dcicutils 8.8.1.1b10__tar.gz → 8.8.1.1b12__tar.gz

{dcicutils-8.8.1.1b10 → dcicutils-8.8.1.1b12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.1.1b10
+Version: 8.8.1.1b12
 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-8.8.1.1b12/dcicutils/progress_constants.py

@@ -0,0 +1,59 @@
+from enum import Enum
+
+
+# Constants for progress tracking for smaht-submitr.
+# Here only to share between smaht-portal, snovault, and smaht-submitr.
+
+class PROGRESS_INGESTER(Enum):
+    VALIDATION = "ingester_validation"
+    INITIATE = "ingester_initiate"
+    PARSE_LOAD_INITIATE = "ingester_parse_initiate"
+    PARSE_LOAD_DONE = "ingester_parse_done"
+    VALIDATE_LOAD_INITIATE = "ingester_validate_initiate"
+    VALIDATE_LOAD_DONE = "ingester_validate_done"
+    LOADXL_INITIATE = "ingester_loadxl_initiate"
+    LOADXL_DONE = "ingester_loadxl_done"
+    MESSAGE = "ingester_message"
+    MESSAGE_VERBOSE = "ingester_message_verbose"
+    MESSAGE_DEBUG = "ingester_message_debug"
+
+
+class PROGRESS_PARSE(Enum):
+    LOAD_START = "parse_start"
+    LOAD_ITEM = "parse_item"
+    LOAD_DONE = "parse_done"
+    LOAD_COUNT_SHEETS = "parse_sheets"
+    LOAD_COUNT_ROWS = "parse_rows"
+    LOAD_COUNT_REFS = "parse_refs"
+    LOAD_COUNT_REFS_FOUND = "parse_refs_found"
+    LOAD_COUNT_REFS_NOT_FOUND = "parse_refs_not_found"
+    LOAD_COUNT_REFS_LOOKUP = "parse_refs_lookup"
+    LOAD_COUNT_REFS_LOOKUP_CACHE_HIT = "parse_refs_lookup_cache_hit"
+    LOAD_COUNT_REFS_EXISTS_CACHE_HIT = "parse_refs_exists_cache_hit"
+    LOAD_COUNT_REFS_INVALID = "parse_refs_invalid"
+    ANALYZE_START = "parse_analyze_start"
+    ANALYZE_COUNT_TYPES = "parse_analyze_types"
+    ANALYZE_COUNT_ITEMS = "parse_analyze_objects"
+    ANALYZE_COUNT_LOOKUP = "parse_analyze_lookups"
+    ANALYZE_CREATE = "parse_analyze_create"
+    ANALYZE_UPDATE = "parse_analyze_update"
+    ANALYZE_DONE = "parse_analyze_done"
+    MESSAGE = "parse_message"
+    MESSAGE_VERBOSE = "parse_message_verbose"
+    MESSAGE_DEBUG = "parse_message_debug"
+
+
+class PROGRESS_LOADXL(Enum):
+    START = "loadxl_start"
+    START_SECOND_ROUND = "loadxl_start_second_round"
+    ITEM = "loadxl_item"
+    ITEM_SECOND_ROUND = "loadxl_item_second_round"
+    GET = "loadxl_lookup"
+    POST = "loadxl_post"
+    PATCH = "loadxl_patch"
+    ERROR = "loadxl_error"
+    DONE = "loadxl_done"
+    TOTAL = "loadxl_total"
+    MESSAGE = "loadxl_message"
+    MESSAGE_VERBOSE = "loadxl_message_verbose"
+    MESSAGE_DEBUG = "loadxl_message_debug"

