[ENH] BIDS Metadata reporting

dandi/bids_utils.py

@@ -1,4 +1,9 @@
-from .utils import pluralize
+from dandi.bids_validator_xs import validate_bids
+from dandi.dandiapi import DandiAPIClient
+
+from .utils import get_logger, pluralize
+
+lgr = get_logger()
 
 
 def is_valid(
@@ -75,3 +80,84 @@ def report_errors(
             bold=True,
             fg="green",
         )
+
+
+def print_summary(
+    summary,
+    sections=[
+        ["subject", "session"],
+        ["session", "subject"],
+        ["subject", "sample"],
+        ["subject", "stain"],
+    ],
+    max_detail=3,
+):
+    out = ""
+    for section in sections:
+        base = section[0]
+        detail = section[1]
+        out += f"Here is the {base} to {detail} summary:\n"
+        for entry in summary[base + "_summary"]:
+            details = entry[detail + "s"]
+            detail_literal = f"{len(details)} ("
+            if len(details) > max_detail:
+                detail_literal += ", ".join(details[:max_detail]) + ", ...)"
+            else:
+                detail_literal += ", ".join(details) + ")"
+            out += f"\t-`{entry[base]}`\t{detail_literal}\n"
+    print(out)
+
+
+def summary(
+    dandi_id,
+    entities=["subject", "session", "sample", "stain"],
+):
+
+    with DandiAPIClient.for_dandi_instance("dandi") as client:
+        dandiset = client.get_dandiset(dandi_id)
+        path_list = []
+        for asset in dandiset.get_assets():
+            i = f"dummy/{asset.path}"
+            if "sub-MITU01h3" in i and "sub-MITU01" in i:
+                lgr.warning("Fixing subject field inconsistencies:")
+                lgr.warning(" - Pre-repair:  %s", i)
+                i = i.replace("sub-MITU01h3", "sub-MITU01")
+                lgr.warning(" + Post-repair: %s", i)
+            # ome.zarr support pending:
+            # https://github.com/dandi/dandi-cli/pull/1050
+            if "ome.zarr" not in i:
+                path_list.append(i)
+
+    result = validate_bids(path_list, dummy_paths=True)
+    for i in result["path_tracking"]:
+        lgr.warning("`%s` was not matched by any BIDS regex pattern.", i)
+    match_listing = result["match_listing"]
+    entity_sets = {}
+    for entity in entities:
+        entity_sets[entity] = set(
+            [i[entity] for i in match_listing if entity in i.keys()]
+        )
+
+    summary_full = {}
+    for entity in entities:
+        sub_summary = []
+        for value in entity_sets[entity]:
+            entry = {}
+            entry[entity] = value
+            for _entity in entities:
+                if _entity == entity:
+                    continue
+                entry[_entity + "s"] = list(
+                    set(
+                        [
+                            i[_entity]
+                            for i in match_listing
+                            if entity in i.keys()
+                            and _entity in i.keys()
+                            and i[entity] == value
+                        ]
+                    )
+                )
+            sub_summary.append(entry)
+        summary_full[entity + "_summary"] = sub_summary
+    print_summary(summary_full)

dandi/bids_validator_xs.py

@@ -364,7 +364,7 @@ def load_all(
 
 
 def validate_all(
-    bids_paths,
+    paths_list,
     regex_schema,
     debug=False,
 ):
@@ -398,7 +398,6 @@ def validate_all(
     """
 
     tracking_schema = deepcopy(regex_schema)
-    paths_list = _get_paths(bids_paths)
     tracking_paths = deepcopy(paths_list)
     if debug:
         itemwise_results = []
@@ -695,6 +694,7 @@ def validate_bids(
     schema_version=None,
     debug=False,
     report_path=False,
+    dummy_paths=False,
 ):
     """
     Validate paths according to BIDS schema.
@@ -743,8 +743,12 @@ def validate_bids(
         bids_paths, schema_reference_root, schema_version
     )
     regex_schema = load_all(bids_schema_dir)
+    if not dummy_paths:
+        paths_list = _get_paths(bids_paths)
+    else:
+        paths_list = bids_paths
     validation_result = validate_all(
-        bids_paths,
+        paths_list,
         regex_schema,
         debug=debug,
     )

dandi/tests/test_bids_utils.py

@@ -0,0 +1,4 @@
+def test_summary():
+    from dandi.bids_utils import summary
+
+    summary("000108")