fair-cli 0.9.7__tar.gz → 0.9.9__tar.gz

{fair_cli-0.9.7 → fair_cli-0.9.9}/CITATION.cff

@@ -36,4 +36,4 @@ license: BSD-2-Clause
 message: If you use this software, please cite it using these metadata.
 repository-code: https://github.com/FAIRDataPipeline/FAIR-CLI/
 title: "The FAIR Data Pipeline command line tool"
-version: 0.9.7
+version: 0.9.9

{fair_cli-0.9.7 → fair_cli-0.9.9}/PKG-INFO

@@ -1,12 +1,13 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: fair-cli
-Version: 0.9.7
+Version: 0.9.9
 Summary: Synchronization interface for the SCRC FAIR Data Pipeline registry
 License: BSD-2-Clause
+License-File: LICENSE
 Keywords: FAIR Data Pipeline,FAIR,Data Management,Provenance
 Author: Richard Reeve
 Author-email: richard.reeve@glasgow.ac.uk
-Requires-Python: >=3.9.0,<4.0.0
+Requires-Python: >=3.10.0,<4.0.0
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
@@ -15,11 +16,12 @@ Classifier: Operating System :: MacOS
 Classifier: Operating System :: OS Independent
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Classifier: Topic :: Database :: Front-Ends
 Classifier: Topic :: Scientific/Engineering
 Provides-Extra: all

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/cli.py

@@ -347,7 +347,7 @@ def purge(glob: bool, debug: bool, yes: bool, data: bool, all: bool) -> None:
         )
     else:
         _purge = click.confirm(
-            "Are you sure you want to reset FAIR tracking, " "this is not reversible?"
+            "Are you sure you want to reset FAIR tracking, this is not reversible?"
         )
         if data:
             data = click.confirm(

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/common.py

@@ -308,7 +308,11 @@ def set_file_permissions(path: str):
 
 def remove_readonly(fn, path, excinfo):
     try:
+        _ = excinfo  # Required to avoid unused variable warning
+        # Remove readonly bit
         os.chmod(path, stat.S_IWRITE)
+        # Call the provided function again
         fn(path)
     except Exception as exc:
+        # Log the error
         print("Skipped:", path, "because:\n", exc)

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/identifiers.py

@@ -30,6 +30,9 @@ from fake_useragent import UserAgent
 
 logger = logging.getLogger("FAIRDataPipeline.Identifiers")
 
+JSON_MIME_TYPE = "application/json"
+JSON_HEADERS = {"Accept": JSON_MIME_TYPE}
+
 ID_URIS = {
     "orcid": "https://orcid.org/",
     "ror": "https://ror.org/",
@@ -57,7 +60,7 @@ def check_orcid(orcid: str) -> typing.Dict:
         metadata from the given ID
     """
     orcid = orcid.replace(ID_URIS["orcid"], "")
-    _header = {"Accept": "application/json"}
+    _header = JSON_HEADERS
     _url = urllib.parse.urljoin(QUERY_URLS["orcid"], orcid)
     requests.packages.urllib3.disable_warnings(category=InsecureRequestWarning)
     _response = requests.get(_url, headers=_header, verify=False, allow_redirects=True)
@@ -95,7 +98,7 @@ def check_github(github: str) -> typing.Dict:
     typing.Dict
         metadata from the given ID
     """
-    _header = {"Accept": "application/json"}
+    _header = JSON_HEADERS
     _url = urllib.parse.urljoin(QUERY_URLS["github"], github)
     requests.packages.urllib3.disable_warnings(category=InsecureRequestWarning)
     _response = requests.get(_url, headers=_header, verify=False, allow_redirects=True)
@@ -104,7 +107,7 @@ def check_github(github: str) -> typing.Dict:
 
     if _response.status_code == 403:
         time.sleep(3)
-        _header = {"Accept": "application/json", "User-Agent": str(UserAgent().chrome)}
+        _header = {"Accept": JSON_MIME_TYPE, "User-Agent": str(UserAgent().chrome)}
         _response = requests.get(
             _url, headers=_header, verify=False, allow_redirects=True
         )
@@ -149,7 +152,7 @@ def check_gitlab(gitlab: str, gitlab_url: str = "https://gitlab.com/") -> typing
 
     if _response.status_code == 403:
         time.sleep(3)
-        _header = {"Accept": "application/json", "User-Agent": str(UserAgent().chrome)}
+        _header = {"Accept": JSON_MIME_TYPE, "User-Agent": str(UserAgent().chrome)}
         _response = requests.get(
             _url, headers=_header, verify=False, allow_redirects=True
         )
@@ -231,7 +234,12 @@ def _check_generic_ror(id: str) -> typing.Dict:
         return _result_dict
 
