From 9ffc2ec0f98da38f8ded2df9b65a7a32da6c2aaa Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Fri, 1 Mar 2024 14:42:26 -0600 Subject: [PATCH 01/12] Add requirements.txt --- requirements.txt | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..5cd1f3ba --- /dev/null +++ b/requirements.txt @@ -0,0 +1,6 @@ +requests==2.20.0 +markupsafe==2.0.1 +Jinja2==2.11.3 +mysqlclient==2.1.0 +PyYAML==6.0.1 +dsnparse==0.1.15 From 9c6df18a12752559a84383f89e1cc8764f55ec31 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:39:45 -0600 Subject: [PATCH 02/12] Add validate-python yml --- .github/workflows/validate-python.yml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/workflows/validate-python.yml diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml new file mode 100644 index 00000000..b06649c9 --- /dev/null +++ b/.github/workflows/validate-python.yml @@ -0,0 +1,21 @@ +name: Python validator + +on: [push, pull_request] + +jobs: + build: + name: Validate Data + runs-on: ubuntu-latest + steps: + - name: 'Checkout Code' + uses: actions/checkout@v4 + - name: 'Validate tests' + working-directory: ./cbioportal + run: | + docker run -v ${PWD}:/cbioportal python:3.6 /bin/sh -c ' + pip install -r requirements.txt && + export PYTHONPATH=/src/main/resources/scripts && + cd /src/test/scripts/ && + python unit_tests_validate_data.py && + python system_tests_validate_data.py && + python system_tests_validate_studies.py' \ No newline at end of file From 35958d0113d11b401b5062b49828c04f966c879f Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:40:37 -0600 Subject: [PATCH 03/12] Fix working-directory --- .github/workflows/validate-python.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index b06649c9..4ae806a4 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -10,7 +10,6 @@ jobs: - name: 'Checkout Code' uses: actions/checkout@v4 - name: 'Validate tests' - working-directory: ./cbioportal run: | docker run -v ${PWD}:/cbioportal python:3.6 /bin/sh -c ' pip install -r requirements.txt && From 7838cd900bdaea70022e6ca7d1279e41720d3aa8 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:44:07 -0600 Subject: [PATCH 04/12] Another directory change --- .github/workflows/validate-python.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 4ae806a4..834528fd 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -11,7 +11,7 @@ jobs: uses: actions/checkout@v4 - name: 'Validate tests' run: | - docker run -v ${PWD}:/cbioportal python:3.6 /bin/sh -c ' + docker run -v ${PWD} python:3.6 /bin/sh -c ' pip install -r requirements.txt && export PYTHONPATH=/src/main/resources/scripts && cd /src/test/scripts/ && From 4f756623caa3fedd8262fafabc233618516b64c7 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:46:12 -0600 Subject: [PATCH 05/12] test and directory --- .github/workflows/validate-python.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 834528fd..0abf8c7b 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -11,7 +11,9 @@ jobs: uses: actions/checkout@v4 - name: 'Validate tests' run: | - docker run -v ${PWD} python:3.6 /bin/sh -c ' + docker run -v ${PWD}:cbioportal-core python:3.6 /bin/sh -c ' + pwd && + ls -lart && pip install -r requirements.txt && export PYTHONPATH=/src/main/resources/scripts && cd /src/test/scripts/ && From e2f808d8f7a48d78bb509198b51b9e08d43496e4 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:47:05 -0600 Subject: [PATCH 06/12] Remove validator --- .github/workflows/validate-python.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 0abf8c7b..7d43eaaf 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -11,7 +11,7 @@ jobs: uses: actions/checkout@v4 - name: 'Validate tests' run: | - docker run -v ${PWD}:cbioportal-core python:3.6 /bin/sh -c ' + docker run -v ${PWD} python:3.6 /bin/sh -c ' pwd && ls -lart && pip install -r requirements.txt && From 0c4de0dc504793c679611a682094917cd25904a9 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:49:52 -0600 Subject: [PATCH 07/12] Paths again --- .github/workflows/validate-python.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 7d43eaaf..5e6397e7 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -9,7 +9,10 @@ jobs: steps: - name: 'Checkout Code' uses: actions/checkout@v4 + with: + path: ./cbioportal-core - name: 'Validate tests' + working-directory: path: ./cbioportal-core run: | docker run -v ${PWD} python:3.6 /bin/sh -c ' pwd && From ec7987fb18d45a54ff2850af03d2d2c32a25e86c Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:50:55 -0600 Subject: [PATCH 08/12] Formatting --- .github/workflows/validate-python.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 5e6397e7..5d3b25c5 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -10,9 +10,9 @@ jobs: - name: 'Checkout Code' uses: actions/checkout@v4 with: - path: ./cbioportal-core + path: ./cbioportal-core - name: 'Validate tests' - working-directory: path: ./cbioportal-core + working-directory: ./cbioportal-core run: | docker run -v ${PWD} python:3.6 /bin/sh -c ' pwd && From dad8eb0060c823a3194bb062a4b1065d11226917 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:53:33 -0600 Subject: [PATCH 09/12] Add docker volume path --- .github/workflows/validate-python.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 5d3b25c5..efda1e5a 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -14,7 +14,7 @@ jobs: - name: 'Validate tests' working-directory: ./cbioportal-core run: | - docker run -v ${PWD} python:3.6 /bin/sh -c ' + docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/sh -c ' pwd && ls -lart && pip install -r requirements.txt && From 486ebff9498fec73b07399947455050b9c09d661 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:54:41 -0600 Subject: [PATCH 10/12] Change dir --- .github/workflows/validate-python.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index efda1e5a..0de2bce2 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -15,6 +15,7 @@ jobs: working-directory: ./cbioportal-core run: | docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/sh -c ' + cd cbioportal-core && pwd && ls -lart && pip install -r requirements.txt && From 689b947bcfe589167e85152f8355b52598f9ed02 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 08:58:58 -0600 Subject: [PATCH 11/12] More directory fixes --- .github/workflows/validate-python.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml index 0de2bce2..7ef914b0 100644 --- a/.github/workflows/validate-python.yml +++ b/.github/workflows/validate-python.yml @@ -19,8 +19,8 @@ jobs: pwd && ls -lart && pip install -r requirements.txt && - export PYTHONPATH=/src/main/resources/scripts && - cd /src/test/scripts/ && + export PYTHONPATH=/cbioportal-core/src/main/resources/scripts && + cd src/test/scripts/ && python unit_tests_validate_data.py && python system_tests_validate_data.py && python system_tests_validate_studies.py' \ No newline at end of file From ac609afc51ac2f3691a129263e87fab84da644b7 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Wed, 6 Mar 2024 11:27:37 -0600 Subject: [PATCH 12/12] Update directory report html --- src/test/scripts/test_data/study_es_0/result_report.html | 4 ++-- src/test/scripts/test_data/study_es_1/result_report.html | 4 ++-- src/test/scripts/test_data/study_es_3/result_report.html | 4 ++-- src/test/scripts/test_data/study_es_3/study_es_3.html | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/test/scripts/test_data/study_es_0/result_report.html b/src/test/scripts/test_data/study_es_0/result_report.html index a73fb794..0def1eae 100644 --- a/src/test/scripts/test_data/study_es_0/result_report.html +++ b/src/test/scripts/test_data/study_es_0/result_report.html @@ -142,7 +142,7 @@

