feat: add numberOfSessions to AssetsSummary by bendichter · Pull Request #409 · dandi/dandi-schema

bendichter · 2026-05-14T00:16:24Z

Summary

Add optional numberOfSessions: int field to AssetsSummary, with a schema description documenting the counting semantics
Bump DANDI_SCHEMA_VERSION to 0.7.1, since 0.7.0 is already published in dandi/schema and the release workflow rejects modifications to published schemata
Aggregator counts unique (subject, session) pairs parsed from BIDS-style sub-* / ses-* tokens in asset paths. Keying on the pair avoids the undercount when two subjects share a session id like ses-1
Filename is parsed first (matching existing sub-/sample- handling); directory components are scanned as a fallback so ses-* tokens that appear only in the path (e.g. sub-X/ses-Y/foo_acq-Z_bold.nii.gz) are still counted

Caveats

Assets whose paths carry no sub-/ses- tokens won't contribute. Note that dandi organize produces sub-X/sub-X_ses-Y.nwb layouts, so organized NWB dandisets with session ids are counted; only datasets that follow neither BIDS nor the organized layout are missed.

Test plan

New test_aggregate_number_of_sessions covers: same subject across sessions, two subjects sharing a session id, ses- only in directory, ses- without any sub-, and the no-ses- case
Existing test_aggregate fixtures updated with expected numberOfSessions values
Existing test_aggregation_bids now asserts numberOfSessions == 2
Full suite: 268 passed, 17 skipped; tox -e lint,typing clean

🤖 Generated with Claude Code

Aggregator counts unique (subject, session) pairs parsed from BIDS-style sub-* and ses-* tokens in asset paths (filename first, then directory components when the session token is omitted from the filename). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

codecov · 2026-05-14T00:16:33Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.36%. Comparing base (54a77c8) to head (8b31bc6).

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #409       +/-   ##
===========================================
+ Coverage   48.27%   97.36%   +49.08%     
===========================================
  Files          19       19               
  Lines        2430     2463       +33     
===========================================
+ Hits         1173     2398     +1225     
+ Misses       1257       65     -1192

Flag	Coverage Δ
unittests	`97.36% <100.00%> (+49.08%)`	⬆️

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# Conflicts: # dandischema/metadata.py

yarikoptic · 2026-05-14T11:57:46Z

+        if not found.get("session") and part.startswith("ses-"):
+            found["session"] = part.split("ses-", 1)[1]
+    # Fallback: ses- tokens that appear only in directory components (e.g.
+    # `sub-X/ses-Y/foo_acq-Z_bold.nii.gz`) should still be counted. To form
+    # the (subject, session) pair we also accept a directory-only subject,
+    # but we do not add such a subject to stats["subjects"] — subject
+    # counting remains driven by the filename and wasAttributedTo, matching
+    # prior behavior.
+    if not found.get("session"):
+        dir_subject = found.get("subject")
+        dir_session: Optional[str] = None
+        for directory in asset_path.parts[:-1]:
+            for part in directory.split("_"):
+                if dir_subject is None and part.startswith("sub-"):
+                    dir_subject = part.split("sub-", 1)[1]
+                if dir_session is None and part.startswith("ses-"):
+                    dir_session = part.split("ses-", 1)[1]
+        if dir_subject is not None and dir_session is not None:
+            found.setdefault("subject", dir_subject)
+            found["session"] = dir_session
+    stats["sessions"] = stats.get("sessions", [])
+    if found.get("subject") and found.get("session"):
+        pair = (found["subject"], found["session"])
+        if pair not in stats["sessions"]:
+            stats["sessions"].append(pair)


too aisloppy -- easier to HI compose the logic but first potentially even generalize 2 prior blocks into a 'for' loop, then if no session was found in filename, go through path's parts and split on ses- and be done if any matches.

Done in cdb37ee — collapsed the sub-/sample-/ses- filename parsing into a single loop over an entities list, and simplified the session fallback to scanning asset_path.parts[:-1] for a ses-X directory and stopping at the first match. Dropped the directory-only subject fallback since BIDS files always carry sub- in the filename.

yarikoptic

THANK YOU for the PR. Needs a little a human touch ;)

Per review feedback: generalize the per-prefix blocks (sub-, sample-, ses-) into a single loop over an entity list, and simplify the session fallback to a direct scan of path parts. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

candleindark · 2026-05-14T16:57:21Z

Is the minor label a bit too much? Since we don't have a major in our version number, patch has been carrying the semantics of a minor.

bendichter · 2026-05-14T16:59:27Z

yes, I think patch makes sense for this while major is 0

candleindark

LGTM as the targeted datasets are valid BIDS datasets. (See other comments for more details).

candleindark · 2026-05-14T19:04:49Z

    numberOfCells: Optional[int] = Field(None, json_schema_extra={"readOnly": True})
+    numberOfSessions: Optional[int] = Field(
+        None, json_schema_extra={"readOnly": True}
+    )  # BIDS ses-* tokens, counted as unique (subject, session) pairs


Possibly add to the comment that this count assumes the dataset is valid BIDS dataset. (For example, a session without subject will not be counted)

well, that's what I wonder -- since we do have sub-..._ses-... even in DANDI names, and we do count on those -- we better count sessions as well in non-BIDS names as well. but "AI logic" above is wrong for that... will comment there

actually my initial read was wrong -- there is a generic handling in the filename at https://github.com/dandi/dandi-schema/pull/409/changes#diff-196e8d7f9869422a0dba629b1f58a9972a300d67308aec783b2847cdb50ef5ffR541

but wouldn't it work for DANDI names (no folder name) as well and thus just a matter of

Suggested change

) # BIDS ses-* tokens, counted as unique (subject, session) pairs

) # BIDS or DANDI ses-* tokens (in file name or path), counted as unique (subject, session) pairs

?

Coverage's `source = dandischema` resolves to the in-repo tree, but the package was installed (non-editable) into the tox venv, so the source modules actually executed from site-packages and fell outside the measured tree. As a result Codecov recorded 0% for every source module (metadata.py, models.py, ...) — only the test files, which run from the repo, were counted. This dragged patch coverage below the project threshold even for fully tested changes. Setting `usedevelop = true` makes the measured source and the executed source the same in-repo files, so metadata.py now reports ~90% instead of 0% and Codecov can map diff lines correctly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Schema 0.7.0 is already published in dandi/schema, so adding the numberOfSessions field to AssetsSummary requires a new schema version (the release workflow guards against modifying published schemata). Also add a schema description for the field documenting the (subject, session) pair counting, mark the new test as ai_generated, and cover the case where ses- appears without any sub- token. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/master' into add-number-of-sessions

c7069f6

# Conflicts: # dandischema/metadata.py

bendichter requested review from candleindark and yarikoptic May 14, 2026 00:21

bendichter marked this pull request as ready for review May 14, 2026 00:29

yarikoptic reviewed May 14, 2026

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yarikoptic requested changes May 14, 2026

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yarikoptic added enhancement New feature or request minor Increment the minor version when merged labels May 14, 2026

bendichter mentioned this pull request May 14, 2026

AssetsSummary: numberOfSamples / numberOfCells under-count when the same id appears across subjects #411

Open

candleindark reviewed May 14, 2026

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bendichter mentioned this pull request Jun 11, 2026

Add num_subjects: advanced-search operator dandi/dandi-archive#2827

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4 tasks

bendichter and others added 5 commits July 7, 2026 09:10

Merge branch 'master' into add-number-of-sessions

6cba609

Merge branch 'master' into add-number-of-sessions

839f861

Merge branch 'master' into add-number-of-sessions

8b31bc6

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feat: add numberOfSessions to AssetsSummary - #409

feat: add numberOfSessions to AssetsSummary#409
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	) # BIDS ses-* tokens, counted as unique (subject, session) pairs
	) # BIDS or DANDI ses-* tokens (in file name or path), counted as unique (subject, session) pairs

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