     _id = _response.json()["items"][0]["id"]
-    _name = _response.json()["items"][0]["name"]
+    # The ROR API lists every name of an organisation, marking the one to show as "ror_display"
+    _names = _response.json()["items"][0]["names"]
+    _name = next(
+        (n["value"] for n in _names if "ror_display" in n["types"]),
+        _names[0]["value"],
+    )
     _result_dict["name"] = _name
     _result_dict["family_name"] = _name
     _result_dict["given_names"] = None

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/logging.py

@@ -99,5 +99,5 @@ class LevelFormatter(logging.Formatter):
 
     def format(self, record: logging.LogRecord) -> str:
         idx = bisect(self.formats, (record.levelno,), hi=len(self.formats) - 1)
-        level, formatter = self.formats[idx]
+        _, formatter = self.formats[idx]  # Tuple unpacking level, then formatter
         return formatter.format(record)

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/registry/requests.py

@@ -632,7 +632,7 @@ def get_author_exists(registry_uri, token=None, name=None, identifier=None) -> s
         The url of the author if they exist else None
     """
     if not name and not identifier:
-        return {}
+        return ""
     if not token:
         token = local_token()
     _params = {}
@@ -643,7 +643,7 @@ def get_author_exists(registry_uri, token=None, name=None, identifier=None) -> s
     _author_exists = get(registry_uri, "author", token, params=_params)
     if _author_exists:
         return _author_exists[0]["url"]
-    return {}
+    return ""
 
 
 def get_auth_provider(registry_uri: str, token: str = None) -> str:

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/registry/sync.py

@@ -350,13 +350,12 @@ def _get_new_url(
             _new_obj_data["authors"].append(_new_author_url)
             _filters["authors"].append(fdp_req.get_obj_id_from_url(_new_author_url))
 
-    if _obj_type == "author":
-        if "identifier" in _new_obj_data:
-            _author = fdp_req.get_author_exists(
-                dest_uri, token=dest_token, identifier=_new_obj_data["identifier"]
-            )
-            if _author:
-                return _author
+    if _obj_type == "author" and "identifier" in _new_obj_data:
+        _author = fdp_req.get_author_exists(
+            dest_uri, token=dest_token, identifier=_new_obj_data["identifier"]
+        )
+        if _author:
+            return _author
 
     return fdp_req.post_else_get(
         dest_uri,
@@ -402,6 +401,8 @@ def sync_user_author(
     author_url: str,
     remote_user: str,
 ) -> None:
+    _ = origin_uri  # prevent unused variable warning
+    _ = origin_token  # prevent unused variable warning
     current_user = fdp_req.get(
         dest_uri, "users", dest_token, params={"username": remote_user}
     )

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/session.py

@@ -64,6 +64,13 @@ import fair.user_config as fdp_user
 import fair.logging as fdp_logging
 import fair.registry.storage as fdp_store
 
+GLOBAL_CONFIG_MESSAGE = (
+    "Setup will now ask you questions regarding the global configuration"
+)
+REPO_CONFIG_MESSAGE = (
+    "Setup will now ask you questions regarding this repo configuration"
+)
+
 
 class FAIR:
     """
@@ -1170,17 +1177,13 @@ class FAIR:
         if not os.path.exists(fdp_com.global_fdpconfig()):
             try:
                 if not self._testing:
-                    click.echo(
-                        "Setup will now ask you questions regarding the global configuration"
-                    )
+                    click.echo(GLOBAL_CONFIG_MESSAGE)
                 self._global_config = fdp_conf.global_config_query(registry, local)
             except (fdp_exc.CLIConfigurationError, click.Abort) as e:
                 self._clean_reset(_fair_dir, e)
             try:
                 if not self._testing:
-                    click.echo(
-                        "Setup will now ask you questions regarding this repo configuration"
-                    )
+                    click.echo(REPO_CONFIG_MESSAGE)
                 self._local_config = fdp_conf.local_config_query(
                     self._global_config,
                     first_time_setup=_first_time,
@@ -1191,9 +1194,7 @@ class FAIR:
         elif not using:
             try:
                 if not self._testing:
-                    click.echo(
-                        "Setup will now ask you questions regarding this repo configuration"
-                    )
+                    click.echo(REPO_CONFIG_MESSAGE)
                 self._local_config = fdp_conf.local_config_query(
                     self._global_config, local=local
                 )
@@ -1208,14 +1209,10 @@ class FAIR:
                 yaml.dump(self._global_config, f)
         else:
             if not self._testing:
-                click.echo(
-                    "Setup will now ask you questions regarding the global configuration"
-                )
+                click.echo(GLOBAL_CONFIG_MESSAGE)
             self._global_config = fdp_conf.read_global_fdpconfig()
             if not self._testing:
-                click.echo(
-                    "Setup will now ask you questions regarding this repo configuration"
-                )
+                click.echo(REPO_CONFIG_MESSAGE)
             self._local_config = fdp_conf.read_local_fdpconfig(self._session_loc)
 
         if export_as:

