From ed04a5e3cbd9ff01ba6f2ab53c7733aed777eda5 Mon Sep 17 00:00:00 2001 From: EddieLF <34049565+EddieLF@users.noreply.github.com> Date: Thu, 22 Aug 2024 13:53:46 +1000 Subject: [PATCH 1/6] Adds user agent to request to igv content (#239) --- seqr/views/apis/igv_api.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/seqr/views/apis/igv_api.py b/seqr/views/apis/igv_api.py index eebcbb248a..ddc038f514 100644 --- a/seqr/views/apis/igv_api.py +++ b/seqr/views/apis/igv_api.py @@ -273,6 +273,8 @@ def igv_genomes_proxy(request, cloud_host, file_path): if range_header: headers['Range'] = range_header + headers['User-Agent'] = request.META.get('HTTP_USER_AGENT', 'Mozilla/5.0') + genome_response = requests.get(f'{CLOUD_STORAGE_URLS[cloud_host]}/{file_path}', headers=headers) proxy_response = HttpResponse( content=genome_response.content, From 069205d9a86c904921badc39a621d714749f6e9a Mon Sep 17 00:00:00 2001 From: EddieLF <34049565+EddieLF@users.noreply.github.com> Date: Wed, 4 Sep 2024 14:45:46 +1000 Subject: [PATCH 2/6] Update IGV reference URLs to new s3 path (#243) --- ui/shared/components/panel/family/constants.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/ui/shared/components/panel/family/constants.js b/ui/shared/components/panel/family/constants.js index a5b870f9de..f78ead46e3 100644 --- a/ui/shared/components/panel/family/constants.js +++ b/ui/shared/components/panel/family/constants.js @@ -93,15 +93,15 @@ const REFERENCE_URLS = [ baseUrl: `${BASE_REFERENCE_URL}/s3`, path: { 37: 'igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt', - 38: 'igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz', + 38: 'igv-genepattern-org/genomes/hg38/cytoBandIdeo.txt.gz', }, }, { key: 'aliasURL', - baseUrl: `${BASE_REFERENCE_URL}/s3/igv.org.genomes`, + baseUrl: `${BASE_REFERENCE_URL}/s3`, path: { 37: 'hg19/hg19_alias.tab', - 38: 'hg38/hg38_alias.tab', + 38: 'igv-genepattern-org/genomes/hg38/hg38_alias.tab', }, }, ] @@ -121,10 +121,10 @@ const REFERENCE_TRACKS = [ { name: 'Refseq', indexPostfix: 'tbi', - baseUrl: `${BASE_REFERENCE_URL}/s3/igv.org.genomes`, + baseUrl: `${BASE_REFERENCE_URL}`, path: { - 37: 'hg19/refGene.sorted.txt.gz', - 38: 'hg38/refGene.sorted.txt.gz', + 37: 's3/igv.org.genomes/hg19/refGene.sorted.txt.gz', + 38: 's3/igv-genepattern-org/genomes/hg38/ncbiRefSeq.txt.gz', }, format: 'refgene', visibilityWindow: -1, From 110bfd7cb187a4f4b30e02244c331019cd1ae2d5 Mon Sep 17 00:00:00 2001 From: EddieLF <34049565+EddieLF@users.noreply.github.com> Date: Thu, 13 Feb 2025 15:48:41 +1100 Subject: [PATCH 3/6] Update the 'feature updates' URL to point to popgen github (#257) --- seqr/views/apis/feature_updates_api.py | 2 +- ui/pages/Public/components/FeatureUpdates.jsx | 6 +++--- ui/shared/components/page/Header.jsx | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/seqr/views/apis/feature_updates_api.py b/seqr/views/apis/feature_updates_api.py index 2fccead30e..5e51832c42 100644 --- a/seqr/views/apis/feature_updates_api.py +++ b/seqr/views/apis/feature_updates_api.py @@ -6,7 +6,7 @@ from seqr.views.utils.json_utils import create_json_response FEED_URL = ( - "https://github.com/broadinstitute/seqr/discussions/categories/feature-updates.atom" + "https://github.com/populationgenomics/seqr/discussions/categories/feature-updates.atom" ) TIMEOUT = 5 diff --git a/ui/pages/Public/components/FeatureUpdates.jsx b/ui/pages/Public/components/FeatureUpdates.jsx index 49f5ecb49e..26a8618a75 100644 --- a/ui/pages/Public/components/FeatureUpdates.jsx +++ b/ui/pages/Public/components/FeatureUpdates.jsx @@ -13,11 +13,11 @@ const getDateFromDateStr = dateStr => ( const FeatureUpdatesFeed = ({ entries }) => (
- Feature Updates + CPG Updates - This page serves as an announcement hub for new seqr functionality, sourced from this + This page serves as an announcement hub for CPG seqr updates, sourced from this   - GitHub Discussion + GitHub Discussion .
