From dbe8032342997c1c9ca398a26b2c18e8692ec325 Mon Sep 17 00:00:00 2001 From: Sijie Date: Thu, 27 Jun 2024 11:03:21 -0700 Subject: [PATCH 01/10] initiate gc_content, dna_size, and md5 --- lib/GenomeFileUtil/core/GenbankToGenome.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/GenomeFileUtil/core/GenbankToGenome.py b/lib/GenomeFileUtil/core/GenbankToGenome.py index 9b74e8cd..4d21230c 100644 --- a/lib/GenomeFileUtil/core/GenbankToGenome.py +++ b/lib/GenomeFileUtil/core/GenbankToGenome.py @@ -81,6 +81,9 @@ def __init__(self): self.assembly_ref = None self.assembly_path = None self.assembly_info = None + self.gc_content = None + self.dna_size = None + self.md5 = None self.input_params = None From e37d86174e42c8a671ed1c3e25c022d93df1cab2 Mon Sep 17 00:00:00 2001 From: Sijie Date: Fri, 19 Jul 2024 18:07:38 -0700 Subject: [PATCH 02/10] fix kb-sdk test --- .github/workflows/kb_sdk_test.yaml | 19 ++----------------- scripts/GHA/kb-sdk | 13 +++++++++++++ scripts/GHA/make_testdir | 17 +++++++++++++++++ 3 files changed, 32 insertions(+), 17 deletions(-) create mode 100644 scripts/GHA/kb-sdk create mode 100644 scripts/GHA/make_testdir diff --git a/.github/workflows/kb_sdk_test.yaml b/.github/workflows/kb_sdk_test.yaml index 2f985601..e1ae205c 100644 --- a/.github/workflows/kb_sdk_test.yaml +++ b/.github/workflows/kb_sdk_test.yaml @@ -16,26 +16,13 @@ jobs: if: "!contains(github.event.head_commit.message, 'skip ci')" uses: actions/checkout@v2 - - name: Check out Actions CI files - if: "!contains(github.event.head_commit.message, 'skip ci')" - uses: actions/checkout@v2 - with: - repository: 'kbaseapps/kb_sdk_actions' - path: 'kb_sdk_actions' - - - name: Set up test environment if: "!contains(github.event.head_commit.message, 'skip ci')" shell: bash env: KBASE_TEST_TOKEN: ${{ secrets.KBASE_CI_TOKEN }} run: | - # Verify kb_sdk_actions clone worked - test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned" - # Pull kb-sdk & create startup script - docker pull kbase/kb-sdk - - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local" + sh scripts/GHA/make_testdir && echo "Created test_local" test -f "test_local/test.cfg" && echo "Confirmed config exists" - name: Configure authentication @@ -55,10 +42,8 @@ jobs: - name: Run tests if: "!contains(github.event.head_commit.message, 'skip ci')" shell: bash - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} run: | - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test + sh scripts/GHA/kb-sdk test --verbose - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 diff --git a/scripts/GHA/kb-sdk b/scripts/GHA/kb-sdk new file mode 100644 index 00000000..b97ad70b --- /dev/null +++ b/scripts/GHA/kb-sdk @@ -0,0 +1,13 @@ +#!/bin/sh + +# TODO pin sdk image when pinnable tags are available +# TODO may want to make the image an env var or argument + +# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/kb-sdk for source + +# Cache the group for the docker file +if [ ! -e $HOME/.kbsdk.cache ] ; then + docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-main -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache +fi + +exec docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-main $@ diff --git a/scripts/GHA/make_testdir b/scripts/GHA/make_testdir new file mode 100644 index 00000000..555d8489 --- /dev/null +++ b/scripts/GHA/make_testdir @@ -0,0 +1,17 @@ +#!