{dcicutils-8.8.1.1b10 → dcicutils-8.8.1.1b12}/dcicutils/structured_data.py

@@ -192,8 +192,8 @@ class StructuredDataSet:
         diffs = {}
         if callable(progress):
             ntypes, nobjects = get_counts()
-            progress({PROGRESS.ANALYZE_START: True,
-                      PROGRESS.ANALYZE_COUNT_TYPES: ntypes, PROGRESS.ANALYZE_COUNT_ITEMS: nobjects})
+            progress({PROGRESS.ANALYZE_START.value: True,
+                      PROGRESS.ANALYZE_COUNT_TYPES.value: ntypes, PROGRESS.ANALYZE_COUNT_ITEMS.value: nobjects})
         if self.data or self.portal:  # TODO: what is this OR biz?
             refs = self.resolved_refs_with_uuids
             # TODO: Need feedback/progress tracking mechanism here.
@@ -212,19 +212,20 @@ class StructuredDataSet:
                                                                        uuid=existing_object.uuid,
                                                                        diffs=object_diffs or None))
                         if callable(progress):
-                            progress({PROGRESS.ANALYZE_UPDATE: True,
-                                      PROGRESS.ANALYZE_COUNT_LOOKUP: nlookups + nlookups_compare})
+                            progress({PROGRESS.ANALYZE_UPDATE.value: True,
+                                      PROGRESS.ANALYZE_COUNT_LOOKUP.value: nlookups + nlookups_compare})
                     elif identifying_path:
                         # If there is no existing object we still create a record for this object
                         # but with no uuid which will be the indication that it does not exist.
                         diffs[type_name].append(create_readonly_object(path=identifying_path, uuid=None, diffs=None))
                         if callable(progress):
-                            progress({PROGRESS.ANALYZE_CREATE: True, PROGRESS.ANALYZE_COUNT_LOOKUP: nlookups})
+                            progress({PROGRESS.ANALYZE_CREATE.value: True,
+                                      PROGRESS.ANALYZE_COUNT_LOOKUP.value: nlookups})
                     else:
                         if callable(progress):
-                            progress({PROGRESS.ANALYZE_COUNT_LOOKUP: nlookups})
+                            progress({PROGRESS.ANALYZE_COUNT_LOOKUP.value: nlookups})
         if callable(progress):
-            progress({PROGRESS.ANALYZE_DONE: True})
+            progress({PROGRESS.ANALYZE_DONE.value: True})
         return diffs
 
     def load_file(self, file: str) -> None:
@@ -271,8 +272,8 @@ class StructuredDataSet:
             return nrows, len(excel.sheet_names)
         if self._progress:  # TODO: Move to _load_reader
             nrows, nsheets = get_counts()
-            self._progress({PROGRESS.LOAD_START: True,
-                            PROGRESS.LOAD_COUNT_SHEETS: nsheets, PROGRESS.LOAD_COUNT_ROWS: nrows})
+            self._progress({PROGRESS.LOAD_START.value: True,
+                            PROGRESS.LOAD_COUNT_SHEETS.value: nsheets, PROGRESS.LOAD_COUNT_ROWS.value: nrows})
         excel = Excel(file)  # Order the sheet names by any specified ordering (e.g. ala snovault.loadxl).
         order = {Schema.type_name(key): index for index, key in enumerate(self._order)} if self._order else {}
         for sheet_name in sorted(excel.sheet_names, key=lambda key: order.get(Schema.type_name(key), sys.maxsize)):
@@ -297,14 +298,14 @@ class StructuredDataSet:
                 del self._errors["ref"]
         if self._progress:
             self._progress({   # TODO: Refactor with same thing below in _load_reader.
-                PROGRESS.LOAD_DONE: True,
-                PROGRESS.LOAD_COUNT_REFS: self.ref_total_count,
-                PROGRESS.LOAD_COUNT_REFS_FOUND: self.ref_total_found_count,
-                PROGRESS.LOAD_COUNT_REFS_NOT_FOUND: self.ref_total_notfound_count,
-                PROGRESS.LOAD_COUNT_REFS_LOOKUP: self.ref_lookup_count,
-                PROGRESS.LOAD_COUNT_REFS_LOOKUP_CACHE_HIT: self.ref_lookup_cache_hit_count,
-                PROGRESS.LOAD_COUNT_REFS_EXISTS_CACHE_HIT: self.ref_exists_cache_hit_count,
-                PROGRESS.LOAD_COUNT_REFS_INVALID: self.ref_invalid_identifying_property_count
+                PROGRESS.LOAD_DONE.value: True,
+                PROGRESS.LOAD_COUNT_REFS.value: self.ref_total_count,
+                PROGRESS.LOAD_COUNT_REFS_FOUND.value: self.ref_total_found_count,
+                PROGRESS.LOAD_COUNT_REFS_NOT_FOUND.value: self.ref_total_notfound_count,
+                PROGRESS.LOAD_COUNT_REFS_LOOKUP.value: self.ref_lookup_count,
+                PROGRESS.LOAD_COUNT_REFS_LOOKUP_CACHE_HIT.value: self.ref_lookup_cache_hit_count,
+                PROGRESS.LOAD_COUNT_REFS_EXISTS_CACHE_HIT.value: self.ref_exists_cache_hit_count,
+                PROGRESS.LOAD_COUNT_REFS_INVALID.value: self.ref_invalid_identifying_property_count
             })
 
