Merge branch 'master' into ras_integration

CHANGELOG.rst

@@ -6,6 +6,168 @@ fourfront
 Change Log
 ----------
 
+8.1.3
+=====
+
+* Added disease_name property to experiment set schema.
+
+
+8.1.2
+=====
+
+* New value "fragments" added in ignored_enum for processed file schema.
+
+
+8.1.1
+=====
+
+* Bug fix to handle non-array children in static content TOC
+
+
+8.1.0
+=====
+
+* 2024-09-03/dmichaels
+  - Update snovault 11.22.0 for fix for running locally; oddity
+    with subprocess.Popen in elasticsearch_fixture; see snovault PR-304.
+
+
+8.0.0
+=====
+
+* Upgrade: React v17 to v18
+* Upgrade: Redux v4 to v5 (there are breaking changes in store and dispatchers. SPC is updated to support both new and legacy usage)
+* Upgrade: HiGlass (React 18-compatible)
+* Upgrade: Vitessce (React 18-compatible)
+* Upgrade: MicroMeta App
+* Upgrade: auth0-Lock v11 to v12
+* Upgrade: gulp.js v4 to v5
+* Upgrade: react-workflow-viz (animation updates to eliminate findDOMNode errors)
+* Fix: User Content updates to fix markdown, jsx, and HTML static section rendering
+* Feature: Improve ExperimentSetDetailPane's raw/processed/supplementary file panels
+* Feature: Display react-workflow-viz version in /health
+* Upgrade: SlideCarousel and BasicCarousel updates upon nuka carousel's breaking changes
+
+
+7.10.1
+=====
+
+* Bug fix to revert schema version of workflow.json back to 7 
+
+
+7.10.0
+=====
+
+* Add cumulative sum and date range options for submission statistics
+* Add cumulative sum and 60 days options for usage statistics
+* Update statistics page style and improve mobile UI
+* Add supplementary files table into /browse details
+* Add raw/processed/supplementary file download options into `Select All` button
+
+
+7.9.0
+=====
+
+* Added 'override_track_title' to file schema
+* Updated track_and_facet calcprop to use the new property if present
+* Added test cases
+
+
+7.8.0
+=====
+
+* Added 'tags' mixing to workflow schema
+* Added 'max_runtime' property to workflow schema
+* Added 'current pipeline' and 'accepted_pipelines' to experiment_type for the names
+  of completed pipelines used by foursight
+
+
+7.7.0
+=====
+
+* Updates related to Python 3.12.
+
+
+7.6.0
+=====
+
+`Add routes page  <https://github.com/4dn-dcic/fourfront/pull/1898>`_
+
+* Add routes page to list all endpoints
+* updated lock file
+
+
+7.5.8
+=====
+
+`Add ignored enum  <https://github.com/4dn-dcic/fourfront/pull/1897>`_
+
+* Add value to ignored_enum for file_type
+
+
+7.5.7
+=====
+
+`Fix command to pull inserts <https://github.com/4dn-dcic/fourfront/pull/1894>`_
+
+* Update snovault and use its updated command to pull inserts
+* Delete nonfunctional command in this repo
+
+
+7.5.6
+=====
+
+`fix cypress 03d  <https://github.com/4dn-dcic/fourfront/pull/1893>`_
+
+* fixes cypress 03d's failing "Select All" step
+* adds OPF coun into Chart's files agg
+
+
+7.5.5
+=====
+
+* bug fix - button "Select All" not turns into "Deselect All" in /browse after QuickInfoBar updates in 7.5.0
+
+
+7.5.4
+=====
+
+* bug fix - analytics impression count calculation fails for the lists having 200+ items
+
+
+7.5.3
+=====
+
+`calcprop update  <https://github.com/4dn-dcic/fourfront/pull/1890>`_
+
+* Updated experiment_categorizer calcprop for ExperimentMic to deal with many targets in imaging paths
+
+
+7.5.2
+=====
+
+* adds two new props to object.CopyWrapper to allow/prevent sending analytics data into GA4
+
+
+7.5.1
+=====
+
+* grab ExpSet accession from source_experiment_sets instead of experiment_sets for FileView's metadata.tsv generation
+
+
+7.5.0
+=====
+
+* changes QuickInfoBar experiment and file links from /browse to /search
+* adds OPF to File counts
+
+
+7.4.2
+=====
+
+* Bug fix - LocalizedTime component cannot handle invalid dates and makes UI failing completely
+
+
 7.4.1
 =====
 

Makefile

@@ -38,52 +38,36 @@ npm-setup:  # runs all front-end setup
 moto-setup:  # optional moto setup that must be done separately
 	pip install "moto[server]==1.3.7"
 
-macpoetry-install:  # Same as 'poetry install' except that on OSX Catalina, an environment variable wrapper is needed
-	bin/macpoetry-install
-
 configure:  # does any pre-requisite installs
 	@#pip install --upgrade pip==21.0.1
 	pip install --upgrade pip
 	@#pip install poetry==1.1.9  # this version is known to work. -kmp 11-Mar-2021
 	# Pin to version 1.1.15 for now to avoid this error:
 	#   Because encoded depends on wheel (>=0.29.0) which doesn't match any versions, version solving failed.
-	pip install wheel==0.40.0
-	pip install poetry==1.7.1
-	pip install setuptools==57.5.0 # this version allows 2to3, any later will break -wrr 20-Sept-2021
+	# pip install wheel==0.40.0
+	# pip install poetry==1.7.1
+	# pip install setuptools==57.5.0 # this version allows 2to3, any later will break -wrr 20-Sept-2021
+	pip install wheel
+	pip install poetry
+	pip install setuptools
 	poetry config virtualenvs.create false --local # do not create a virtualenv - the user should have already done this -wrr 20-Sept-2021
 
 build-poetry:
 	make configure
 	poetry install
 
-macbuild-poetry:
-	make configure
-	make macpoetry-install
-
 build:  # builds
 	make build-poetry
 	make build-after-poetry
 