diff --git a/ui/shared/components/page/Header.jsx b/ui/shared/components/page/Header.jsx index 0a1b6578c9..ea8a8db8f4 100644 --- a/ui/shared/components/page/Header.jsx +++ b/ui/shared/components/page/Header.jsx @@ -28,7 +28,7 @@ const PageHeader = React.memo(({ user, onSubmit }) => ( , ] : null } - + {Object.keys(user).length ? [ Date: Tue, 18 Mar 2025 12:51:07 +1100 Subject: [PATCH 4/6] Update gh actions in unit-tests and add setup-java distribution (#265) * Update gh actions in unit-tests and add setup-java distribution * remove mkdir ../static from build UI in unit-tests.yml action --- .github/workflows/unit-tests.yml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index 05557e01e6..d0d2d5dd70 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -42,18 +42,19 @@ jobs: - 5432:5432 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - uses: actions/setup-java@v1 + - uses: actions/setup-java@v4 with: java-version: '8' # The JDK version needed by hail java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk + distribution: 'temurin' architecture: x64 # (x64 or x86) - defaults to x64 - name: Use pip cache - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: ~/.cache/pip key: pip-${{ hashFiles('**/requirements*.txt') }} @@ -65,7 +66,7 @@ jobs: pip install -r requirements.txt pip install -r requirements-dev.txt - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 with: node-version: 16 - name: Build UI @@ -88,9 +89,9 @@ jobs: node-version: [14] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Use Node.js ${{ matrix.node-version }} - uses: actions/setup-node@v3 + uses: actions/setup-node@v4 with: node-version: ${{ matrix.node-version }} cache: "npm" @@ -99,4 +100,4 @@ jobs: - run: npm ci working-directory: ./ui - run: npm test - working-directory: ./ui + working-directory: ./ui \ No newline at end of file From b8965b6b02790113db115d546d88ad5dbeab7921 Mon Sep 17 00:00:00 2001 From: EddieLF <34049565+EddieLF@users.noreply.github.com> Date: Tue, 18 Mar 2025 14:15:32 +1100 Subject: [PATCH 5/6] Update panelapp URL to new panelapp-aus URL (#264) --- deploy/docker/seqr/deploy_cloudrun_jobs.sh | 2 +- seqr/fixtures/1kg_project.json | 2 +- ui/shared/utils/panelAppUtils.test.ts | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/deploy/docker/seqr/deploy_cloudrun_jobs.sh b/deploy/docker/seqr/deploy_cloudrun_jobs.sh index 70f24b45b4..e602781f0b 100644 --- a/deploy/docker/seqr/deploy_cloudrun_jobs.sh +++ b/deploy/docker/seqr/deploy_cloudrun_jobs.sh @@ -70,7 +70,7 @@ gcloud beta run jobs create \ ${ENV_NAME}-reference-import-panels \ --image=${IMAGE} \ --task-timeout 3600 \ - --command=python --args="-u,manage.py,import_all_panels,https://panelapp.agha.umccr.org/api/v1,--label=AU" \ + --command=python --args="-u,manage.py,import_all_panels,https://panelapp-aus.org/api/v1,--label=AU" \ --region=australia-southeast1 \ --service-account=${SERVICE_ACCOUNT} \ --vpc-connector=projects/seqr-308602/locations/australia-southeast1/connectors/seqr-cloud-run-to-sql \ diff --git a/seqr/fixtures/1kg_project.json b/seqr/fixtures/1kg_project.json index 82398e19f4..f7fd6dfc8f 100644 --- a/seqr/fixtures/1kg_project.json +++ b/seqr/fixtures/1kg_project.json @@ -2364,7 +2364,7 @@ "status": "public", "version": "1.0", "version_created": "2018-04-28T00:03:25.347Z", - "url": "https://panelapp.agha.umccr.org/api/v1/panels/254/genes" + "url": "https://panelapp-aus.org/api/v1/panels/254/genes" } }, { diff --git a/ui/shared/utils/panelAppUtils.test.ts b/ui/shared/utils/panelAppUtils.test.ts index d91656b23a..f87b296194 100644 --- a/ui/shared/utils/panelAppUtils.test.ts +++ b/ui/shared/utils/panelAppUtils.test.ts @@ -55,15 +55,15 @@ describe('Test moiToMoiInitials()', () => { }) const panelAppData = [{ - url: 'https://panelapp.agha.umccr.org/api/v1/panels/40/genes', + url: 'https://panelapp-aus.org/api/v1/panels/40/genes', panel: 40, gene: 'SLC2A1', - result: 'https://panelapp.agha.umccr.org/panels/40/gene/SLC2A1', + result: 'https://panelapp-aus.org/panels/40/gene/SLC2A1', }, { - url: 'https://panelapp.agha.umccr.org/api/v1/panels/40/genes', + url: 'https://panelapp-aus.org/api/v1/panels/40/genes', panel: 40, gene: 'SLC1A3', - result: 'https://panelapp.agha.umccr.org/panels/40/gene/SLC1A3', + result: 'https://panelapp-aus.org/panels/40/gene/SLC1A3', }, { url: 'https://panelapp.genomicsengland.co.uk/api/v1', panel: 486, From 4aa9f24d9897b2dbc6e2d8cb7457755d1dfdd6c4 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Thu, 15 May 2025 17:23:41 +1000 Subject: [PATCH 6/6] maxDiff=None for failing test --- seqr/utils/search/hail_search_utils_tests.py | 1 + 1 file changed, 1 insertion(+) diff --git a/seqr/utils/search/hail_search_utils_tests.py b/seqr/utils/search/hail_search_utils_tests.py index a2ef9bfe7a..8da1eb69d3 100644 --- a/seqr/utils/search/hail_search_utils_tests.py +++ b/seqr/utils/search/hail_search_utils_tests.py @@ -75,6 +75,7 @@ def _test_expected_search_call(self, search_fields=None, gene_ids=None, interval @mock.patch('seqr.utils.search.hail_search_utils.MAX_FAMILY_COUNTS', {'WES': 2, 'WGS': 1}) @responses.activate def test_query_variants(self): + self.maxDiff = None variants, total = query_variants(self.results_model, user=self.user) self.assertListEqual(variants, HAIL_BACKEND_VARIANTS) self.assertEqual(total, 5)