Merge pull request #1529 from BRCAChallenge/fix_circleci

Fix circleci
BRCAChallenge · Nov 28, 2024 · 2881cea · 2881cea
2 parents 8e32b3a + ede8d0e
commit 2881cea
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Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/pipeline/clinvar/clinvar_common.py b/pipeline/clinvar/clinvar_common.py
@@ -41,13 +41,17 @@ def findUniqueElement(name, parent):
     return(child)
 
 
-
-#def build_xpath_filter_for_cv_assertions(gene_symbols):
-##    symbols_str = [ f'text()="{s}"' for s in gene_symbols] ### HERE
-#    symbols_pred = ' or '.join(symbols_str)
+#
+# This function is outdated (11/25/2024), but is currently part of an
+# ENIGMA unit test
+#
+def build_xpath_filter_for_cv_assertions(gene_symbols):
+    symbols_str = [ f'text()="{s}"' for s in gene_symbols] ### HERE
+    symbols_pred = ' or '.join(symbols_str)
 
     # filter assertion if it contains a Symbol we are interested in
-#    return f"ReferenceClinVarAssertion/MeasureSet/Measure/MeasureRelationship/Symbol/ElementValue[({symbols_pred}) and @Type=\"Preferred\"]"
+    return f"ReferenceClinVarAssertion/MeasureSet/Measure/MeasureRelationship/Symbol/ElementValue[({symbols_pred}) and @Type=\"Preferred\"]"
+
 
 def extractSynonyms(el):
     include_types = {'ProteinChange3LetterCode', 'ProteinChange1LetterCode',
@@ -89,9 +93,9 @@ def extract_genomic_coordinates_from_location(loc):
             )
     # if no reference/alternate allele found, compute (assuming genomic coordinates
     # are either present for all assemblies or for none)
-    #if not coords:
-    #    coords = _extract_genomic_coordinates_from_non_genomic_fields(meas_el)
-    return coords
+#    if not coords:
+#        coords = _extract_genomic_coordinates_from_non_genomic_fields(meas_el)
+#    return coords
 
 
 def _preprocess_element_value(var_str):

diff --git a/pipeline/clinvar/test_clinvar.py b/pipeline/clinvar/test_clinvar.py
@@ -17,7 +17,7 @@ def test_simple_genomic_coordinate_extraction():
       </Location>
     """
 
-    measure_el = ET.fromstring(sample_measure)
+    location_el = ET.fromstring(sample_location)
 
     genomic_coords = clinvar_common.extract_genomic_coordinates_from_location(location_el)
 
@@ -34,7 +34,7 @@ def test_genomic_coordinate_extraction_from_NM():
     """
     measure_el = ET.fromstring(sample_measure)
 
-    genomic_coords = clinvar_common.extract_genomic_coordinates_from_measure(measure_el)
+    genomic_coords = clinvar_common._extract_genomic_coordinates_from_non_genomic_fields(measure_el)
 
     assert genomic_coords[hgvs_utils.HgvsWrapper.GRCh38_Assem] == variant_utils.VCFVariant(13, 32340945, "CTG", "C")