zombie-squirrel 0.4.7__py3-none-any.whl → 0.5.1__py3-none-any.whl

zombie_squirrel/__init__.py

@@ -3,7 +3,7 @@
 Provides functions to fetch and cache project names, subject IDs, and asset
 metadata from the AIND metadata database with support for multiple backends."""
 
-__version__ = "0.4.7"
+__version__ = "0.5.1"
 
 from zombie_squirrel.squirrels import (  # noqa: F401
     asset_basics,

zombie_squirrel/squirrels.py

@@ -143,6 +143,9 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
         "subject.subject_id",
         "acquisition.acquisition_start_time",
         "acquisition.acquisition_end_time",
+        "processing.data_processes.start_date_time",
+        "subject.subject_details.genotype",
+        "location",
     ]
 
     if df.empty or force_update:
@@ -157,6 +160,9 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
                 "subject_id",
                 "acquisition_start_time",
                 "acquisition_end_time",
+                "process_date",
+                "genotype",
+                "location",
             ]
         )
         client = MetadataDbClient(
@@ -183,7 +189,7 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
         asset_records = []
         for i in range(0, len(keep_ids), BATCH_SIZE):
             logging.info(f"Fetching asset basics batch {i // BATCH_SIZE + 1}...")
-            batch_ids = keep_ids[i : i + BATCH_SIZE]
+            batch_ids = keep_ids[i: i + BATCH_SIZE]
             batch_records = client.retrieve_docdb_records(
                 filter_query={"_id": {"$in": batch_ids}},
                 projection={field: 1 for field in FIELDS + ["_id", "_last_modified"]},
@@ -197,6 +203,16 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
             modalities = record.get("data_description", {}).get("modalities", [])
             modality_abbreviations = [modality["abbreviation"] for modality in modalities if "abbreviation" in modality]
             modality_abbreviations_str = ", ".join(modality_abbreviations)
+
+            # Get the process date, convert to YYYY-MM-DD if present
+            data_processes = record.get("processing", {}).get("data_processes", [])
+            if data_processes:
+                latest_process = data_processes[-1]
+                process_datetime = latest_process.get("start_date_time", None)
+                process_date = process_datetime.split("T")[0]
+            else:
+                process_date = None
+
             flat_record = {
                 "_id": record["_id"],
                 "_last_modified": record.get("_last_modified", None),
@@ -206,6 +222,9 @@ def asset_basics(force_update: bool = False) -> pd.DataFrame:
                 "subject_id": record.get("subject", {}).get("subject_id", None),
                 "acquisition_start_time": record.get("acquisition", {}).get("acquisition_start_time", None),
                 "acquisition_end_time": record.get("acquisition", {}).get("acquisition_end_time", None),
+                "process_date": process_date,
+                "genotype": record.get("subject", {}).get("subject_details", {}).get("genotype", None),
+                "location": record.get("location", None),
             }
             records.append(flat_record)
 
@@ -300,6 +319,8 @@ def raw_to_derived(force_update: bool = False) -> pd.DataFrame:
         raw_to_derived_map = {raw_id: [] for raw_id in raw_ids}
         for derived_record in derived_records:
             source_data_list = derived_record.get("data_description", {}).get("source_data", [])
+            if not source_data_list:
+                continue
             derived_id = derived_record["_id"]
             # Add this derived record to each raw record it depends on
             for source_id in source_data_list:

{zombie_squirrel-0.4.7.dist-info → zombie_squirrel-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: zombie-squirrel
-Version: 0.4.7
+Version: 0.5.1
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -17,7 +17,7 @@ Dynamic: license-file
 ![Code Style](https://img.shields.io/badge/code%20style-black-black)
 [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
 ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
-![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen)
+![Coverage](https://img.shields.io/badge/coverage-99%25-brightgreen)
 ![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)
 
 <img src="zombie-squirrel_logo.png" width="400" alt="Logo (image from ChatGPT)">

zombie_squirrel-0.5.1.dist-info/RECORD

@@ -0,0 +1,10 @@
+zombie_squirrel/__init__.py,sha256=ihoDdnYVX9vzrIOTRGU1EFj_vGu_6OgJHeOC_6bVyLQ,409
+zombie_squirrel/acorns.py,sha256=4uBzYtYgW2oD5sOohNQUw4qfjmNjmAIK2RlL1Ge1Udo,2597
+zombie_squirrel/squirrels.py,sha256=xFGckcm4hcmFVxQneqeloSZjoY6Qc2wvHT9Wws9L-Rk,12088
+zombie_squirrel/sync.py,sha256=84Ta5beHiPuGBVzp9SCo7G1b4McTUohcUIf_TJbNIV8,518
+zombie_squirrel/utils.py,sha256=woPxU4vYMUv-T0XOjV5ieViksU_q7It_n_5Ll4zpocA,289
+zombie_squirrel-0.5.1.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
+zombie_squirrel-0.5.1.dist-info/METADATA,sha256=CgLCs4WxISN0rMMXSCw0H-E90W8V87bXErZbRbZ26XU,1902
+zombie_squirrel-0.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+zombie_squirrel-0.5.1.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
+zombie_squirrel-0.5.1.dist-info/RECORD,,

zombie_squirrel-0.4.7.dist-info/RECORD

@@ -1,10 +0,0 @@
-zombie_squirrel/__init__.py,sha256=IbDiH8pqVLYYrcBbidXKEabMpxdtSRAY28A9CFDmaTY,409
-zombie_squirrel/acorns.py,sha256=4uBzYtYgW2oD5sOohNQUw4qfjmNjmAIK2RlL1Ge1Udo,2597
-zombie_squirrel/squirrels.py,sha256=b1kQ2itTBo4o0e0r8Fg56YcJsiJAIqxzs86CSv0ExXE,11181
-zombie_squirrel/sync.py,sha256=84Ta5beHiPuGBVzp9SCo7G1b4McTUohcUIf_TJbNIV8,518
-zombie_squirrel/utils.py,sha256=woPxU4vYMUv-T0XOjV5ieViksU_q7It_n_5Ll4zpocA,289
-zombie_squirrel-0.4.7.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
-zombie_squirrel-0.4.7.dist-info/METADATA,sha256=82LMU9_1DwFxTv77PusoaeV9CHHw0Q10CEpmmFdP3h4,1903
-zombie_squirrel-0.4.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-zombie_squirrel-0.4.7.dist-info/top_level.txt,sha256=FmM0coe4AangURZLjM4JwwRv2B8H6oINYCoZLKLDCKA,16
-zombie_squirrel-0.4.7.dist-info/RECORD,,