-macbuild:  # builds for Catalina
-	make macbuild-poetry
-	make build-after-poetry
-
 rebuild:
 	make clean  # Among other things, this assures 'make npm-setup' will run, but it also does other cleanup.
 	make build
 
-macrebuild:
-	make clean  # Among other things, this assures 'make npm-setup' will run, but it also does other cleanup.
-	make macbuild
-
 build-full:  # rebuilds for Catalina, addressing zlib possibly being in an alternate location.
 	make clean-node-modules  # This effectively assures that 'make npm-setup' will need to run.
 	make build
 
-macbuild-full:  # rebuilds for Catalina, addressing zlib possibly being in an alternate location.
-	make clean-node-modules  # This effectively assures that 'make npm-setup' will need to run.
-	make macbuild
-
 build-after-poetry:  # continuation of build after poetry install
 	make moto-setup
 	make npm-setup-if-needed
@@ -98,10 +82,6 @@ build-dev:  # same as build, but sets up locust as well
 	make build
 	make build-locust
 
-macbuild-dev:  # same as macbuild, but sets up locust as well
-	make macbuild
-	make build-locust
-
 build-locust:  # just pip installs locust - may cause instability
 	pip install locust
 

conftest.py

@@ -43,7 +43,7 @@ def pytest_configure():
 if not my_selected_account or my_selected_account == "643366669028":
     PRINT("The legacy account is correctly selected for testing Fourfront.")
 elif not my_selected_env:
-    print("ENV_NAME was not set. It is being set to {desired_env}.")
+    print(f"ENV_NAME was not set. It is being set to {desired_env}.")
     os.environ['ENV_NAME'] = desired_env
 elif my_selected_env != desired_env:
     PRINT(f"ENV_NAME must be set to {desired_env} (or left unset) for testing. (It is set to {my_selected_env}.)")

deploy/post_deploy_testing/cypress/e2e/01b_static_content.cy.js

@@ -17,6 +17,17 @@ describe('Static Page & Content Tests', function () {
     it('Click & visit each page from menu, ensure ToC exists somewhere, ensure ToC works.', function(){
 
         cy.on('uncaught:exception', function(err, runnable){
+            // TODO: Investigate hydration errors occurring during SSR in Cypress tests.
+            // It appears that Cypress injects a prop into the div on the client side, which doesn't exist on the server side, leading to hydration issues.
+            // This suppression is temporary and should be removed once the issue is resolved.
+            // https://github.com/cypress-io/cypress/issues/27204
+            if (
+                /hydrat/i.test(err.message) ||
+                /Minified React error #418/.test(err.message) ||
+                /Minified React error #423/.test(err.message)
+            ) {
+                return false;
+            }
 
             expect(err.message).to.include("return response;");
 
@@ -57,7 +68,7 @@ describe('Static Page & Content Tests', function () {
                                 cy.get(helpNavBarItemSelectorStr).click().should('have.class', 'dropdown-open-for').then(()=>{
                                     //TODO: Remove wait() when a better workaround finds out
                                     //TODO: May apply possible solutions described in https://www.cypress.io/blog/2018/02/05/when-can-the-test-start
-                                    cy.get('div.big-dropdown-menu a#' + escapeElementWithNumericId(allLinkElementIDs[count])).wait(500).click().then(($nextListItem)=>{
+                                    cy.get('div.big-dropdown-menu a#' + escapeElementWithNumericId(allLinkElementIDs[count])).wait(1000).click().then(($nextListItem)=>{
                                         const linkHref = $nextListItem.attr('href');
                                         cy.location('pathname').should('equal', linkHref);
                                         testVisit();

deploy/post_deploy_testing/cypress/e2e/03a_browse_views_basic.cy.js

@@ -80,6 +80,7 @@ describe('Browse Views - Basic Tests', function () {
         it('Select a grouping term in Experiment Type facet, then check whether the sub-terms are also selected', function () {
 
             cy.visit('/browse').get('#slow-load-container').should('not.have.class', 'visible').end()
+                .get('.facet-charts.loading').should('not.exist')
                 .get(".facets-header .facets-title").should('have.text', 'Included Properties').end()
                 .get('.facet.closed[data-field="experiments_in_set.experiment_type.display_title"] > h5').scrollIntoView().should('be.visible').click().end()
                 .get('.facet.open[data-field="experiments_in_set.experiment_type.display_title"] .facet-list-element[data-is-grouping="true"] a').first().within(($term) => {
@@ -118,6 +119,7 @@ describe('Browse Views - Basic Tests', function () {
         it('Exclude a grouping term in Experiment Type facet, then check whether the sub-terms are also excluded', function () {
 
             cy.visit('/browse').get('#slow-load-container').should('not.have.class', 'visible').end()
+                .get('.facet-charts.loading').should('not.exist')
                 .get(".facets-header button").first().click().end()
                 .get(".facets-header .facets-title").should('have.text', 'Excluded Properties').end()
                 .get('.facet.closed[data-field="experiments_in_set.experiment_type.display_title"] > h5').scrollIntoView().should('be.visible').click().end()