7") rt==1.0.13 simplegeneric==0.8.1; python_version >= "3.4" -six==1.16.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" -stone==3.2.1 -tablib==3.1.0; python_version >= "3.6" -toml==0.10.2; python_full_version >= "3.6.2" -tomli==1.2.3; python_version >= "3.6" and python_full_version >= "3.6.2" -traitlets==4.3.3; python_version >= "3.4" -typed-ast==1.5.1; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.6" -typing-extensions==4.0.1 +six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7" +sqlparse==0.4.3; python_version >= "3.6" +stone==3.3.1 +tablib==3.3.0; python_version >= "3.7" +toml==0.10.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +tomli==1.2.3; python_version >= "3.6" and python_full_version >= "3.7.2" and python_version < "3.11" +tomlkit==0.11.6; python_version >= "3.6" and python_full_version >= "3.7.2" +traitlets==5.9.0; python_version >= "3.7" +typed-ast==1.5.4; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.7.2" and python_version >= "3.6" +typing-extensions==4.4.0 unidecode==1.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" -uritemplate==4.1.1; python_version >= "3.6" -urllib3==1.26.7; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" -uwsgi==2.0.20 +uritemplate==4.1.1; python_version >= "3.7" +urllib3==1.26.14; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7" +uwsgi==2.0.21 uwsgitop==0.11 -vine==5.0.0; python_version >= "3.6" -wcwidth==0.2.5; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" +vine==5.0.0; python_version >= "3.7" +wcwidth==0.2.6; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" -websocket-client==1.2.3; python_version >= "3.6" -wrapt==1.13.3; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.2" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") -zipp==3.6.0; python_version < "3.8" and python_version >= "3.6" -zope.event==4.5.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" -zope.interface==5.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version > "3.5" +websocket-client==1.5.1; python_version >= "3.7" +wrapt==1.14.1 +zipp==3.13.0; python_version < "3.8" and python_version >= "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_version < "3.8" and python_version >= "3.7" and python_full_version >= "3.5.0") and python_full_version >= "3.6.2" +zope.event==4.6; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" +zope.interface==5.5.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_version > "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version > "3.5" From 258622ba18232531fbf6d370e055a9d106f41655 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Tue, 3 Oct 2023 10:42:55 -0500 Subject: [PATCH 17/23] Pass backend explicitly during JWT auth --- designsafe/apps/api/decorators.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/designsafe/apps/api/decorators.py b/designsafe/apps/api/decorators.py index 8681b5b450..f931f421e0 100644 --- a/designsafe/apps/api/decorators.py +++ b/designsafe/apps/api/decorators.py @@ -103,8 +103,7 @@ def decorated_function(request, *args, **kwargs): user = None if user is not None: - user.backend = 'django.contrib.auth.backends.ModelBackend', - login(request, user) + login(request, user, backend="django.contrib.auth.backends.ModelBackend") return func(request, *args, **kwargs) From 9daf83a94f4380480d7b0436076e642ca99551e9 Mon Sep 17 00:00:00 2001 From: Wesley B <62723358+wesleyboar@users.noreply.github.com> Date: Thu, 5 Oct 2023 09:58:33 -0500 Subject: [PATCH 18/23] =?UTF-8?q?fix:=20DES-2598=20text=20editor=20too=20s?= =?UTF-8?q?hort=20(=E2=9A=A0=EF=B8=8F=20untested)=20(#1102)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix: DES-2598 text editor too short — ⚠️ untested 1. stole code from https://github.com/TACC/Core-CMS/pull/573/files#diff-b613bf1b786994b3d51a81e982cf9106f4a09f8adcc65fd9c14f4f8d54bdfa72R6-R8 2. applied code like https://github.com/TACC/Core-CMS/blob/v4.0.0/taccsite_cms/static/djangocms_text_ckeditor/ckeditor/contents.css * fix import path --------- Co-authored-by: Jake Rosenberg --- .../css/cms.ckeditor.css | 5 + .../css/cms.ckeditor.original.css | 109 ++++++++++++++++++ 2 files changed, 114 insertions(+) create mode 100644 designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.css create mode 100644 designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.original.css diff --git a/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.css