More ruff

libraries/client/biomodels_info.py

@@ -2,20 +2,15 @@
 Script to get Biomodels project info
 """
 
-import sys
 import json
-
-import osb
-import operator
 import pprint
+from loadbiomodels import get_model_identifiers, get_model_info
 
 verbose = True  #
 verbose = False
 
 info_all = {}
 
-from loadbiomodels import get_model_identifiers, get_model_info
-
 
 if __name__ == "__main__":
     min_index = 0

libraries/client/cached_info/osb_gh.json

@@ -209517,8 +209517,8 @@
         "name": "OSBv2",
         "node_id": "MDEwOlJlcG9zaXRvcnkyNDMzMTY0MTM=",
         "notifications_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/notifications{?since,all,participating}",
-        "open_issues": 130,
-        "open_issues_count": 130,
+        "open_issues": 129,
+        "open_issues_count": 129,
         "owner": {
             "avatar_url": "https://avatars.githubusercontent.com/u/1565478?v=4",
             "events_url": "https://api.github.com/users/OpenSourceBrain/events{/privacy}",
@@ -209549,9 +209549,9 @@
         },
         "private": false,
         "pulls_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/pulls{/number}",
-        "pushed_at": "2025-01-09T14:17:02Z",
+        "pushed_at": "2025-01-22T10:32:09Z",
         "releases_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/releases{/id}",
-        "size": 47905,
+        "size": 48835,
         "ssh_url": "[email protected]:OpenSourceBrain/OSBv2.git",
         "stargazers_count": 12,
         "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/stargazers",
@@ -211069,8 +211069,8 @@
         "name": "SBMLShowcase",
         "node_id": "MDEwOlJlcG9zaXRvcnk5ODMzNTU3",
         "notifications_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/notifications{?since,all,participating}",
-        "open_issues": 11,
-        "open_issues_count": 11,
+        "open_issues": 10,
+        "open_issues_count": 10,
         "owner": {
             "avatar_url": "https://avatars.githubusercontent.com/u/1565478?v=4",
             "events_url": "https://api.github.com/users/OpenSourceBrain/events{/privacy}",
@@ -211101,9 +211101,9 @@
         },
         "private": false,
         "pulls_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/pulls{/number}",
-        "pushed_at": "2025-01-21T16:15:51Z",
+        "pushed_at": "2025-01-22T10:44:21Z",
         "releases_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/releases{/id}",
-        "size": 2048,
+        "size": 2049,
         "ssh_url": "[email protected]:OpenSourceBrain/SBMLShowcase.git",
         "stargazers_count": 1,
         "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/stargazers",

libraries/client/info_all.sh

@@ -3,6 +3,9 @@ set -ex
 
 ## A script to refresh all the cached info json files
 
+ruff format *.py
+ruff check  *.py
+
 python osbv1_info.py
 
 python osb_info.py

libraries/client/loadbiomodels.py

@@ -50,9 +50,11 @@ def main():
             if "BIOMD" in model_id:
                 model_link = f"[{model_id}](https://www.ebi.ac.uk/biomodels/{model_id})"
                 info = get_model_info(model_id)
-                model_name = info["name"]
+                # model_name = info["name"]
                 print("\n===============================================")
-                print(f"  {model_id}: \n{pprint.pprint(info['name'])}--")
+                print(
+                    f"  {model_id} ({model_link}): \n{pprint.pformat(info['name'])}--"
+                )
                 count += 1
 
 

libraries/client/loadddandi.py

@@ -6,14 +6,13 @@
 import logging
 import json
 import sys
+import csv
 
 from utils import get_tags_info
 from utils import known_users, lookup_user
 
 from workspaces_cli.models import (
     OSBRepository,
-    RepositoryType,
-    Tag,
     RepositoryContentType,
 )
 # Defining the host is optional and defaults to http://localhost/api
@@ -76,7 +75,6 @@
 dandishowcase_csv_url = "https://raw.githubusercontent.com/OpenSourceBrain/DANDIArchiveShowcase/main/validation_folder/dandiset_summary.csv"
 response = urlopen(dandishowcase_csv_url)
 