     def _load_json_file(self, file: str) -> None:
@@ -334,14 +335,14 @@ class StructuredDataSet:
             self._add(type_name, structured_row)
             if self._progress:
                 self._progress({
-                    PROGRESS.LOAD_ITEM: True,
-                    PROGRESS.LOAD_COUNT_REFS: self.ref_total_count,
-                    PROGRESS.LOAD_COUNT_REFS_FOUND: self.ref_total_found_count,
-                    PROGRESS.LOAD_COUNT_REFS_NOT_FOUND: self.ref_total_notfound_count,
-                    PROGRESS.LOAD_COUNT_REFS_LOOKUP: self.ref_lookup_count,
-                    PROGRESS.LOAD_COUNT_REFS_LOOKUP_CACHE_HIT: self.ref_lookup_cache_hit_count,
-                    PROGRESS.LOAD_COUNT_REFS_EXISTS_CACHE_HIT: self.ref_exists_cache_hit_count,
-                    PROGRESS.LOAD_COUNT_REFS_INVALID: self.ref_invalid_identifying_property_count
+                    PROGRESS.LOAD_ITEM.value: True,
+                    PROGRESS.LOAD_COUNT_REFS.value: self.ref_total_count,
+                    PROGRESS.LOAD_COUNT_REFS_FOUND.value: self.ref_total_found_count,
+                    PROGRESS.LOAD_COUNT_REFS_NOT_FOUND.value: self.ref_total_notfound_count,
+                    PROGRESS.LOAD_COUNT_REFS_LOOKUP.value: self.ref_lookup_count,
+                    PROGRESS.LOAD_COUNT_REFS_LOOKUP_CACHE_HIT.value: self.ref_lookup_cache_hit_count,
+                    PROGRESS.LOAD_COUNT_REFS_EXISTS_CACHE_HIT.value: self.ref_exists_cache_hit_count,
+                    PROGRESS.LOAD_COUNT_REFS_INVALID.value: self.ref_invalid_identifying_property_count
                 })
         self._note_warning(reader.warnings, "reader")
         if schema:

{dcicutils-8.8.1.1b10 → dcicutils-8.8.1.1b12}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.1.1b10"  # TODO: To become 8.8.2
+version = "8.8.1.1b12"  # TODO: To become 8.8.2
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

dcicutils-8.8.1.1b10/dcicutils/progress_constants.py

@@ -1,53 +0,0 @@
-from enum import Enum
-
-
-# Constants for progress tracking for smaht-submitr.
-# Here only to share between smaht-portal, snovault, and smaht-submitr.
-
-class PROGRESS_INGESTER(Enum):
-    VALIDATION = "ingester_validation"
-    INITIATE = "ingester_initiate"
-    PARSE_LOAD_INITIATE = "ingester_parse_initiate"
-    PARSE_LOAD_DONE = "ingester_parse_done"
-    VALIDATE_LOAD_INITIATE = "ingester_validate_initiate"
-    VALIDATE_LOAD_DONE = "ingester_validate_done"
-    LOADXL_INITIATE = "ingester_loadxl_initiate"
-    LOADXL_DONE = "ingester_loadxl_done"
-
-
-class PROGRESS_PARSE(Enum):
-    LOAD_START = "start"
-    LOAD_ITEM = "parse"
-    LOAD_DONE = "finish"
-    LOAD_COUNT_SHEETS = "sheets"
-    LOAD_COUNT_ROWS = "rows"
-    LOAD_COUNT_REFS = "refs"
-    LOAD_COUNT_REFS_FOUND = "refs_found"
-    LOAD_COUNT_REFS_NOT_FOUND = "refs_not_found"
-    LOAD_COUNT_REFS_LOOKUP = "refs_lookup"
-    LOAD_COUNT_REFS_LOOKUP_CACHE_HIT = "refs_lookup_cache_hit"
-    LOAD_COUNT_REFS_EXISTS_CACHE_HIT = "refs_exists_cache_hit"
-    LOAD_COUNT_REFS_INVALID = "refs_invalid"
-    ANALYZE_START = "start"
-    ANALYZE_COUNT_TYPES = "types"
-    ANALYZE_COUNT_ITEMS = "objects"
-    ANALYZE_CREATE = "create"
-    ANALYZE_COUNT_LOOKUP = "lookups"
-    ANALYZE_UPDATE = "update"
-    ANALYZE_DONE = "finish"
-
-
-class PROGRESS_LOADXL(Enum):
-    START = "loadxl_start"
-    START_SECOND_ROUND = "loadxl_start_second_round"
-    ITEM = "loadxl_item"
-    ITEM_SECOND_ROUND = "loadxl_item_second_round"
-    GET = "loadxl_lookup"
-    POST = "loadxl_post"
-    PATCH = "loadxl_patch"
-    ERROR = "loadxl_error"
-    DONE = "loadxl_done"
-    TOTAL = "loadxl_total"
-    MESSAGE = "loadxl_message"
-    MESSAGE_VERBOSE = "loadxl_message_verbose"
-    MESSAGE_DEBUG = "loadxl_message_debug"