Merge branch 'master' into enh/MEG_support

brainlife · Jan 18, 2024 · c6a0cc9 · c6a0cc9
2 parents befac12 + cc34072
commit c6a0cc9
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Showing 3 changed files with 19 additions and 14 deletions.
diff --git a/.prettierignore b/.prettierignore
@@ -1,2 +1,3 @@
+.vscode/settings.json
 node_modules
 ui/node_modules
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -7,5 +7,9 @@
     "[typescript]": {
         "editor.formatOnSave": true,
         "editor.defaultFormatter": "esbenp.prettier-vscode"
-    }
+    },
+    "flake8.args": [
+        "--max-line-length", "125",
+        "--extend-ignore", "E722"
+    ]
 }
diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py
@@ -941,13 +941,8 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
             age = "n/a"
             if "PatientAge" in json_data:
                 patient_age = json_data["PatientAge"]
-                if not patient_age.isalnum():  # if true, is alphanumeric, so not age
-                    try:
-                        # if age is over 100, probably made up
-                        if (isinstance(patient_age, int) or isinstance(patient_age, float)) and int(patient_age) < 100:
-                            age = patient_age
-                    except:
-                        pass
+                if (isinstance(patient_age, int) or isinstance(patient_age, float)):
+                    age = patient_age
 
             if age == "n/a" and "PatientBirthDate" in json_data:
                 patient_birth_date = json_data["PatientBirthDate"]  # ISO 8601 "YYYY-MM-DD"
@@ -1424,8 +1419,13 @@ def determine_sub_ses_IDs(dataset_list, bids_compliant):
         subject_ids_info = {
             "subject": sub,
             "PatientInfo": patient_info,
-            "phenotype": list({"species": x["PatientSpecies"], "sex": x["PatientSex"], "age": x["PatientAge"],
-                               "handedness": x["PatientHandedness"]} for x in sub_dics_list)[0],
+            "phenotype": list(
+                {
+                    "species": x["PatientSpecies"],
+                    "sex": x["PatientSex"],
+                    "age": x["PatientAge"],
+                    "handedness": x["PatientHandedness"]
+                } for x in sub_dics_list)[0],
             "exclude": False,
             "sessions": [
                 {k: v for k, v in d.items()
@@ -1671,11 +1671,11 @@ def template_configuration(dataset_list_unique_series, subjects_information, con
             unique_dic["finalized_match"] = True
             if "localizer" in ref_message:
                 unique_dic["message"] = "Datatype, suffix, and entity information was determined based on match "\
-                    "with corresponding data in ezBIDS configuration (ezBIDS_template.json) file. This data is believed to "\
-                    "be a localizer. Please modify if incorrect"
+                    "with corresponding data in ezBIDS configuration (ezBIDS_template.json) file. This data is "\
+                    "believe to be a localizer. Please modify if incorrect"
             else:
                 unique_dic["message"] = "Datatype, suffix, and entity information was determined based on match "\
-                    "with corresponding data in ezBIDS configuration (ezBIDS_template.json) file. Please modify if incorrect"
+                    "with corresponding data in ezBIDS configuration file. Please modify if incorrect"
 
             """
             If metadata information was added in, find it and add to the json file.
@@ -2259,7 +2259,7 @@ def datatype_suffix_identification(dataset_list_unique_series, lookup_dic, confi
                 if len(bids_guess) == 2:  # should always be length of 2, but just to be safe
                     datatype = str(bids_guess[0]).lower()  # in case BidsGuess doesn't make datatype lowercase
                     suffix = bids_guess[1].split("_")[-1]
-                    for bids_ref_suffix in suffixes_yaml:  # in case BidsGuess not use correct suffix case format (e.g PET)
+                    for bids_ref_suffix in suffixes_yaml:  # in case BidsGuess not use proper suffix case format (e.g PET)
                         if bids_ref_suffix != suffix and bids_ref_suffix.lower() == suffix.lower():
                             suffix = bids_ref_suffix
                     # Issue with BidsGuess and func/sbref identification