-import csv
 
 dandishowcase_info_reader = csv.DictReader(codecs.iterdecode(response, "utf-8"))
 dandishowcase_info = list(dandishowcase_info_reader)
@@ -104,7 +102,7 @@ def add_dandiset(dandishowcase_entry, index):
             dandi_api_info = api_instance.get_info(
                 uri=dandiset_url, repository_type="dandi"
             )
-        except:
+        except Exception:
             but_ok = (
                 " (known to be missing...)"
                 if dandiset_url in known_missing_dandisets
@@ -159,7 +157,7 @@ def add_dandiset(dandishowcase_entry, index):
                     "    %s already exists (owner: %s); updating..."
                     % (dandiset_url, lookup_user(r.user_id, url_info))
                 )
-            except:
+            except Exception:
                 exit(-1)
             print(url_info)
             all_updated.append(url_info)
@@ -236,7 +234,7 @@ def add_dandiset(dandishowcase_entry, index):
                 continue
             try:
                 added = add_dandiset(dandishowcase_entry, index)
-            except Exception as e:
+            except Exception:
                 logging.exception(
                     "Error adding/updating %s" % dandishowcase_entry["url"]
                 )

libraries/client/loadmodeldb.py

@@ -1,5 +1,3 @@
-from urllib.request import urlopen
-import codecs
 import workspaces_cli
 from pprint import pprint
 from workspaces_cli.api import rest_api, k8s_api
@@ -12,8 +10,6 @@
 
 from workspaces_cli.models import (
     OSBRepository,
-    RepositoryType,
-    Tag,
     RepositoryContentType,
 )
 # Defining the host is optional and defaults to http://localhost/api
@@ -82,7 +78,7 @@
 
     def add_modeldb_model(modeldb_model, index):
         modeldb_model_id = modeldb_model["id"]
-        if not "osbv2_gh_repo" in modeldb_model or not modeldb_model["osbv2_gh_repo"]:
+        if "osbv2_gh_repo" not in modeldb_model or not modeldb_model["osbv2_gh_repo"]:
             all_errors.append(
                 "  %i, %s (%s) doesn't have a Github repo..."
                 % (index, modeldb_model["name"], modeldb_model_id)
@@ -149,7 +145,7 @@ def add_modeldb_model(modeldb_model, index):
                     "    %s already exists (owner: %s); updating..."
                     % (modeldb_model_id, lookup_user(existing_repo.user_id, url_info))
                 )
-            except:
+            except Exception:
                 exit(-1)
             print(url_info)
             all_updated.append(url_info)
@@ -239,7 +235,7 @@ def add_modeldb_model(modeldb_model, index):
                 print("----------")
                 print("Error: %s" % str(e))
                 print("----------")
-                if not "context_resources" in str(e):
+                if "context_resources" not in str(e):
                     print("Exiting due to unknown error...")
                     exit()
                 else:

libraries/client/loadosbv1.py

@@ -1,23 +1,20 @@
-from urllib.request import urlopen
-import codecs
 import workspaces_cli
 from pprint import pprint
 from workspaces_cli.api import rest_api, k8s_api
 import logging
 import json
 import sys
+from workspaces_cli.models import (
+    OSBRepository,
+    RepositoryContentType,
+)
 
 from utils import get_tags_info
 from utils import known_users, lookup_user
 
 known_ignores = ["dentate", "nc_superdeep", "tvb_neuroml"]
 
-from workspaces_cli.models import (
-    OSBRepository,
-    RepositoryType,
-    Tag,
-    RepositoryContentType,
-)
+
 # Defining the host is optional and defaults to http://localhost/api
 # See configuration.py for a list of all supported configuration parameters.
 