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/staging.py

@@ -171,7 +171,7 @@ class Stager:
         self.add_to_staging(job_id, "job")
         self.change_stage_status(job_id, "job", stage)
 
-    def find_registry_entry_for_file(self, local_uri: str, file_path: str) -> str:
+    def find_registry_entry_for_file(self, local_uri: str, file_path: str) -> dict:
         """Performs a rough search for a file in the local registry
 
         Parameters
@@ -312,7 +312,7 @@ class Stager:
 
         _config_url = self.find_registry_entry_for_file(
             fdp_conf.get_local_uri(), _config_rel_path
-        )["url"]
+        ).get("url")
 
         # Check for job script file
         _config_yaml = os.path.join(_directory, fdp_com.USER_CONFIG_FILE)
@@ -355,7 +355,9 @@ class Stager:
         _rel_script_path = _script_path.split(fdp_com.JOBS_DIR)[1]
         _rel_script_path = f"{fdp_com.JOBS_DIR}{_rel_script_path}"
 
-        result = self.find_registry_entry_for_file(local_uri, _rel_script_path)["url"]
+        result = self.find_registry_entry_for_file(local_uri, _rel_script_path).get(
+            "url"
+        )
 
         self._logger.debug("Script URL: %s", result)
 

{fair_cli-0.9.7 → fair_cli-0.9.9}/fair/user_config/__init__.py

@@ -318,7 +318,7 @@ class JobConfiguration(MutableMapping):
         for register_entry in register_block:
             _new_entry = register_entry.copy()
             if "namespace_name" not in register_entry:
-                if not "use" in register_entry:
+                if "use" not in register_entry:
                     _new_entry["use"] = {}
                 else:
                     if "namespace" in register_entry["use"]:
@@ -569,8 +569,8 @@ class JobConfiguration(MutableMapping):
 
         if not _cmd or not _out_file:
             raise fdp_exc.UserConfigError(
-                "Configuration file must contain either a valid "
-                "'script' or 'script_path' entry under 'run_metadata'"
+                "Configuration file must contain either a valid \
+                'script' or 'script_path' entry under 'run_metadata'"
             )
 
         self.set_script(_out_file)
@@ -808,7 +808,13 @@ class JobConfiguration(MutableMapping):
         # Additional parser for formatted datetime
         _regex_fmt = re.compile(r"\$\{\{\s*([^}${\s]+)\s*\}\}")
 
-        if _unparsed := _regex_fmt.findall(_conf_str):
+        # RUN_ID is the code run's UUID, which does not exist until the API
+        # creates the code run, so the API substitutes it at finalise
+        _unparsed = [
+            var for var in _regex_fmt.findall(_conf_str) if var != "RUN_ID"
+        ]
+
+        if _unparsed:
             raise fdp_exc.InternalError(f"Failed to parse variables '{_unparsed}'")
 
     def _subst_cli_vars(self, job_time: datetime.datetime) -> str:

{fair_cli-0.9.7 → fair_cli-0.9.9}/pyproject.toml

@@ -10,7 +10,6 @@ authors = [
 classifiers = [
   "License :: OSI Approved :: BSD License",
   "Intended Audience :: Science/Research",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -24,7 +23,7 @@ classifiers = [
 ]
 description = "Synchronization interface for the SCRC FAIR Data Pipeline registry"
 name = "fair-cli"
-version = "0.9.7"
+version = "0.9.9"
 
 homepage = "https://www.fairdatapipeline.org/"
 
@@ -56,7 +55,7 @@ click = "^8.0.0"
 email-validator = "^1.1.3"
 pre-commit = "^3"
 pydantic = {extras = ["email"], version = "^1.9.0"}
-python = "^3.9.0,<4.0"
+python = "^3.10.0,<4.0"
 requests = "^2.23.0"
 rich = ">=10.2.3,<12.0.0"
 semver = "^2.13.0"