Merge pull request #142 from bcgsc/bugfix/SDEV-4041_gsc_report_fail_P…

…OG1650

Bugfix/sdev 4041 gsc report fail pog1650

.github/workflows/automerge_back_to_dev.yml

@@ -0,0 +1,52 @@
+# This will trigger when master branch gets updated, it will make a PR to develop
+name: Auto-pr-master-develop
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the develop branch
+  pull_request:
+    branches: [master]
+    types: [closed]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  merge-master-to-dev:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # If master pull request is merged
+    if: github.event.pull_request.merged == true
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+        with:
+          ref: develop
+
+      - name: Set Git config
+        run: |
+            git config --local user.email "[email protected]"
+            git config --local user.name "Github Actions"
+
+      - name: Reset master branch
+        run: |
+          git fetch origin master:master
+          git reset --hard master
+
+      - name: Read and set version
+        id: versioning
+        run: |
+          PACKAGE_VERSION=$(node -p "require('./package.json').version")
+          echo ::set-output name=tag::${PACKAGE_VERSION}
+
+      - name: Create Pull Request
+        uses: peter-evans/[email protected]
+        with:
+          branch: merge-master-to-dev-${{ steps.versioning.outputs.tag }}
+          title: update develop from master-${{ steps.versioning.outputs.tag }}
+          commit-message: auto PR master to develop

ipr/connection.py

@@ -116,4 +116,4 @@ def get_spec(self) -> Dict:
         """
         Get the current IPR spec, for the purposes of current report upload fields
         """
-        return self.request(f'/spec.json', method='GET')
+        return self.request('/spec.json', method='GET')

ipr/main.py

@@ -35,10 +35,15 @@
 )
 from .summary import summarize
 from .therapeutic_options import create_therapeutic_options
-from .types import IprVariant, KbMatch, IprGene
+from .types import IprVariant, KbMatch
 from .util import LOG_LEVELS, logger, trim_empty_values
 
 CACHE_GENE_MINIMUM = 5000
+RENAMED_GENE_PROPERTIES = {
+    # old_name: new_name
+    'cancerRelated': 'kbStatementRelated',
+    'cancerGene': 'cancerGeneListMatch',
+}
 
 
 def file_path(path: str) -> str:
@@ -105,9 +110,9 @@ def command_interface() -> None:
     )
 
 
-def clean_unsupported_content(upload_content: Dict, ipr_spec: json = {}) -> Dict:
-    """
-    Remove unsupported content. This content is either added to facilitate creation
+def clean_unsupported_content(upload_content: Dict, ipr_spec: Dict = {}) -> Dict:
+    """Remove unsupported content.
+    This content is either added to facilitate creation
     or to support upcoming and soon to be supported content that we would like
     to implement but is not yet supported by the upload
     """
@@ -121,30 +126,39 @@ def clean_unsupported_content(upload_content: Dict, ipr_spec: json = {}) -> Dict
         genes_spec = ipr_spec['components']['schemas']['genesCreate']['properties'].keys()
 
         # check what ipr report upload expects and adjust contents to match
-        # TODO: remove this code after IPR-API is released with DEVSU-2143
-        if 'cancerRelated' in genes_spec:
-            for gene in upload_content['genes']:
-                logger.warning(
-                    f"Renamed property 'kbStatementRelated' to 'cancerRelated' for upload in gene {gene['name']}"
-                )
-                gene['cancerRelated'] = gene['kbStatementRelated']
-                gene.pop('kbStatementRelated')
-        if 'cancerGene' in genes_spec:
-            for gene in upload_content['genes']:
+        for old_name, new_name in RENAMED_GENE_PROPERTIES.items():
+            if old_name in genes_spec:
                 logger.warning(
-                    f"Renamed property 'cancerGeneListMatch' to 'cancerGene' for upload in gene {gene['name']}"
+                    f"Legacy IPR - Renaming property {new_name} to {old_name} for compatibility to ipr_spec"
                 )
-                gene['cancerGene'] = gene['cancerGeneListMatch']
-                gene.pop('cancerGeneListMatch')
+                for gene in upload_content['genes']:
+                    if new_name in gene:
+                        gene[old_name] = gene[new_name]
+                        gene.pop(new_name)
+            else:
+                outdate_properties = 0
+                for gene in upload_content['genes']:
+                    if old_name in gene:
+                        gene[new_name] = gene[old_name]
+                        gene.pop(old_name)
+                        outdate_properties += 1
+                if outdate_properties:
+                    logger.warning(
+                        f"Renamed property {old_name} to {new_name} on {outdate_properties} genes for ipr_spec"
+                    )
 