General

Debug – – - Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json' + Retrieving chromosome lengths from '/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json' – @@ -150,7 +150,7 @@

General

Debug – – - Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json' + Retrieving chromosome lengths from '/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json' – diff --git a/src/test/scripts/test_data/study_es_1/result_report.html b/src/test/scripts/test_data/study_es_1/result_report.html index 38588c01..9de476a2 100644 --- a/src/test/scripts/test_data/study_es_1/result_report.html +++ b/src/test/scripts/test_data/study_es_1/result_report.html @@ -36,7 +36,7 @@ - cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_1' + cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_1' @@ -46,7 +46,7 @@

cBioPortal validation report

-

Study directory:
/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_1

+

Study directory:
/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_1

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version -- offline instance

diff --git a/src/test/scripts/test_data/study_es_3/result_report.html b/src/test/scripts/test_data/study_es_3/result_report.html index b76f3fd4..358f9a47 100644 --- a/src/test/scripts/test_data/study_es_3/result_report.html +++ b/src/test/scripts/test_data/study_es_3/result_report.html @@ -36,7 +36,7 @@ - cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3' + cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3' @@ -46,7 +46,7 @@

cBioPortal validation report

-

Study directory:
/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3

+

Study directory:
/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version unknown -- offline instance

diff --git a/src/test/scripts/test_data/study_es_3/study_es_3.html b/src/test/scripts/test_data/study_es_3/study_es_3.html index 9d9ed928..00e52944 100644 --- a/src/test/scripts/test_data/study_es_3/study_es_3.html +++ b/src/test/scripts/test_data/study_es_3/study_es_3.html @@ -36,7 +36,7 @@ - cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3' + cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3' @@ -46,7 +46,7 @@

cBioPortal validation report

-

Study directory:
/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3

+

Study directory:
/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 1.19.0-SNAPSHOT