/bin/sh + +# TODO pin sdk image when pinnable tags are available +# TODO may want to make the image an env var or argument + +# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/make_testdir for source + +# Disable the default `return 1` when creating `test_local` +set +e + +# Cache the group for the docker file +if [ ! -e $HOME/.kbsdk.cache ] ; then + docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-main -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache +fi + +exec docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-main test +exit From ca4dfd61c76fd5c1678b3a50061fa4f8139b3fcc Mon Sep 17 00:00:00 2001 From: Sijie Date: Mon, 22 Jul 2024 11:42:51 -0700 Subject: [PATCH 03/10] retry kb-sdk test --- lib/GenomeFileUtil/core/GenbankToGenome.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/GenomeFileUtil/core/GenbankToGenome.py b/lib/GenomeFileUtil/core/GenbankToGenome.py index 4d21230c..ea64567a 100644 --- a/lib/GenomeFileUtil/core/GenbankToGenome.py +++ b/lib/GenomeFileUtil/core/GenbankToGenome.py @@ -82,9 +82,9 @@ def __init__(self): self.assembly_path = None self.assembly_info = None self.gc_content = None - self.dna_size = None - self.md5 = None - self.input_params = None + # self.dna_size = None + # self.md5 = None + # self.input_params = None class GenbankToGenome: From d4bc8a3b22ffbccc884c2884435c16e399b17a21 Mon Sep 17 00:00:00 2001 From: Sijie Date: Mon, 22 Jul 2024 13:04:00 -0700 Subject: [PATCH 04/10] update kb-sdk tag ver --- lib/GenomeFileUtil/core/GenbankToGenome.py | 6 +++--- scripts/GHA/kb-sdk | 4 ++-- scripts/GHA/make_testdir | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/lib/GenomeFileUtil/core/GenbankToGenome.py b/lib/GenomeFileUtil/core/GenbankToGenome.py index ea64567a..4d21230c 100644 --- a/lib/GenomeFileUtil/core/GenbankToGenome.py +++ b/lib/GenomeFileUtil/core/GenbankToGenome.py @@ -82,9 +82,9 @@ def __init__(self): self.assembly_path = None self.assembly_info = None self.gc_content = None - # self.dna_size = None - # self.md5 = None - # self.input_params = None + self.dna_size = None + self.md5 = None + self.input_params = None class GenbankToGenome: diff --git a/scripts/GHA/kb-sdk b/scripts/GHA/kb-sdk index b97ad70b..08359f4d 100644 --- a/scripts/GHA/kb-sdk +++ b/scripts/GHA/kb-sdk @@ -7,7 +7,7 @@ # Cache the group for the docker file if [ ! -e $HOME/.kbsdk.cache ] ; then - docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-main -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache + docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache fi -exec docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-main $@ +exec docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 $@ diff --git a/scripts/GHA/make_testdir b/scripts/GHA/make_testdir index 555d8489..862d4b6e 100644 --- a/scripts/GHA/make_testdir +++ b/scripts/GHA/make_testdir @@ -10,8 +10,8 @@ set +e # Cache the group for the docker file if [ ! -e $HOME/.kbsdk.cache ] ; then - docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-main -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache + docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache fi -exec docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-main test +exec docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test exit From 642246935f136065d89d86f6e284684b8193be30 Mon Sep 17 00:00:00 2001 From: Sijie Date: Tue, 23 Jul 2024 10:30:05 -0700 Subject: [PATCH 05/10] remove code --- lib/GenomeFileUtil/core/GenbankToGenome.