Black formatting

Author: tmorrell

caltechdata_api/cli.py

@@ -360,7 +360,9 @@ def create_record():
                         existing_data, token, production=False, publish=False
                     )
                 rec_id = response
-                print(f'You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}')
+                print(
+                    f"You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}"
+                )
                 break
             else:
                 print("Going back to the main menu.")
@@ -421,7 +423,9 @@ def create_record():
                         metadata, token, production=False, publish=False
                     )
                 rec_id = response
-                print(f'You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}')
+                print(
+                    f"You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}"
+                )
                 with open(response + ".json", "w") as file:
                     json.dump(metadata, file, indent=2)
                 break
@@ -434,15 +438,15 @@ def create_record():
 def edit_record():
     record_id = input("Enter the CaltechDATA record ID: ")
     token = get_or_set_token()
-    file_name = download_file_by_id(record_id,token)
+    file_name = download_file_by_id(record_id, token)
     if file_name:
         try:
             # Read the edited metadata file
             with open(file_name, "r") as file:
                 metadata = json.load(file)
             response = caltechdata_edit(
-                    record_id, metadata, token, production=False, publish=False
-                )
+                record_id, metadata, token, production=False, publish=False
+            )
             if response:
                 print("Metadata edited successfully.")
             else:
@@ -469,12 +473,14 @@ def edit_record():
                 publish=False,
             )
         rec_id = response
-        print(f'You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}')
+        print(
+            f"You can view and publish this record at https://data.caltechlibrary.dev/uploads/{rec_id}"
+        )
 
 
-def download_file_by_id(record_id,token=None):
+def download_file_by_id(record_id, token=None):
     url = f"https://data.caltechlibrary.dev/api/records/{record_id}"
-    
+
     headers = {
         "accept": "application/vnd.datacite.datacite+json",
     }
@@ -483,12 +489,12 @@ def download_file_by_id(record_id,token=None):
         headers["Authorization"] = "Bearer %s" % token
 
     try:
-        response = requests.get(url,headers=headers)
+        response = requests.get(url, headers=headers)
         if response.status_code != 200:
             # Might have a draft
             response = requests.get(
-            url + "/draft",
-            headers=headers,
+                url + "/draft",
+                headers=headers,
             )
             if response.status_code != 200:
                 raise Exception(f"Record {record_id} does not exist, cannot edit")

caltechdata_api/md_to_json.py

@@ -16,13 +16,19 @@ def camel_case(s):
 def expand_special_keys(key, value):
     """Expand special keys into their structured format (affiliation, nameIdentifiers)."""
     if key == "affiliation":
-        if 'ror.org' not in value:
-            raise ValueError('Affiliation Identifier is not a ROR')
-        ror = value.split('ror.org/')[1].split(']')[0]
-        response = requests.get(f'https://api.ror.org/organizations/{ror}').json()
-        return [{"affiliationIdentifier": ror, "affiliationIdentifierScheme": "ROR","name":response['name']}]
+        if "ror.org" not in value:
+            raise ValueError("Affiliation Identifier is not a ROR")
+        ror = value.split("ror.org/")[1].split("]")[0]
+        response = requests.get(f"https://api.ror.org/organizations/{ror}").json()
+        return [
+            {
+                "affiliationIdentifier": ror,
+                "affiliationIdentifierScheme": "ROR",
+                "name": response["name"],
+            }
+        ]
     elif key == "nameIdentifiers":
-        orcid = value.split('orcid.org/')[1].split(']')[0]
+        orcid = value.split("orcid.org/")[1].split("]")[0]
         return [
             {
                 "nameIdentifier": orcid,
@@ -44,10 +50,10 @@ def parse_readme_to_json(readme_path):
     current_object = {}
 
     title_line = lines.pop(0)
-    if title_line.startswith('#') == False:
+    if title_line.startswith("#") == False:
         raise ValueError('README.md needs to start with "# Title"')
     else:
-        json_data['titles'] = [{'title':title_line.replace("# ","")}]
+        json_data["titles"] = [{"title": title_line.replace("# ", "")}]
 
     section_pattern = re.compile(r"^##\s+(.*)$")
     key_value_pattern = re.compile(r"^-\s+(.*?):\s+(.*)$")
@@ -61,7 +67,7 @@ def parse_readme_to_json(readme_path):
                 elif len(current_object) == 1:
                     key, value = next(iter(current_object.items()))
                     if key in ["language", "publicationYear", "publisher", "version"]:
-                        json_data[current_section]=value
+                        json_data[current_section] = value
                     else:
                         json_data[current_section].append(current_object)
                 else:
@@ -120,7 +126,8 @@ def parse_readme_to_json(readme_path):
 
     return json_data
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     readme_path = "exampleREADME.md"
     try:
         json_data = parse_readme_to_json(readme_path)

process_tomograms.py

@@ -11,6 +11,7 @@
 # Set OpenAI API key from environment variable
 openai.api_key = os.getenv("OPENAI_API_KEY")
 
+
 # Function to parse collaborators using OpenAI API
 def parse_collaborators(collaborator_string):
     # Using OpenAI API to extract names and contributions
@@ -55,6 +56,7 @@ def parse_collaborators(collaborator_string):
                         formatted.append(new)
     return formatted
 
+
 # Function to create a description based on the metadata
 def create_detailed_description(information, annotation):
     keywords = []
@@ -142,6 +144,7 @@ def create_detailed_description(information, annotation):
             )
     return description, keywords
 
+
 # Function for processing files and extracting information
 def process_files(files, embargoed):
     formats = []
@@ -206,6 +209,7 @@ def process_files(files, embargoed):
         default_preview,
     )
 
+
 # List of funding resources
 funding = [
     {"funderName": "NIH"},
@@ -228,6 +232,7 @@ def process_files(files, embargoed):
     },
 ]
 
+
 # Function for processing a single tomogram record
 def process_record(source, edit=None):
     # Extract information from the record
@@ -414,6 +419,7 @@ def process_record(source, edit=None):
             except FileNotFoundError:
                 print("Not deleting remaned files")
 
+
 # Read record IDs from a file
 with open("tomogram_ids.json", "r") as infile:
     record_ids = json.load(infile)

setup.py

@@ -67,7 +67,7 @@ def package_files(package, directory):
     "pyyaml",
     "s3fs",
     "configparser",
-    "awscli"
+    "awscli",
 ]
 
 # What packages are optional?