b/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.css new file mode 100644 index 0000000000..bcea5033dd --- /dev/null +++ b/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.css @@ -0,0 +1,5 @@ +@import url("./cms.ckeditor.original.css"); + +/* To stretch source editor textarea height */ +/* https://github.com/django-cms/djangocms-text-ckeditor/pull/590 */ +textarea.cke_source { max-height: inherit; } diff --git a/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.original.css b/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.original.css new file mode 100644 index 0000000000..59fac00860 --- /dev/null +++ b/designsafe/static/djangocms_text_ckeditor/css/cms.ckeditor.original.css @@ -0,0 +1,109 @@ +/*! https://raw.githubusercontent.com/django-cms/djangocms-text-ckeditor/3.10.0/djangocms_text_ckeditor/static/djangocms_text_ckeditor/css/cms.ckeditor.css */ + +@charset "utf-8"; +/* everything has to be !important because of the way css is loaded */ + +/* float left with the label */ +.cke_chrome { + float: left !important; + width: 100% !important; +} + +/* special case when inside a text plugin */ +.djangocms_text_ckeditor-text .form-row label { + display: none !important; +} +.djangocms_text_ckeditor-text .cke_chrome { + float: none !important; +} + +/* ensure dialog has relative positioning for absolute positioned content */ +.cms-ckeditor-dialog .cke_dialog { + position: fixed !important; +} +.cke_dialog_contents { + user-select: none !important; +} +.cke_dialog_contents_body { + position: relative !important; +} + +/* show cmsplugin label */ +.cke_button__cmsplugins .cke_button_label { + display: inline !important; + padding-right: 5px !important; + padding-left: 5px !important; +} + +/* make dropdow larger */ +.cke_combopanel, +.cke_panel { + min-width: 200px !important; +} + + +/* add / edit plugin modal */ +.cke_dialog_body { + border: 1px solid #d1d1d1 !important; +} +.cms-ckeditor-dialog .cke_dialog_contents_body { + padding: 3px 0 !important; +} +.cms-ckeditor-dialog .cke_dialog_page_contents { + width: 100% !important; + height: 100% !important; +} +.cms-ckeditor-dialog .cke_dialog_page_contents table { + display: block !important; + position: absolute !important; + top: 0 !important; + left: 0 !important; + width: 100% !important; + height: 100% !important; +} +.cms-ckeditor-dialog .cke_dialog_page_contents table tbody, +.cms-ckeditor-dialog .cke_dialog_page_contents table tr, +.cms-ckeditor-dialog .cke_dialog_page_contents table td { + display: block !important; + height: 100% !important; +} +.cms-ckeditor-dialog .cke_dialog_page_contents table .cke_dialog_ui_vbox_child { + display: block !important; + overflow-y: auto !important; + height: 100% !important; + padding: 0 !important; + + -webkit-overflow-scrolling: touch !important; +} +.cms-ckeditor-dialog .cke_dialog_page_contents table .cke_dialog_ui_vbox_child iframe { + display: block !important; + position: static !important; + width: 100% !important; + height: 100% !important; +} + +/* scrollable dropdowns on touch */ +.cke_panel { + overflow-y: auto !important; + height: auto !important; + max-height: 300px !important; + + -webkit-overflow-scrolling: touch !important; +} +.cke_panel .cke_panel_frame { + display: block !important; + position: static !important; + overflow: hidden !important; + width: 100% !important; + height: 100% !important; + min-height: 100% !important; +} + +/* cms-resizer */ +.cms-ckeditor-resizer { + overflow: auto !important; + font-size: 12px !important; + width: auto !important; + height: auto !important; + border: none !important; +} From 665bb45c2eb93a0552400e61f8f5d696e7c3d425 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Thu, 5 Oct 2023 09:58:46 -0500 Subject: [PATCH 19/23] use service client instead of envision user for public listings (#1100) Co-authored-by: Jake Rosenberg --- designsafe/apps/api/datafiles/views.