Merge pull request #297 from 4dn-dcic/dmichaels-20240103

Modified publish script to allow untracked gitinfo.json file.

CHANGELOG.rst

@@ -6,6 +6,17 @@ dcicutils
 Change Log
 ----------
 
+
+8.7.1
+=====
+
+* Changed scripts/publish_to_pypi.py to allow gitinfo.json to have unstaged changes;
+  this is so we can optionally have repos write relevant git (repo, branch, commit) info
+  to this file (via GitHub Actions) and make it accessible to the package for inspection.
+* Added is_schema_type and is_specified_schema to portal_utils.Portal.
+* Refactoring in portal_utils; added portal_object_utils; added file_utils.py.
+
+
 8.7.0
 =====
 

dcicutils/file_utils.py

@@ -0,0 +1,54 @@
+import glob
+import os
+import pathlib
+from typing import List, Optional, Union
+
+
+def search_for_file(file: str,
+                    location: Union[str, Optional[List[str]]] = None,
+                    recursive: bool = False,
+                    single: bool = False) -> Union[List[str], Optional[str]]:
+    """
+    Searches for the existence of the given file name, first directly in the given directory or list
+    of directories, if specified, and if not then just in the current (working) directory; if the
+    given recursive flag is True then also searches all sub-directories of these directories;
+    returns the full path name to the file if found. If the single flag is True then just the
+    first file which is found is returns (as a string), or None if none; if the single flag
+    is False, then all matched files are returned in a list, or and empty list if none.
+    """
+    if file and isinstance(file, (str, pathlib.PosixPath)):
+        if os.path.isabs(file):
+            if os.path.exists(file):
+                return file if single else [file]
+            return None if single else []
+        files_found = []
+        if not location:
+            location = ["."]
+        elif isinstance(location, (str, pathlib.PosixPath)):
+            location = [location]
+        elif not isinstance(location, list):
+            location = []
+        for directory in location:
+            if isinstance(directory, (str, pathlib.PosixPath)) and os.path.exists(os.path.join(directory, file)):
+                file_found = os.path.abspath(os.path.normpath(os.path.join(directory, file)))
+                if single:
+                    return file_found
+                if file_found not in files_found:
+                    files_found.append(file_found)
+        if recursive:
+            for directory in location:
+                if not directory.endswith("/**") and not file.startswith("**/"):
+                    path = f"{directory}/**/{file}"
+                else:
+                    path = f"{directory}/{file}"
+                files = glob.glob(path, recursive=recursive)
+                if files:
+                    for file_found in files:
+                        file_found = os.path.abspath(file_found)
+                        if single:
+                            return file_found
+                        if file_found not in files_found:
+                            files_found.append(file_found)
+        if files_found:
+            return files_found[0] if single else files_found
+        return None if single else []

dcicutils/portal_object_utils.py

@@ -0,0 +1,112 @@
+from functools import lru_cache
+from typing import List, Optional, Tuple, Type, Union
+from dcicutils.portal_utils import Portal
+
+PortalObject = Type["PortalObject"]  # Forward type reference for type hints.
+
+
+class PortalObject:
+
+    def __init__(self, portal: Portal, portal_object: dict, portal_object_type: Optional[str] = None) -> None:
+        self._portal = portal
+        self._data = portal_object
+        self._type = portal_object_type if isinstance(portal_object_type, str) and portal_object_type else None
+
+    @property
+    def data(self):
+        return self._data
+
+    @property
+    @lru_cache(maxsize=1)
+    def type(self):
+        return self._type or Portal.get_schema_type(self._data)
+
+    @property
+    @lru_cache(maxsize=1)
+    def types(self):
+        return self._type or Portal.get_schema_types(self._data)
+
+    @property
+    @lru_cache(maxsize=1)
+    def uuid(self) -> Optional[str]:
+        return self._data.get("uuid") if isinstance(self._data, dict) else None
+
+    @property
+    @lru_cache(maxsize=1)
+    def schema(self):
+        return self._portal.get_schema(self.type)
+
+    @property
+    @lru_cache(maxsize=1)
+    def identifying_properties(self) -> List[str]:
+        """
+        Returns the list of all identifying property names of this Portal object which actually have values.
+        Implicitly include "uuid" and "identifier" properties as identifying properties if they are actually
+        properties in the object schema, and favor these (first); defavor "aliases"; no other ordering defined.
+        """
+        if not (schema := self.schema) or not (schema_identifying_properties := schema.get("identifyingProperties")):
+            return []
+        identifying_properties = []
+        for identifying_property in schema_identifying_properties:
+            if identifying_property not in ["uuid", "identifier", "aliases"]:
+                if self._data.get(identifying_property):
+                    identifying_properties.append(identifying_property)
+        if self._data.get("identifier"):
+            identifying_properties.insert(0, "identifier")
+        if self._data.get("uuid"):
+            identifying_properties.insert(0, "uuid")
+        if "aliases" in schema_identifying_properties and self._data.get("aliases"):
+            identifying_properties.append("aliases")
+        return identifying_properties
+
+    @property
+    @lru_cache(maxsize=1)
+    def identifying_paths(self) -> List[str]:
+        """
+        Returns a list of the possible Portal URL paths identifying this Portal object.
+        """
+        if not (identifying_properties := self.identifying_properties):
+            return []
+        identifying_paths = []
+        for identifying_property in identifying_properties:
+            if (identifying_value := self._data.get(identifying_property)):
+                if identifying_property == "uuid":
+                    identifying_paths.append(f"/{self.type}/{identifying_value}")
+                    identifying_paths.append(f"/{identifying_value}")
+                # For now at least we include the path both with and without the schema type component,
+                # as for some identifying values, it works (only) with, and some, it works (only) without.
+                # For example: If we have FileSet with "accession", an identifying property, with value
+                # SMAFSFXF1RO4 then /SMAFSFXF1RO4 works but /FileSet/SMAFSFXF1RO4 does not; and
+                # conversely using "submitted_id", also an identifying property, with value
+                # UW_FILE-SET_COLO-829BL_HI-C_1 then /UW_FILE-SET_COLO-829BL_HI-C_1 does
+                # not work but /FileSet/UW_FILE-SET_COLO-829BL_HI-C_1 does work.
+                elif isinstance(identifying_value, list):
+                    for identifying_value_item in identifying_value:
+                        identifying_paths.append(f"/{self.type}/{identifying_value_item}")
+                        identifying_paths.append(f"/{identifying_value_item}")
+                else:
+                    identifying_paths.append(f"/{self.type}/{identifying_value}")
+                    identifying_paths.append(f"/{identifying_value}")
+        return identifying_paths
+
+    @property
+    @lru_cache(maxsize=1)
+    def identifying_path(self) -> Optional[str]:
+        if identifying_paths := self.identifying_paths:
+            return identifying_paths[0]
+
+    def lookup(self, include_identifying_path: bool = False,
+               raw: bool = False) -> Optional[Union[Tuple[PortalObject, str], PortalObject]]:
+        return self._lookup(raw=raw) if include_identifying_path else self._lookup(raw=raw)[0]
+
+    def lookup_identifying_path(self) -> Optional[str]:
+        return self._lookup()[1]
+
+    def _lookup(self, raw: bool = False) -> Tuple[Optional[PortalObject], Optional[str]]:
+        try:
+            for identifying_path in self.identifying_paths:
+                if (value := self._portal.get(identifying_path, raw=raw)) and (value.status_code == 200):
+                    return PortalObject(self._portal, value.json(), self.type if raw else None), identifying_path
+        except Exception:
+            pass
+        return None, self.identifying_path