run black

any2eln/__main__.py

@@ -14,13 +14,14 @@ def main():
     parser.add_argument('--out_dir', required=False, help='output directory', default='.')
     args = parser.parse_args()
 
-    if (args.src == 'labfolder'):
+    if args.src == 'labfolder':
         username = env_or_ask('LABFOLDER_USERNAME', 'Your Labfolder username or email: ')
         password = env_or_ask('LABFOLDER_PASSWORD', 'Your Labfolder password: ')
         lf = Labfolder(username, password, out_dir=args.out_dir)
         lf.extract()
     else:
         print('Not implemented.')
 
+
 if __name__ == "__main__":
     main()

any2eln/labfolder/labfolder.py

@@ -25,7 +25,7 @@
 
 
 class Labfolder:
-    def __init__(self, username: str, password: str, out_dir = '.'):
+    def __init__(self, username: str, password: str, out_dir='.'):
         self.username = username
         self.password = password
         self.token = self.__get_token()
@@ -205,7 +205,9 @@ def extract(self) -> Path:
                                 # save the full json
                                 with entry_folder.joinpath(f"{json_metadata['id']}").open('w') as json_file:
                                     json.dump(json_metadata, json_file, indent=2)
-                                node['sha256'] = hashlib.sha256(json.dumps(json_metadata, indent=2).encode()).hexdigest()
+                                node['sha256'] = hashlib.sha256(
+                                    json.dumps(json_metadata, indent=2).encode()
+                                ).hexdigest()
                                 crate_metadata['@graph'].append(node)
                                 files.append(node['@id'])
 
@@ -230,7 +232,9 @@ def extract(self) -> Path:
                                 node = self.__get_node_from_metadata(json_metadata, entry_folder)
                                 with entry_folder.joinpath(f"{json_metadata['id']}").open('w') as json_file:
                                     json.dump(json_metadata, json_file, indent=2)
-                                node['sha256'] = hashlib.sha256(json.dumps(json_metadata, indent=2).encode()).hexdigest()
+                                node['sha256'] = hashlib.sha256(
+                                    json.dumps(json_metadata, indent=2).encode()
+                                ).hexdigest()
                                 crate_metadata['@graph'].append(node)
                                 files.append(node['@id'])
 
@@ -290,18 +294,19 @@ def extract(self) -> Path:
     def __get_links_script(self) -> str:
         lines = []
         for category in self.categories:
-            lines.append(f"""
+            lines.append(
+                f"""
 INSERT INTO experiments_links (item_id, link_id)
 SELECT
   experiments.id,
   (SELECT items.id FROM items WHERE title = "{category}" LIMIT 1)
 FROM experiments
 LEFT JOIN tags2entity ON tags2entity.item_id = experiments.id AND tags2entity.item_type = 'experiments'
 LEFT JOIN tags ON tags2entity.tag_id = tags.id
-WHERE tags.tag = "{category}";""")
+WHERE tags.tag = "{category}";"""
+            )
         return '\n'.join(lines)
 
-
     def __get_project_script(self) -> str:
         header = """#!/usr/bin/env python
 import elabapi_python
@@ -348,7 +353,7 @@ def __get_dataset_node(self, entry: dict[str, Any], content: list[str], files: l
             self.categories.append(project_title)
         node['keywords'] = ','.join(entry.get('tags', []))
         # use this to create a Category with the Project title
-        #node['category'] = entry.get('project', {}).get('title', {})
+        # node['category'] = entry.get('project', {}).get('title', {})
         node['dateCreated'] = entry['creation_date']
         node['dateModified'] = entry['version_date']
         node['hasPart'] = [{'@id': file} for file in files]
@@ -402,7 +407,7 @@ def __get_csvs_from_json(self, json_metadata: dict[str, Any]) -> list[tuple[str,
                 debug('Skipping csv that has no dataTable in data:')
                 debug(json.dumps(json_metadata, indent=2))
                 continue
-            #column_names = [str(table_data['0'][str(i)].get('value', '')) for i in range(len(table_data['0']))]
+            # column_names = [str(table_data['0'][str(i)].get('value', '')) for i in range(len(table_data['0']))]
             rows = []
             for key, values in table_data.items():
                 row = {}
@@ -413,7 +418,7 @@ def __get_csvs_from_json(self, json_metadata: dict[str, Any]) -> list[tuple[str,
             # Create DataFrame from the list of dictionaries
             df = pd.DataFrame(rows)
             # drop first row
-            #df = df.drop(0)
+            # df = df.drop(0)
             # None as first arg will return the csv as string instead of writing a file
             csvs.append((sheet_name + '.csv', df.to_csv(None, index=False)))
         return csvs

any2eln/utils/rocrate.py

@@ -5,6 +5,7 @@
 from datetime import datetime
 from typing import Any
 
+
 def get_crate_metadata() -> dict[str, Any]:
     crate_metadata: dict[str, Any] = {}
     crate_metadata['@context'] = 'https://w3id.org/ro/crate/1.1/context'