black spm_parser

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+-   repo: https://github.com/python/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.7

bids_prov/spm_parser.py

@@ -1,24 +1,20 @@
-import os
 import sys
 import click
 import json
 import re
 
 from collections import defaultdict
-import pyld as ld
-import warnings
-
-dir_path = os.path.dirname(os.path.realpath(__file__))
 
 import random
 import string
 
-get_id = lambda : ''.join(random.choice(string.ascii_letters) for i in range(10))
+get_id = lambda: "".join(random.choice(string.ascii_letters) for i in range(10))
+
 
 def realines(filename):
     with open(filename) as fd:
         for line in fd:
-            if line.startswith('matlabbatch'):
+            if line.startswith("matlabbatch"):
                 yield line[:-1]  # remove "\n"
 
 
@@ -27,56 +23,55 @@ def group_lines(lines):
     key = lambda line: re.finditer(r"\{\d+\}", line)
     for line in lines:
         a = next(re.finditer(r"\{\d+\}", line), None)
-        b = line.split('.')[2]
+        b = line.split(".")[2]
         if a and b:
             g = a.group()
             k = (b, g)
-            res[k].append(line[len(f"matlabbatch{g}."):])
+            res[k].append(line[len(f"matlabbatch{g}.") :])
 
     return dict(res)
 
+
 def get_records(task_groups, records=defaultdict(list)):
     entities_ids = set()
     for _, values in task_groups.items():
-        activity_name = ''.join(_)
+        activity_name = "".join(_)
         activity_id = "niiri:" + activity_name + get_id()
         activity = {
-            "@id" : activity_id,
-            "label" : ''.join(activity_name),
+            "@id": activity_id,
+            "label": "".join(activity_name),
         }
         # TODO : add time to activity
-        #import pdb; pdb.set_trace()
+        # import pdb; pdb.set_trace()
         used = list()
         entities = []
         for v in values:
-            entity_split = v.split(' = ')
+            entity_split = v.split(" = ")
             if len(entity_split) == 2:
                 left, right = entity_split
-                entity_label = left.split('/')[-1].split('.')[0]
+                entity_label = left.split("/")[-1].split(".")[0]
                 entity = {
-                    "@id" : "niiri:" + entity_label + get_id(),
-                    "label": entity_label,   
+                    "@id": "niiri:" + entity_label + get_id(),
+                    "label": entity_label,
                     "prov:atLocation": right[2:-3],
                     "wasGeneratedBy": activity_id,
                 }
 
                 entities.append(entity)
 
-        activity['used'] = [e["@id"] for e in entities]
+        activity["used"] = [e["@id"] for e in entities]
         records["prov:Activity"].append(activity)
         for e in entities:
             if e["@id"] not in entities_ids:
                 records["prov:Entity"].append(e)
             entities_ids.add(e["@id"])
 
-
     return records
 
 
-
 @click.command()
-@click.argument('filenames', nargs=-1)
-@click.option('--output-file', '-o', required=True)
+@click.argument("filenames", nargs=-1)
+@click.option("--output-file", "-o", required=True)
 def spm_to_bids_prov(filenames, output_file):
     filename = filenames[0]  # FIXME
 
@@ -91,30 +86,30 @@ def spm_to_bids_prov(filenames, output_file):
             "wasAssociatedWith": {
                 "@id": "NIH",
                 "@type": "Organization",
-                "hadRole": "Funding"
-            }
+                "hadRole": "Funding",
+            },
         },
         "records": {
-            "prov:Agent": [{
-                "@id": "RRID:SCR_007037",  # TODO query for version
-                "@type": "prov:SoftwareAgent",
-                "label": "SPM"
-            }],
+            "prov:Agent": [
+                {
+                    "@id": "RRID:SCR_007037",  # TODO query for version
+                    "@type": "prov:SoftwareAgent",
+                    "label": "SPM",
+                }
+            ],
             "prov:Activity": [],
             "prov:Entity": [],
-        }
+        },
     }
 
     lines = realines(filename)
     tasks = group_lines(lines)
     records = get_records(tasks)
     graph["records"].update(records)
 
-    with open(output_file, 'w') as fd:
+    with open(output_file, "w") as fd:
         json.dump(graph, fd, indent=2)
 
-
-
 
-if __name__ == '__main__':
-    sys.exit(spm_to_bids_prov())
+if __name__ == "__main__":
+    sys.exit(spm_to_bids_prov())

dev-requirements.txt

@@ -0,0 +1,2 @@
+black
+pre-commit