dcicutils 8.8.2.1b6__tar.gz → 8.8.2.1b8__tar.gz

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.2.1b6
+Version: 8.8.2.1b8
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/dcicutils/deployment_utils.py

@@ -430,6 +430,7 @@ class IniFileManager:
                                      auth0_allowed_connections=None,
                                      re_captcha_key=None, re_captcha_secret=None,
                                      redis_server=None,
+                                     google_api_key=None,
                                      file_upload_bucket=None, file_wfout_bucket=None,
                                      blob_bucket=None, system_bucket=None, metadata_bundles_bucket=None):
 
@@ -506,6 +507,7 @@ class IniFileManager:
                                                re_captcha_key=re_captcha_key,
                                                re_captcha_secret=re_captcha_secret,
                                                redis_server=redis_server,
+                                               google_api_key=google_api_key,
                                                file_upload_bucket=file_upload_bucket,
                                                file_wfout_bucket=file_wfout_bucket,
                                                blob_bucket=blob_bucket,
@@ -576,6 +578,7 @@ class IniFileManager:
                                        auth0_allowed_connections=None,
                                        re_captcha_key=None, re_captcha_secret=None,
                                        redis_server=None,
+                                       google_api_key=None,
                                        file_upload_bucket=None,
                                        file_wfout_bucket=None, blob_bucket=None, system_bucket=None,
                                        metadata_bundles_bucket=None):
@@ -632,6 +635,7 @@ class IniFileManager:
         higlass_server = higlass_server or os.environ.get('ENCODED_HIGLASS_SERVER', "MISSING_ENCODED_HIGLASS_SERVER")
         es_server = es_server or os.environ.get('ENCODED_ES_SERVER', "MISSING_ENCODED_ES_SERVER")
         redis_server = redis_server or os.environ.get('ENCODED_REDIS_SERVER', '')  # optional
+        google_api_key = google_api_key or os.environ.get('GOOGLE_API_KEY', '')  # optional
         env_bucket = (env_bucket
                       or EnvBase.global_env_bucket_name()
                       or ("MISSING_GLOBAL_ENV_BUCKET"
@@ -773,6 +777,7 @@ class IniFileManager:
             'HIGLASS_SERVER': higlass_server,
             'ES_SERVER': es_server,
             'REDIS_SERVER': redis_server,
+            'GOOGLE_API_KEY': google_api_key,
             'ENV_BUCKET': env_bucket,
             'ENV_ECOSYSTEM': env_ecosystem,
             'ENV_NAME': env_name,
@@ -945,6 +950,9 @@ class IniFileManager:
             parser.add_argument("--redis_server",
                                 help="server URL to a Redis Cluster",
                                 default=None)
+            parser.add_argument("--google_api_key",
+                                help="Google API key to get smaht-submitr metadata template version",
+                                default=None)
             parser.add_argument("--tibanna_cwls_bucket",
                                 help="the name of a Tibanna CWLs bucket to use",
                                 default=None)
@@ -1024,6 +1032,7 @@ class IniFileManager:
                                              auth0_allowed_connections=args.auth0_allowed_connections,
                                              re_captcha_key=args.recaptcha_key, re_captcha_secret=args.recaptcha_secret,
                                              redis_server=args.redis_server,
+                                             google_api_key=args.google_api_key,
                                              file_upload_bucket=args.file_upload_bucket,
                                              file_wfout_bucket=args.file_wfout_bucket,
                                              blob_bucket=args.blob_bucket, system_bucket=args.system_bucket,

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/dcicutils/portal_utils.py

@@ -45,6 +45,7 @@ class Portal:
     DEFAULT_APP = APP_SMAHT
     KEYS_FILE_DIRECTORY = "~"
     MIME_TYPE_JSON = "application/json"
+    FILE_TYPE_SCHEMA_NAME = "File"
 
     # Object lookup strategies; on a per-reference (type/value) basis, used currently ONLY by
     # structured_data.py; controlled by an optional ref_lookup_strategy callable; default is
@@ -342,6 +343,9 @@ class Portal:
                             return True
         return False
 
+    def is_schema_file_type(self, schema_name_or_portal_object: Union[str, dict]) -> bool:
+        return self.is_schema_type(schema_name_or_portal_object, self.FILE_TYPE_SCHEMA_NAME)
+
     def isinstance_schema(self, portal_object: dict, target_schema_name: str) -> bool:
         """
         Returns True iff the given object isa type of the given schema type.

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/dcicutils/progress_bar.py

@@ -64,7 +64,7 @@ class ProgressBar:
         self._started = time.time()
         self._stop_requested = False
         # Interrupt handling. We do not do the actual (signal) interrupt setup
-        # in self._initialiaze as that could be called from a (sub) thread; and in
+        # in self._initialize as that could be called from a (sub) thread; and in
         # Python we can only set a signal (SIGINT in our case) on the main thread.
         self._catch_interrupt = (catch_interrupt is True)
         self._interrupt = interrupt if callable(interrupt) else None

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/dcicutils/structured_data.py

@@ -40,7 +40,6 @@ DOTTED_NAME_DELIMITER_CHAR = "."
 
 
 # TODO: Should probably pass this knowledge in from callers.
-FILE_TYPE_NAME = "File"
 FILE_TYPE_PROPERTY_NAME = "filename"
 
 # Forward type references for type hints.
@@ -162,7 +161,7 @@ class StructuredDataSet:
         result = []
         if self._portal:
             for type_name in self.data:
-                if self._portal.is_file_schema(type_name):
+                if self._portal.is_schema_file_type(type_name):
                     for item in self.data[type_name]:
                         if (file_name := item.get(FILE_TYPE_PROPERTY_NAME)):
                             result.append({"type": type_name, "file": file_name})
@@ -872,12 +871,6 @@ class Portal(PortalBase):
                     schemas[user_specified_schema["title"]] = user_specified_schema
         return schemas
 
-    def is_file_schema(self, schema_name: str) -> bool:
-        """
-        Returns True iff the given schema name isa File type, i.e. has an ancestor which is of type File.
-        """
-        return self.is_schema_type(schema_name, FILE_TYPE_NAME)
-
     def ref_exists(self, type_name: str, value: Optional[str] = None,
                    called_from_map_ref: bool = False) -> Optional[dict]:
         if not value:

{dcicutils-8.8.2.1b6 → dcicutils-8.8.2.1b8}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.2.1b6"  # TODO: To become 8.8.3
+version = "8.8.2.1b8"  # TODO: To become 8.8.3
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"