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/lib/GenomeFileUtil/core/GenbankToGenome.py b/lib/GenomeFileUtil/core/GenbankToGenome.py index 4d21230c..9b74e8cd 100644 --- a/lib/GenomeFileUtil/core/GenbankToGenome.py +++ b/lib/GenomeFileUtil/core/GenbankToGenome.py @@ -81,9 +81,6 @@ def __init__(self): self.assembly_ref = None self.assembly_path = None self.assembly_info = None - self.gc_content = None - self.dna_size = None - self.md5 = None self.input_params = None From c680d557b22b10e543da9095072e639e206d04dd Mon Sep 17 00:00:00 2001 From: Sijie Date: Fri, 26 Jul 2024 17:07:52 -0700 Subject: [PATCH 06/10] rerun kb-sdk test after new images registered --- scripts/GHA/kb-sdk | 1 - scripts/GHA/make_testdir | 1 - 2 files changed, 2 deletions(-) diff --git a/scripts/GHA/kb-sdk b/scripts/GHA/kb-sdk index 08359f4d..07972231 100644 --- a/scripts/GHA/kb-sdk +++ b/scripts/GHA/kb-sdk @@ -1,6 +1,5 @@ #!/bin/sh -# TODO pin sdk image when pinnable tags are available # TODO may want to make the image an env var or argument # See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/kb-sdk for source diff --git a/scripts/GHA/make_testdir b/scripts/GHA/make_testdir index 862d4b6e..83a0709d 100644 --- a/scripts/GHA/make_testdir +++ b/scripts/GHA/make_testdir @@ -1,6 +1,5 @@ #!/bin/sh -# TODO pin sdk image when pinnable tags are available # TODO may want to make the image an env var or argument # See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/make_testdir for source From ae56d064f0035a542382137ef757dc19293eaaf5 Mon Sep 17 00:00:00 2001 From: Sijie Date: Fri, 26 Jul 2024 17:49:26 -0700 Subject: [PATCH 07/10] set the constructor to dev --- lib/installed_clients/GenomeAnnotationAPIClient.py | 2 +- lib/installed_clients/WSLargeDataIOClient.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/installed_clients/GenomeAnnotationAPIClient.py b/lib/installed_clients/GenomeAnnotationAPIClient.py index 44f92b82..08ccd9a5 100644 --- a/lib/installed_clients/GenomeAnnotationAPIClient.py +++ b/lib/installed_clients/GenomeAnnotationAPIClient.py @@ -24,7 +24,7 @@ def __init__( password=None, token=None, ignore_authrc=False, trust_all_ssl_certificates=False, auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', - service_ver='release', + service_ver='dev', async_job_check_time_ms=100, async_job_check_time_scale_percent=150, async_job_check_max_time_ms=300000): if url is None: diff --git a/lib/installed_clients/WSLargeDataIOClient.py b/lib/installed_clients/WSLargeDataIOClient.py index c185bfee..8ae85be4 100644 --- a/lib/installed_clients/WSLargeDataIOClient.py +++ b/lib/installed_clients/WSLargeDataIOClient.py @@ -24,7 +24,7 @@ def __init__( password=None, token=None, ignore_authrc=False, trust_all_ssl_certificates=False, auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', - service_ver='beta', + service_ver='dev', async_job_check_time_ms=100, async_job_check_time_scale_percent=150, async_job_check_max_time_ms=300000): if url is None: From facdafefc33797acd2c8787d094d9859129f176d Mon Sep 17 00:00:00 2001 From: Sijie Date: Fri, 26 Jul 2024 18:33:44 -0700 Subject: [PATCH 08/10] add dev in _PROV_SUBACTION_VERSION_PATTERN --- test/supplemental_genbank_tests/genbank_upload_full_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/supplemental_genbank_tests/genbank_upload_full_test.py b/test/supplemental_genbank_tests/genbank_upload_full_test.py index 7a55066e..6bd86625 100644 --- a/test/supplemental_genbank_tests/genbank_upload_full_test.py +++ b/test/supplemental_genbank_tests/genbank_upload_full_test.py @@ -20,7 +20,7 @@ _UPA_PATTERN = re.compile(r'^[0-9]+\/[0-9]+\/[0-9]$') _OBJECT_VERSION_PATTERN = re.compile(r'^[0-9]+\/[0-9]+\/1$') -_PROV_SUBACTION_VERSION_PATTERN = re.compile(r'^\d+\.\d+\.\d+-(release|beta)$') +_PROV_SUBACTION_VERSION_PATTERN = re.compile(r'^\d+\.\d+\.\d+-(release|beta|dev)$') class GenomeFileUtilTest(unittest.TestCase): @classmethod From ab4923a6d838a5293f6c3aa567a1e0745d3a0265 Mon Sep 17 00:00:00 2001 From: Sijie Date: Mon, 29 Jul 2024 18:30:28 -0700 Subject: [PATCH 09/10] revert service version back to release --- lib/installed_clients/GenomeAnnotationAPIClient.py | 2 +- lib/installed_clients/WSLargeDataIOClient.py | 2 +- test/supplemental_genbank_tests/genbank_upload_full_test.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/installed_clients/GenomeAnnotationAPIClient.py b/lib/installed_clients/GenomeAnnotationAPIClient.py index 08ccd9a5..44f92b82 100644 --- a/lib/installed_clients/GenomeAnnotationAPIClient.py +++ b/lib/installed_clients/GenomeAnnotationAPIClient.py @@ -24,7 +24,7 @@ def __init__( password=None, token=None, ignore_authrc=False, trust_all_ssl_certificates=False, auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', - service_ver='dev', + service_ver='release', async_job_check_time_ms=100, async_job_check_time_scale_percent=150, async_job_check_max_time_ms=300000): if url is None: diff --git a/lib/installed_clients/WSLargeDataIOClient.py b/lib/installed_clients/WSLargeDataIOClient.py index 8ae85be4..2b571378 100644 --- a/lib/installed_clients/WSLargeDataIOClient.py +++ b/lib/installed_clients/WSLargeDataIOClient.py @@ -24,7 +24,7 @@ def __init__( password=None, token=None, ignore_authrc=False, trust_all_ssl_certificates=False, auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', - service_ver='dev', + service_ver='release', async_job_check_time_ms=100, async_job_check_time_scale_percent=150, async_job_check_max_time_ms=300000): if url is None: diff --git a/test/supplemental_genbank_tests/genbank_upload_full_test.py b/test/supplemental_genbank_tests/genbank_upload_full_test.py index 6bd86625..7a55066e 100644 --- a/test/supplemental_genbank_tests/genbank_upload_full_test.py +++ b/test/supplemental_genbank_tests/genbank_upload_full_test.py @@ -20,7 +20,7 @@ _UPA_PATTERN = re.compile(r'^[0-9]+\/[0-9]+\/[0-9]$') _OBJECT_VERSION_PATTERN = re.compile(r'^[0-9]+\/[0-9]+\/1$') -_PROV_SUBACTION_VERSION_PATTERN = re.compile(r'^\d+\.\d+\.\d+-(release|beta|dev)$') +_PROV_SUBACTION_VERSION_PATTERN = re.compile(r'^\d+\.\d+\.\d+-(release|beta)$') class GenomeFileUtilTest(unittest.TestCase): @classmethod From 674cb8f30907b1f7ba63515e27bf39f96d6f46a3 Mon Sep 17 00:00:00 2001 From: Sijie Date: Mon, 29 Jul 2024 18:31:41 -0700 Subject: [PATCH 10/10] revert service version --- lib/installed_clients/WSLargeDataIOClient.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/installed_clients/WSLargeDataIOClient.py b/lib/installed_clients/WSLargeDataIOClient.py index 2b571378..c185bfee 100644 --- a/lib/installed_clients/WSLargeDataIOClient.py +++ b/lib/installed_clients/WSLargeDataIOClient.py @@ -24,7 +24,7 @@ def __init__( password=None, token=None, ignore_authrc=False, trust_all_ssl_certificates=False, auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', - service_ver='release', + service_ver='beta', async_job_check_time_ms=100, async_job_check_time_scale_percent=150, async_job_check_max_time_ms=300000): if url is None: