Adjustments for new Plugins

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Update MERFISH directory schema
 - Update Phenocycler docs
 - Update MERFISH directory schema
+- Adding support for EPIC's new plugin
 
 ## v0.0.23
 - Add token to validation_utils.get_assaytype_data, replace URL string concatenation with urllib

src/ingest_validation_tools/plugin_validator.py

@@ -3,7 +3,7 @@
 from collections.abc import Iterator
 from importlib import util
 from pathlib import Path
-from typing import List, Optional, Tuple, Type, Union
+from typing import Dict, List, Optional, Tuple, Type, Union
 
 from ingest_validation_tools.schema_loader import SchemaVersion
 
@@ -53,6 +53,9 @@ def __init__(
         assay_type: str,
         contains: List = [],
         verbose: bool = False,
+        metadata_tsv: SchemaVersion = None,
+        globus_token: str = None,
+        app_context: Dict[str, str] = {},
         **kwargs,
     ):
         """
@@ -72,6 +75,9 @@ def __init__(
         self.assay_type = assay_type
         self.contains = contains
         self.verbose = verbose
+        self.metadata_tsv = metadata_tsv
+        self.token = globus_token
+        self.app_context = app_context
 
     def _log(self, message):
         if self.verbose:
@@ -99,6 +105,8 @@ def run_plugin_validators_iter(
     plugin_dir: PathOrStr,
     is_shared_upload: bool,
     verbose: bool = True,
+    globus_token: str = None,
+    app_context: Dict[str, str] = {},
     **kwargs,
 ) -> Iterator[KeyValuePair]:
     """
@@ -134,7 +142,15 @@ def run_plugin_validators_iter(
                     raise ValidatorError(f"{data_path} should be the base directory of a dataset")
                 data_paths.append(data_path)
             for k, v in validation_error_iter(
-                data_paths, sv.dataset_type, plugin_dir, sv.contains, verbose=verbose, **kwargs
+                data_paths,
+                sv.dataset_type,
+                plugin_dir,
+                sv.contains,
+                verbose=verbose,
+                metadata_tsv=sv,
+                globus_token=globus_token,
+                app_context=app_context,
+                **kwargs,
             ):
                 yield k, v
         else:
@@ -179,6 +195,9 @@ def validation_error_iter(
     plugin_dir: PathOrStr,
     contains: List,
     verbose: bool = False,
+    metadata_tsv: SchemaVersion = None,
+    globus_token: str = None,
+    app_context: Dict[str, str] = {},
     **kwargs,
 ) -> Iterator[KeyValuePair]:
     """
@@ -195,6 +214,8 @@ def validation_error_iter(
     error messages
     """
     for cls in validation_class_iter(plugin_dir):
-        validator = cls(paths, assay_type, contains, verbose)
+        validator = cls(
+            paths, assay_type, contains, verbose, metadata_tsv, globus_token, app_context
+        )
         for err in validator.collect_errors(**kwargs):
             yield cls, err

src/ingest_validation_tools/upload.py

@@ -181,7 +181,7 @@ def get_app_context(self, submitted_app_context: Dict):
         Ensure that all default values are present, but privilege any
         submitted values (after making a basic validity check).
         """
-        for url_type in ["entities_url", "ingest_url", "constraints_url"]:
+        for url_type in ["entities_url", "ingest_url", "constraints_url", "uuid_url"]:
             if submitted_app_context.get(url_type):
                 split_url = urlsplit(submitted_app_context[url_type])
                 assert (
@@ -193,6 +193,7 @@ def get_app_context(self, submitted_app_context: Dict):
             "request_header": {"X-Hubmap-Application": "ingest-pipeline"},
             # TODO: does not work in HuBMAP currently
             "constraints_url": None,
+            "uuid_url": "https://uuid.api.hubmapconsortium.org/uuid/",
         } | submitted_app_context
 
     def validation_routine(
@@ -444,6 +445,8 @@ def _get_plugin_errors(self, **kwargs) -> dict:
                         plugin_path,
                         self.is_shared_upload,
                         verbose=self.verbose,
+                        globus_token=self.globus_token,
+                        app_context=self.app_context,
                         **kwargs,
                     ):
                         if v is None: