small update: only include 'empty' report when no other reports are s…

…pecified
uio-bmi · Nov 8, 2023 · ab27ec5 · ab27ec5
1 parent 6e90ce1
commit ab27ec5
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Showing 2 changed files with 9 additions and 10 deletions.
diff --git a/immuneML/api/galaxy/build_dataset_overview_yaml.py b/immuneML/api/galaxy/build_dataset_overview_yaml.py
@@ -27,10 +27,7 @@ def build_specs(args):
         "instructions": {
             "my_dataset_generation_instruction": {
                 "type": "ExploratoryAnalysis",
-                "analyses":{
-                    "dataset_overview":{
-                        "dataset": args.dataset_name,
-                        "report": None}}
+                "analyses": dict()
             }
         }
     }
@@ -53,6 +50,9 @@ def build_specs(args):
     if args.amino_acid_report == "True":
         add_report_with_label(specs, args, report_name="AminoAcidFrequencyDistribution", report_key="amino_acid")
 
+    if len(specs["instructions"]["my_dataset_generation_instruction"]["analyses"]) == 0:
+        specs["instructions"]["my_dataset_generation_instruction"]["analyses"] = {"dataset_overview":{"dataset": args.dataset_name, "report": None}}
+
     return specs
 
 

diff --git a/test/api/galaxy/test_build_dataset_overview_yaml.py b/test/api/galaxy/test_build_dataset_overview_yaml.py
@@ -67,9 +67,6 @@ def test_sequencedataset(self):
             self.assertDictEqual(loaded_specs["instructions"], {"my_dataset_generation_instruction": {
                                                                      "type":"ExploratoryAnalysis",
                                                                      "analyses":{
-                                                                         "dataset_overview":
-                                                                              {"dataset": "dataset",
-                                                                               "report": None},
                                                                          "sequence_length_analysis":
                                                                               {"dataset": "dataset",
                                                                                "report": "sequence_length_report"},
@@ -126,7 +123,7 @@ def test_repertoiredataset(self):
 
         os.chdir(path)
 
-        yamlbuilder_main(["-r", "VDJdb", "-o", str(path), "-f", "repertoire.yaml", "-m", "metadata.csv", "-i", "True"])
+        yamlbuilder_main(["-r", "VDJdb", "-o", str(path), "-f", "repertoire.yaml", "-m", "metadata.csv", "-i", "True", "-q", "True"])
 
         with open(path / "repertoire.yaml", "r") as file:
             loaded_specs = yaml.load(file, Loader=yaml.FullLoader)
@@ -135,12 +132,14 @@ def test_repertoiredataset(self):
                 {"path": "./", "metadata_file": "metadata.csv", "is_repertoire": True, "region_type": RegionType.IMGT_CDR3.name,
                  "result_path": "./"}}})
 
+            self.assertDictEqual(loaded_specs["definitions"]["reports"], {"amino_acid_report": "AminoAcidFrequencyDistribution"})
+
             self.assertDictEqual(loaded_specs["instructions"], {"my_dataset_generation_instruction":
                                                                     {"type": "ExploratoryAnalysis",
                                                                      "analyses":
-                                                                         {"dataset_overview":
+                                                                         {"amino_acid_analysis":
                                                                               {"dataset": "dataset",
-                                                                               "report": None}}}})
+                                                                               "report": "amino_acid_report"}}}})
 
         ImmuneMLParser.parse_yaml_file(path / "repertoire.yaml")