Dandi export fixes

CHANGELOG.md

@@ -27,6 +27,7 @@ dj.FreeTable(dj.conn(), "common_session.session_group").drop()
 - Enforce match between ingested nwb probe geometry and existing table entry
     #1074
 - Update DataJoint install and password instructions #1131
+- Fix dandi upload process for nwb's with video or linked objects #1095
 - Minor docs fixes #1145
 
 ### Pipelines

src/spyglass/common/common_dandi.py

@@ -1,6 +1,7 @@
 import os
 import shutil
 from pathlib import Path
+from typing import Optional
 
 import datajoint as dj
 import fsspec
@@ -9,7 +10,7 @@
 from fsspec.implementations.cached import CachingFileSystem
 
 from spyglass.common.common_usage import Export, ExportSelection
-from spyglass.settings import export_dir
+from spyglass.settings import export_dir, raw_dir
 from spyglass.utils import SpyglassMixin, logger
 from spyglass.utils.sql_helper_fn import SQLDumpHelper
 
@@ -21,7 +22,8 @@
     from dandi.consts import known_instances
     from dandi.dandiapi import DandiAPIClient
     from dandi.metadata.nwb import get_metadata
-    from dandi.organize import OrganizeInvalid
+    from dandi.organize import CopyMode, FileOperationMode, OrganizeInvalid
+    from dandi.pynwb_utils import nwb_has_external_links
     from dandi.validate_types import Severity
 
 except (ImportError, ModuleNotFoundError) as e:
@@ -31,8 +33,11 @@
         DandiAPIClient,
         get_metadata,
         OrganizeInvalid,
+        CopyMode,
+        FileOperationMode,
         Severity,
-    ) = [None] * 6
+        nwb_has_external_links,
+    ) = [None] * 9
     logger.warning(e)
 
 
@@ -87,6 +92,7 @@ def compile_dandiset(
         dandiset_id: str,
         dandi_api_key: str = None,
         dandi_instance: str = "dandi",
+        skip_raw_files: bool = False,
     ):
         """Compile a Dandiset from the export.
         Parameters
@@ -100,6 +106,8 @@ def compile_dandiset(
             DANDI_API_KEY is set.
         dandi_instance : str, optional
             What instance of Dandi the dandiset is on. Defaults to dev server.
+        skip_raw_files : bool, optional
+            Dev tool to skip raw files in the export. Defaults to False.
         """
         key = (Export & key).fetch1("KEY")
         paper_id = (Export & key).fetch1("paper_id")
@@ -137,9 +145,14 @@ def compile_dandiset(
 
         os.makedirs(destination_dir, exist_ok=False)
         for file in source_files:
-            if not os.path.exists(
-                f"{destination_dir}/{os.path.basename(file)}"
-            ):
+            if os.path.exists(f"{destination_dir}/{os.path.basename(file)}"):
+                continue
+            if skip_raw_files and raw_dir in file:
+                continue
+            # copy the file if it has external links so can be safely edited
+            if nwb_has_external_links(file):
+                shutil.copy(file, f"{destination_dir}/{os.path.basename(file)}")
+            else:
                 os.symlink(file, f"{destination_dir}/{os.path.basename(file)}")
 
         # validate the dandiset
@@ -154,11 +167,16 @@ def compile_dandiset(
 
         # organize the files in the dandiset directory
         dandi.organize.organize(
-            destination_dir, dandiset_dir, invalid=OrganizeInvalid.WARN
+            destination_dir,
+            dandiset_dir,
+            update_external_file_paths=True,
+            invalid=OrganizeInvalid.FAIL,
+            media_files_mode=CopyMode.SYMLINK,
+            files_mode=FileOperationMode.COPY,
         )
 
         # get the dandi name translations
-        translations = translate_name_to_dandi(destination_dir)
+        translations = lookup_dandi_translation(destination_dir, dandiset_dir)
 
         # upload the dandiset to the dandi server
         if dandi_api_key:
@@ -200,7 +218,7 @@ def write_mysqldump(self, export_key: dict):
             docker_id=None,
             spyglass_version=spyglass_version,
         )
-        sql_dump.write_mysqldump(self & key, file_suffix="_dandi")
+        sql_dump.write_mysqldump([self & key], file_suffix="_dandi")
 
 
 def _get_metadata(path):
@@ -229,6 +247,7 @@ def translate_name_to_dandi(folder):
     dict
         dictionary of filename to dandi_path translations
     """
+
     files = Path(folder).glob("*")
     metadata = list(map(_get_metadata, files))
     metadata, skip_invalid = dandi.organize.filter_invalid_metadata_rows(
@@ -243,6 +262,39 @@ def translate_name_to_dandi(folder):
     ]
 