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/designsafe/apps/api/datafiles/views.py b/designsafe/apps/api/datafiles/views.py index 9326896932..2ce9139292 100644 --- a/designsafe/apps/api/datafiles/views.py +++ b/designsafe/apps/api/datafiles/views.py @@ -8,6 +8,7 @@ from designsafe.apps.api.datafiles.notifications import notify from designsafe.apps.api.datafiles.models import DataFilesSurveyResult, DataFilesSurveyCounter from designsafe.apps.api.views import BaseApiView +from designsafe.apps.api.agave import service_account from dropbox.exceptions import AuthError as DropboxAuthError from google.auth.exceptions import GoogleAuthError from requests.exceptions import HTTPError @@ -56,7 +57,7 @@ def get(self, request, api, operation=None, scheme='private', system=None, path= except AttributeError: raise resource_unconnected_handler(api) elif api == 'agave': - client = get_user_model().objects.get(username='envision').agave_oauth.client + client = service_account() else: return JsonResponse({'message': 'Please log in to access this feature.'}, status=403) From b85ed8da9ff267ab82f59eacd0f10f0d14b1c5e5 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Thu, 5 Oct 2023 11:32:15 -0500 Subject: [PATCH 20/23] Bump django-cms to 3.8 and fix admin UI (#1101) * Bump django-cms to 3.8 and fix admin UI * Fix form export and admin login page --------- Co-authored-by: Jake Rosenberg Co-authored-by: Jake Rosenberg --- designsafe/settings/common_settings.py | 8 +++++++- designsafe/urls.py | 2 ++ poetry.lock | 23 +++++++++++------------ pyproject.toml | 3 ++- 4 files changed, 22 insertions(+), 14 deletions(-) diff --git a/designsafe/settings/common_settings.py b/designsafe/settings/common_settings.py index 583048f105..4d293e61f1 100644 --- a/designsafe/settings/common_settings.py +++ b/designsafe/settings/common_settings.py @@ -16,6 +16,7 @@ import json from django.urls import reverse_lazy from django.utils.text import format_lazy +from django.utils.translation import gettext_lazy as _ gettext = lambda s: s @@ -337,7 +338,12 @@ DJANGOCMS_FORMS_TEMPLATES = ( ('djangocms_forms/form_template/default.html', 'Default'), ) -DJANGOCMS_FORMS_FORMAT_CHOICES = () +DJANGOCMS_FORMS_FORMAT_CHOICES = ( + ("csv", _("CSV")), + ("json", _("JSON")), + ("yaml", _("YAML")), + ("xlsx", _("Microsoft Excel")), +) DJANGOCMS_FORMS_USE_HTML5_REQUIRED = False DJANGOCMS_FORMS_WIDGET_CSS_CLASSES = { 'text': ('form-control', ), diff --git a/designsafe/urls.py b/designsafe/urls.py index 47fdba6768..a6cf7f1dd0 100644 --- a/designsafe/urls.py +++ b/designsafe/urls.py @@ -29,6 +29,7 @@ from django.views.generic import RedirectView, TemplateView from django.urls import reverse from django.http import HttpResponse, HttpResponseRedirect +from django.shortcuts import redirect from designsafe.apps.auth.views import login_options as des_login_options from django.contrib.auth.views import LogoutView as des_logout from designsafe.views import project_version as des_version, redirect_old_nees @@ -49,6 +50,7 @@ urlpatterns = [ # admin + url(r'^admin/login/', lambda _: redirect("/login/?next=/admin/")), url(r'^admin/', admin.site.urls), url(r'^admin/impersonate/', include('impersonate.urls')), diff --git a/poetry.lock b/poetry.lock index 54ce95234a..976cf5aac0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -814,24 +814,23 @@ django = ">=2.2" [[package]] name = "django-cms" -version = "3.7.4" -description = "An Advanced Django CMS" +version = "3.8.2" +description = "Lean enterprise content management powered by Django." category = "main" optional = false python-versions = "*" files = [ - {file = "django-cms-3.7.4.tar.gz", hash = "sha256:9374af5a35bac590f1891031fb0878a0e6c2dc5309a6907929c6a036493694f6"}, - {file = "django_cms-3.7.4-py2.py3-none-any.whl", hash = "sha256:9302f0e21153fc9afca55d9c3424ca3654b51d274a1af6ec39f4fbb05059fe46"}, + {file = "django-cms-3.8.2.tar.gz", hash = "sha256:b32a979a3ce9516a907cd9b481a3291f158e797c2b92c157561bcff2c43f36ae"}, + {file = "django_cms-3.8.2-py2.py3-none-any.whl", hash = "sha256:af80688c5e1a2a1151f122746482d7a40a43c2537c91220347e4272b1a5a627d"}, ] [package.dependencies] -Django = ">=1.11,<4" +Django = ">=2.2" django-classy-tags = ">=0.7.2" django-formtools = ">=2.1" django-sekizai = ">=0.7" -django-treebeard = ">=4.3" +django-treebeard = ">=4.3,<4.5" djangocms-admin-style = ">=1.2" -six = "*" [[package]] name = "django-filer" @@ -1069,14 +1068,14 @@ wsaccel = ["wsaccel (>=0.6.2)"] [[package]] name = "djangocms-admin-style" -version = "3.2.5" +version = "2.0.0" description = "Adds pretty CSS styles for the django CMS admin interface." category = "main" optional = false -python-versions = ">=3.7" +python-versions = "*" files = [ - {file = "djangocms-admin-style-3.2.5.tar.gz", hash = "sha256:abbe89d369c0779f7e5f839887a77bdb21660b547e83605d6a4a6df958ace7a5"}, - {file = "djangocms_admin_style-3.2.5-py3-none-any.whl", hash = "sha256:fc51677f12dbec6996590c430c90c9fe8efa32ceadfee383a576ed092be07526"}, + {file = "djangocms-admin-style-2.0.0.tar.gz", hash = "sha256:080f55fe2b643cf608ee8feeb1407bf20e1e76c0f2c058a1bf360b4aa0c90cf4"}, + {file = "djangocms_admin_style-2.0.0-py3-none-any.whl", hash = "sha256:78c64b4e2adba59a7c2e4d5b34e68dc32ab3e2d677f8a94403a2ae9d211aa212"}, ] [[package]] @@ -3529,4 +3528,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] [metadata] lock-version = "2.0" python-versions = "^3.7.12" -content-hash = "92b39fa1042f98ce79752aad3d0abf7e62da11410e515c524b3a46caa86ff774" +content-hash = "9cfa2e07d0ceb7e4c250783d7365ef9ac541471222fd053b36bfebbcf1c3b804" diff --git a/pyproject.toml b/pyproject.toml index 64306fbc30..96995f82cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ python = "^3.7.12" agavepy = "1.0.0a12" Django = "^2.2.28" cryptography = "^2.3.1" -django-cms = "3.7.4" +django-cms = "3.8.2" importlib-resources = "^5.4.0" django-filer = "^1.7.1" django-formtools = "2.2" @@ -66,6 +66,7 @@ opf-fido = "1.4.1" asgiref = "^3.6.0" importlib-metadata = "2.1.3" django-select2 = "6.3.1" +djangocms-admin-style = "2.0.0" [build-system] requires = ["poetry-core>=1.0.0"] From 17dbeeb9e1179311bfe040632054f5692f40532f Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Thu, 5 Oct 2023 12:51:25 -0500 Subject: [PATCH 21/23] Revert admin redirect to /login --- designsafe/urls.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/designsafe/urls.py b/designsafe/urls.py index a6cf7f1dd0..47fdba6768 100644 --- a/designsafe/urls.py +++ b/designsafe/urls.py @@ -29,7 +29,6 @@ from django.views.generic import RedirectView, TemplateView from django.urls import reverse from django.http import HttpResponse, HttpResponseRedirect -from django.shortcuts import redirect from designsafe.apps.auth.views import login_options as des_login_options from django.contrib.auth.views import LogoutView as des_logout from designsafe.views import project_version as des_version, redirect_old_nees @@ -50,7 +49,6 @@ urlpatterns = [ # admin - url(r'^admin/login/', lambda _: redirect("/login/?next=/admin/")), url(r'^admin/', admin.site.urls), url(r'^admin/impersonate/', include('impersonate.urls')), From 576932e88e44639b26016bf3018c725e9587866f Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Thu, 5 Oct 2023 15:06:39 -0500 Subject: [PATCH 22/23] Fix argument order in auth backend --- designsafe/apps/auth/backends.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/designsafe/apps/auth/backends.py b/designsafe/apps/auth/backends.py index 55ea6d8895..8df77eda72 100644 --- a/designsafe/apps/auth/backends.py +++ b/designsafe/apps/auth/backends.py @@ -50,7 +50,7 @@ def __init__(self): # Create an authentication method # This is called by the standard Django login procedure - def authenticate(self, username=None, password=None, request=None, **kwargs): + def authenticate(self, request, username=None, password=None, **kwargs): user = None if username is not None and password is not None: tas_user = None From 742bb2262fef9985bb1a96c8f52e4cbeca02be48 Mon Sep 17 00:00:00 2001 From: Jake Rosenberg Date: Thu, 5 Oct 2023 20:14:28 -0500 Subject: [PATCH 23/23] fix logout buton --- designsafe/settings/common_settings.py | 1 + designsafe/urls.py | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/designsafe/settings/common_settings.py b/designsafe/settings/common_settings.py index 4d293e61f1..63ca1cc24d 100644 --- a/designsafe/settings/common_settings.py +++ b/designsafe/settings/common_settings.py @@ -123,6 +123,7 @@ ) LOGIN_REDIRECT_URL = os.environ.get('LOGIN_REDIRECT_URL', '/account/') +LOGOUT_REDIRECT_URL = os.environ.get('LOGOUT_REDIRECT_URL', '/auth/logged-out/') CACHES = { 'default': { diff --git a/designsafe/urls.py b/designsafe/urls.py index 47fdba6768..d1cea41a6a 100644 --- a/designsafe/urls.py +++ b/designsafe/urls.py @@ -126,8 +126,7 @@ url(r'^auth/', include(('designsafe.apps.auth.urls', 'designsafe.apps.auth'), namespace='designsafe_auth')), url(r'^login/$', des_login_options, name='login'), - url(r'^logout/$', des_logout, - {'next_page': '/auth/logged-out/'}, name='logout'), + url(r'^logout/$', des_logout.as_view(), name='logout'), # help url(r'^help/', include(('designsafe.apps.djangoRT.urls', 'designsafe.apps.djangoRT'), namespace='djangoRT')),