fix more tests

EBIvariation · Jul 9, 2024 · 9a044ed · 9a044ed
1 parent 2930ffa
commit 9a044ed
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Showing 5 changed files with 55 additions and 84 deletions.
diff --git a/bin/xlsx2json.py b/bin/xlsx2json.py
@@ -241,7 +241,7 @@ def get_sample_json_data(self):
         json_key = self.xlsx_conf[WORKSHEETS_KEY_NAME][SAMPLE]
         sample_json = {json_key: []}
         for row in self.get_rows():
-            row.pop('row_num')
+            row_num = row.pop('row_num')
             json_value = {self.translate_header(SAMPLE, k): v for k, v in row.items() if v is not None}
             bio_sample_acc = self.xlsx_conf[SAMPLE][OPTIONAL_HEADERS_KEY_NAME][SAMPLE_ACCESSION_KEY]
 
@@ -262,12 +262,12 @@ def get_sample_json_data(self):
                 if sample_name not in json_value:
                     self.add_error(f'If BioSample Accession is not provided, the {SAMPLE} worksheet should have '
                                    f'{SAMPLE_NAME_KEY} populated',
-                                   sheet=SAMPLE, column=SAMPLE_NAME_KEY)
+                                   sheet=SAMPLE, row=row_num, column=SAMPLE_NAME_KEY)
                     return None
                 if scientific_name not in json_value:
                     self.add_error(f'If BioSample Accession is not provided, the {SAMPLE} worksheet should have '
                                    f'{SCIENTIFIC_NAME_KEY} populated',
-                                   sheet=SAMPLE, column=SCIENTIFIC_NAME_KEY)
+                                   sheet=SAMPLE, row=row_num, column=SCIENTIFIC_NAME_KEY)
                     return None
 
                 biosample_obj = self.get_biosample_object(json_value)

diff --git a/eva_sub_cli/metadata_utils.py b/eva_sub_cli/metadata_utils.py
@@ -10,7 +10,8 @@ def get_samples_per_analysis(metadata):
     """Returns mapping of analysis alias to sample names, based on metadata."""
     samples_per_analysis = defaultdict(list)
     for sample_info in metadata.get('sample', []):
-        samples_per_analysis[sample_info.get('analysisAlias')].append(sample_info.get('sampleInVCF'))
+        for analysis_alias in sample_info.get('analysisAlias', []):
+            samples_per_analysis[analysis_alias].append(sample_info.get('sampleInVCF'))
     return {
         analysis_alias: set(samples)
         for analysis_alias, samples in samples_per_analysis.items()

diff --git a/tests/resources/EVA_Submission_test_with_asm_report.json b/tests/resources/EVA_Submission_test_with_asm_report.json
@@ -64,90 +64,73 @@
   ],
   "sample": [
     {
-      "analysisAlias": "VD1",
-      "sampleInVCF": "sample1",
-      "bioSampleAccession": "SAME00001"
-    },
-    {
-      "analysisAlias": "VD2",
-      "sampleInVCF": "sample1",
-      "bioSampleAccession": "SAME00001"
-    },
-    {
-      "analysisAlias": "VD3",
+      "analysisAlias": [
+        "VD1",
+        "VD2",
+        "VD3"
+      ],
       "sampleInVCF": "sample1",
       "bioSampleAccession": "SAME00001"
     },
     {
-      "analysisAlias": "VD1",
-      "sampleInVCF": "sample2",
-      "bioSampleAccession": "SAME00002"
-    },
-    {
-      "analysisAlias": "VD2",
+      "analysisAlias": [
+        "VD1",
+        "VD2",
+        "VD3"
+      ],
       "sampleInVCF": "sample2",
       "bioSampleAccession": "SAME00002"
     },
     {
-      "analysisAlias": "VD3",
-      "sampleInVCF": "sample2",
-      "bioSampleAccession": "SAME00002"
-    },
-    {
-      "analysisAlias": "VD3",
+      "analysisAlias": [
+        "VD3"
+      ],
       "sampleInVCF": "sample3",
       "bioSampleAccession": "SAME00003"
     },
     {
-      "analysisAlias": "VD4",
+      "analysisAlias": [
+        "VD4",
+        "VD5"
+      ],
       "sampleInVCF": "sample4",
       "bioSampleObject": {
         "name": "Lm_17_S8",
         "characteristics": {
-          "bioSampleName": "Lm_17_S8",
           "title": [
-            "Bastet normal sample"
+            {
+              "text": "Bastet normal sample"
+            }
           ],
           "description": [
-            "Test Description"
+            {
+              "text": "Test Description"
+            }
           ],
           "taxId": [
-            9447
+            {
+              "text": "9447"
+            }
           ],
           "scientificName": [
-            "Lemur catta"
+            {
+              "text": "Lemur catta"
+            }
           ],
-          "sex": "Female",
-          "tissueType": "skin",
-          "species": [
-            "Lemur catta"
-          ]
-        }
-      }
-    },
-    {
-      "analysisAlias": "VD5",
-      "sampleInVCF": "sample4",
-      "bioSampleObject": {
-        "name": "Lm_17_S8",
-        "characteristics": {
-          "bioSampleName": "Lm_17_S8",
-          "title": [
-            "Bastet normal sample"
+          "sex": [
+            {
+              "text": "Female"
+            }
           ],
-          "description": [
-            "Test Description"
-          ],
-          "taxId": [
-            9447
-          ],
-          "scientificName": [
-            "Lemur catta"
+          "tissueType": [
+            {
+              "text": "skin"
+            }
           ],
-          "sex": "Female",
-          "tissueType": "skin",
           "species": [
-            "Lemur catta"
+            {
+              "text": "Lemur catta"
+            }
           ]
         }
       }

diff --git a/tests/resources/sample_checker/metadata.json b/tests/resources/sample_checker/metadata.json
@@ -23,37 +23,17 @@
   },
   "sample": [
     {
-      "analysisAlias":  "VD1",
+      "analysisAlias":  ["VD1", "VD2", "VD3"],
       "sampleInVCF":  "sample1",
       "BioSampleAccession": "SAME00001"
     },
     {
-      "analysisAlias":  "VD1",
+      "analysisAlias":  ["VD1", "VD2", "VD3"],
       "sampleInVCF":  "sample2",
       "BioSampleAccession": "SAME00002"
     },
     {
-      "analysisAlias":  "VD2",
-      "sampleInVCF":  "sample1",
-      "BioSampleAccession": "SAME00001"
-    },
-    {
-      "analysisAlias":  "VD2",
-      "sampleInVCF":  "sample2",
-      "BioSampleAccession": "SAME00002"
-    },
-    {
-      "analysisAlias":  "VD3",
-      "sampleInVCF":  "sample1",
-      "BioSampleAccession": "SAME00001"
-    },
-    {
-      "analysisAlias":  "VD3",
-      "sampleInVCF":  "sample2",
-      "BioSampleAccession": "SAME00002"
-    },
-    {
-      "analysisAlias":  "VD3",
+      "analysisAlias":  ["VD3"],
       "sampleInVCF":  "sample3",
       "BioSampleAccession": "SAME00003"
     }

diff --git a/tests/test_xlsx2json.py b/tests/test_xlsx2json.py
@@ -29,7 +29,14 @@ def test_conversion_2_json(self) -> None:
         xls_filename = os.path.join(self.resource_dir, 'EVA_Submission_test.xlsx')
         self.parser = XlsxParser(xls_filename, self.conf_filename)
         output_json = os.path.join(self.resource_dir, 'EVA_Submission_test_output.json')
+        errors_yaml = os.path.join(self.resource_dir, 'EVA_Submission_test_errors.yml')
         self.parser.json(output_json)
+        self.parser.save_errors(errors_yaml)
+
+        # confirm no errors
+        with open(errors_yaml) as open_file:
+            errors_data = yaml.safe_load(open_file)
+            assert errors_data == []
 
         with open(output_json) as open_file:
             json_data = json.load(open_file)