 
+def lookup_dandi_translation(source_dir: str, dandiset_dir: str):
+    """Get the dandi_path for each nwb file in the source_dir from
+    the organized dandi directory
+
+    Parameters
+    ----------
+    source_dir : str
+        location of the source files
+    dandiset_dir : str
+        location of the organized dandiset directory
+
+    Returns
+    -------
+    dict
+        dictionary of filename to dandi_path translations
+    """
+    # get the obj_id and dandipath for each nwb file in the dandiset
+    dandi_name_dict = {}
+    for dandi_file in Path(dandiset_dir).rglob("*.nwb"):
+        dandi_path = dandi_file.relative_to(dandiset_dir).as_posix()
+        with pynwb.NWBHDF5IO(dandi_file, "r") as io:
+            nwb = io.read()
+            dandi_name_dict[nwb.object_id] = dandi_path
+    # for each file in the source_dir, lookup the dandipath based on the obj_id
+    name_translation = {}
+    for file in Path(source_dir).glob("*"):
+        with pynwb.NWBHDF5IO(file, "r") as io:
+            nwb = io.read()
+            dandi_path = dandi_name_dict[nwb.object_id]
+            name_translation[file.name] = dandi_path
+    return name_translation
+
+
 def validate_dandiset(
     folder, min_severity="ERROR", ignore_external_files=False
 ):

src/spyglass/common/common_usage.py

@@ -22,6 +22,7 @@
     unique_dicts,
     update_analysis_for_dandi_standard,
 )
+from spyglass.utils.nwb_helper_fn import get_linked_nwbs
 from spyglass.utils.sql_helper_fn import SQLDumpHelper
 
 schema = dj.schema("common_usage")
@@ -236,6 +237,7 @@ class File(SpyglassMixin, dj.Part):
 
     def populate_paper(self, paper_id: Union[str, dict]):
         """Populate Export for a given paper_id."""
+        self.load_shared_schemas()
         if isinstance(paper_id, dict):
             paper_id = paper_id.get("paper_id")
         self.populate(ExportSelection().paper_export_id(paper_id))
@@ -272,6 +274,21 @@ def make(self, key):
             query.list_file_paths(paper_key) + restr_graph.file_paths
         )
 
+        # Check for linked nwb objects and add them to the export
+        unlinked_files = set()
+        for file in file_paths:
+            if not (links := get_linked_nwbs(file["file_path"])):
+                unlinked_files.add(file)
+                continue
+            logger.warning(
+                "Dandi not yet supported for linked nwb objects "
+                + f"excluding {file['file_path']} from export "
+                + f" and including {links} instead"
+            )
+            for link in links:
+                unlinked_files.add(link)
+        file_paths = {"file_path": link for link in unlinked_files}
+
         table_inserts = [
             {**key, **rd, "table_id": i}
             for i, rd in enumerate(restr_graph.as_dict)

src/spyglass/utils/dj_helper_fn.py

@@ -355,6 +355,7 @@ def get_child_tables(table):
 def update_analysis_for_dandi_standard(
     filepath: str,
     age: str = "P4M/P8M",
+    resolve_external_table: bool = True,
 ):
     """Function to resolve common nwb file format errors within the database
 
@@ -364,6 +365,9 @@ def update_analysis_for_dandi_standard(
         abs path to the file to edit
     age : str, optional
         age to assign animal if missing, by default "P4M/P8M"
+    resolve_external_table : bool, optional
+        whether to update the external table. Set False if editing file
+        outside the database, by default True
     """
     from spyglass.common import LabMember
 
@@ -394,7 +398,7 @@ def update_analysis_for_dandi_standard(
             )
             file["/general/subject/species"][()] = new_species_value
 
-        if not (
+        elif not (
             len(species_value.split(" ")) == 2 or "NCBITaxon" in species_value
         ):
             raise ValueError(
@@ -427,7 +431,9 @@ def update_analysis_for_dandi_standard(
             file["/general/experimenter"][:] = new_experimenter_value
 
     # update the datajoint external store table to reflect the changes
-    _resolve_external_table(filepath, file_name)
+    if resolve_external_table:
+        location = "raw" if filepath.endswith("_.nwb") else "analysis"
+        _resolve_external_table(filepath, file_name, location)
 
 
 def dandi_format_names(experimenter: List) -> List:
@@ -510,7 +516,10 @@ def make_file_obj_id_unique(nwb_path: str):
     new_id = str(uuid4())
     with h5py.File(nwb_path, "a") as f:
         f.attrs["object_id"] = new_id
-    _resolve_external_table(nwb_path, nwb_path.split("/")[-1])
+    location = "raw" if nwb_path.endswith("_.nwb") else "analysis"
+    _resolve_external_table(
+        nwb_path, nwb_path.split("/")[-1], location=location
+    )
     return new_id
 
 

src/spyglass/utils/nwb_helper_fn.py

@@ -69,6 +69,14 @@ def get_nwb_file(nwb_file_path):
                 from ..common.common_dandi import DandiPath
 
                 dandi_key = {"filename": os.path.basename(nwb_file_path)}
+                if not DandiPath() & dandi_key:
+                    # Check if non-copied raw file is in Dandi
+                    dandi_key = {
+                        "filename": Path(nwb_file_path).name.replace(
+                            "_.nwb", ".nwb"
+                        )
+                    }
+
                 if not DandiPath & dandi_key:
                     # If not in Dandi, then we can't find the file
                     raise FileNotFoundError(
@@ -101,6 +109,16 @@ def file_from_dandi(filepath):
     return False
 
 
+def get_linked_nwbs(path):
+    """Return a list of paths to NWB files that are linked by objects in
+    the file at the given path."""
+    with pynwb.NWBHDF5IO(path, "r") as io:
+        # open the nwb file (opens externally linked files as well)
+        nwb = io.read()
+        # get the linked files
+        return [x for x in io._HDF5IO__built if x != path]
+
+
 def get_config(nwb_file_path, calling_table=None):
     """Return a dictionary of config settings for the given NWB file.
     If the file does not exist, return an empty dict.