         # remove any unhandled incompatible keys
-        ipr_gene_keys = IprGene.__required_keys__ | IprGene.__optional_keys__
-        unexpected_keys = [item for item in genes_spec if item not in ipr_gene_keys]
+        removed_keys: Dict[str, int] = {}
         for gene in upload_content['genes']:
-            for key in unexpected_keys:
-                if key in gene.keys():
-                    logger.warning(f"Unexpected property '{key}' removed from gene {gene['name']}")
-                    gene.pop(key)
+            unsupported_keys = [key for key in gene.keys() if key not in genes_spec]
+            for key in unsupported_keys:
+                if key in removed_keys:
+                    removed_keys[key] += 1
+                else:
+                    removed_keys[key] = 1
+                gene.pop(key)
+        for key, count in removed_keys.items():
+            logger.warning(f"IPR unsupported property '{key}' removed from {count} genes.")
 
     drop_columns = ['variant', 'variantType', 'histogramImage']
     # DEVSU-2034 - use a 'displayName'
@@ -375,25 +389,6 @@ def ipr_report(
     logger.info('fetching gene annotations')
     gene_information = get_gene_information(graphkb_conn, sorted(genes_with_variants))
 
-    # handle old and new column names coming in from GraphKB.
-    # TODO: remove this code when GraphKB is released with KBDEV-1136
-    def update_old_field_name(gene):
-        if 'cancerRelated' in gene.keys():
-            logger.warning(
-                f"Property 'kbStatementRelated' obtained as 'cancerRelated' in gene {gene['name']}"
-            )
-            gene['kbStatementRelated'] = gene['cancerRelated']
-            gene.pop('cancerRelated')
-        if 'cancerGene' in gene.keys():
-            logger.warning(
-                f"Property 'cancerGeneListMatch' obtained as 'cancerGene' in gene {gene['name']}"
-            )
-            gene['cancerGeneListMatch'] = gene['cancerGene']
-            gene.pop('cancerGene')
-        return gene
-
-    gene_information = [update_old_field_name(gene) for gene in gene_information]
-
     if generate_therapeutics:
         logger.info('generating therapeutic options')
         targets = create_therapeutic_options(graphkb_conn, gkb_matches, all_variants)

setup.cfg

@@ -18,7 +18,7 @@ known_standard_library = requests
 
 [metadata]
 name = ipr
-version = 3.12.1
+version = 3.12.2
 author_email = [email protected]
 author = ipr
 maintainer_email = [email protected]

tests/test_main.py

@@ -8,10 +8,19 @@
 
 from ipr.connection import IprConnection
 from ipr.main import command_interface
+from ipr.types import IprGene
 
 from .constants import EXCLUDE_INTEGRATION_TESTS
 
 
+def get_test_spec():
+    ipr_spec = {'components': {'schemas': {'genesCreate': {'properties': {}}}}}
+    ipr_gene_keys = IprGene.__required_keys__ | IprGene.__optional_keys__
+    for key in ipr_gene_keys:
+        ipr_spec['components']['schemas']['genesCreate']['properties'][key] = ""
+    return ipr_spec
+
+
 def get_test_file(name: str) -> str:
     return os.path.join(os.path.dirname(__file__), 'test_data', name)
 
@@ -65,7 +74,7 @@ def report_upload_content(tmp_path_factory) -> Dict:
         ],
     ):
         with patch.object(IprConnection, 'upload_report', new=mock):
-            with patch.object(IprConnection, 'get_spec', return_value={}):
+            with patch.object(IprConnection, 'get_spec', return_value=get_test_spec()):
                 command_interface()
 
     assert mock.called