@@ -84,7 +81,7 @@
 
     def add_osbv1_project(osbv1_proj, index):
         osbv1_proj_id = osbv1_proj["identifier"]
-        if not "GitHub repository" in osbv1_proj:
+        if "GitHub repository" not in osbv1_proj:
             but_ok = (
                 " (but it is in the list of known projects to ignore)"
                 if osbv1_proj_id in known_ignores
@@ -150,7 +147,7 @@ def add_osbv1_project(osbv1_proj, index):
                     "    %s already exists (owner: %s); updating..."
                     % (osbv1_proj_id, lookup_user(r.user_id, url_info))
                 )
-            except:
+            except Exception:
                 exit(-1)
             print(url_info)
             all_updated.append(url_info)
@@ -230,7 +227,7 @@ def add_osbv1_project(osbv1_proj, index):
                 print("----------")
                 print("Error: %s" % str(e))
                 print("----------")
-                if not "context_resources" in str(e):
+                if "context_resources" not in str(e):
                     print("Exiting due to unknown error...")
                     exit()
                 else:

libraries/client/modeldb_info.py

@@ -5,8 +5,6 @@
 import sys
 import json
 
-import osb
-import operator
 import pprint
 
 from utils import get_github
@@ -87,7 +85,7 @@
 
                 info[model]["osbv2_gh_repo"] = repo_to_use.html_url
                 info[model]["osbv2_gh_branch"] = repo_to_use.default_branch
-            except:
+            except Exception:
                 print(
                     "    Missing fork: %s, forking now: %s"
                     % (possible_osbgh_repo, fork_if_missing)
@@ -110,7 +108,7 @@
                     to_be_forked.append(msg)
 
             if (not mdb_repo.forks == expected_forks) and (
-                not (info[model]["id"] in known_to_have_other_forks)
+                info[model]["id"] not in known_to_have_other_forks
             ):
                 msg = "    Unexpected forks for %i (%s != %s)..." % (
                     info[model]["id"],
@@ -120,7 +118,7 @@
                 print(msg)
                 many_forks.append(msg)
 
-        except:
+        except Exception:
             msg = "    Problem locating repo for: %i (%i/%i) %s" % (
                 info[model]["id"],
                 index,

libraries/client/osb_info.py

@@ -3,22 +3,12 @@
 # the current contents. Makes it easier to track (small) changes following API calls
 ######################################################################################
 
-from urllib.request import urlopen
-import codecs
 import workspaces_cli
 from pprint import pprint
 from workspaces_cli.api import rest_api, k8s_api
-import logging
-import datetime
 import json
 import sys
 
-from workspaces_cli.models import (
-    OSBRepository,
-    RepositoryType,
-    Tag,
-    RepositoryContentType,
-)
 # Defining the host is optional and defaults to http://localhost/api
 # See configuration.py for a list of all supported configuration parameters.
 
@@ -70,14 +60,14 @@
         try:
             print("Checking page %i" % page)
             found = api_instance.osbrepository_get(
-                q=f"uri__like=/", per_page=500, page=page
+                q="uri__like=/", per_page=500, page=page
             )
             for f in found.osbrepositories:
                 all_found.append(f)
             print("Found so far: %i" % len(all_found))
             page += 1
             # if page>3: break
-        except:
+        except Exception:
             print("All done")
             break
 

libraries/client/osbv1_info.py

@@ -77,7 +77,7 @@
                 print("    Project has tags: %s" % (project.tags))
                 with_tags += 1
                 for tag in project.tags:
-                    if not tag in tags:
+                    if tag not in tags:
                         tags[tag] = 0
                     tags[tag] += 1
 

libraries/client/utils.py

@@ -13,7 +13,7 @@
 
 
 def lookup_user(uid, url):
-    if not uid in known_users.values():
+    if uid not in known_users.values():
         raise Exception("Unknown user: %s;%s" % (uid, url))
     for user in known_users:
         if uid == known_users[user]:
@@ -51,10 +51,10 @@ def get_tags_info(
         for field in ["Original format", "Cell type", "Brain region", "Specie"]:
             if field in osbv1_info:
                 val = osbv1_info[field]
-                if not val in ["None", "Other", ""]:
+                if val not in ["None", "Other", ""]:
                     val = val.replace("PV+", "PV")
                     val = val.replace("C++", "Cplusplus")
-                    if not val in tags:
+                    if val not in tags:
                         tags.append(val)
 
     if dandi_api_info is not None:

libraries/client/workspaces/workspaces_cli/model/osb_repository_base.py

@@ -312,7 +312,7 @@ def __init__(self, name, repository_type, content_types, uri, *args, **kwargs):
                 continue
             try:
                 setattr(self, var_name, var_value)
-            except:
+            except Exception:
 
                 pass
             if var_name in self.read_only_vars: