np_codeocean 0.2.0__tar.gz → 0.3.0__tar.gz

{np_codeocean-0.2.0 → np_codeocean-0.3.0}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: np_codeocean
-Version: 0.2.0
+Version: 0.3.0
 Summary: Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
-Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>
+Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>, Chris Mochizuki <chrism@alleninstitute.org>, Arjun Sridhar <arjun.sridhar@alleninstitute.org>
 License: MIT
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
@@ -13,16 +13,25 @@ Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX :: Linux
 Project-URL: Source, https://github.com/AllenInstitute/np_codeocean
 Project-URL: Issues, https://github.com/AllenInstitute/np_codeocean/issues
-Requires-Python: >=3.9
-Requires-Dist: np_session>=0.6.4
-Requires-Dist: np-tools>=0.1.21
-Requires-Dist: np-config>=0.4.24
+Requires-Python: >=3.10
+Requires-Dist: np_session>=0.6.44
+Requires-Dist: np-tools>=0.1.23
+Requires-Dist: np-config>=0.4.33
 Requires-Dist: requests>=2.31.0
 Requires-Dist: npc-session>=0.1.34
 Requires-Dist: polars>=0.20.16
+Requires-Dist: npc-lims>=0.1.168
+Requires-Dist: npc-ephys>=0.1.28
+Provides-Extra: dev
 Requires-Dist: bump>=1.3.2; extra == "dev"
 Requires-Dist: pdm>=2.4.9; extra == "dev"
-Provides-Extra: dev
+Provides-Extra: dynamic-routing-metadata
+Requires-Dist: np-aind-metadata>=0.1.17; extra == "dynamic-routing-metadata"
+Requires-Dist: npc-lims>=0.1.154; extra == "dynamic-routing-metadata"
+Requires-Dist: npc-sessions>=0.0.253; extra == "dynamic-routing-metadata"
+Requires-Dist: aind-data-transfer-models>=0.13.1; extra == "dynamic-routing-metadata"
+Requires-Dist: aind-codeocean-pipeline-monitor[full]>=0.5.0; extra == "dynamic-routing-metadata"
+Requires-Dist: aind-metadata-mapper==0.18.2; extra == "dynamic-routing-metadata"
 Description-Content-Type: text/markdown
 
 # np_codeocean

{np_codeocean-0.2.0 → np_codeocean-0.3.0}/pyproject.toml

@@ -1,3 +1,7 @@
+[tool.pdm.resolution.overrides]
+aind_data_transfer_models = ">=0.13.1"
+aind-metadata-mapper = "0.18.2"
+
 [tool.pdm.scripts]
 ruff = "ruff --fix src"
 blue = "blue src"
@@ -40,20 +44,24 @@ composite = [
 
 [project]
 name = "np_codeocean"
-version = "0.2.0"
+version = "0.3.0"
 description = "Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean"
 authors = [
     { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitute.org" },
+    { name = "Chris Mochizuki", email = "chrism@alleninstitute.org" },
+    { name = "Arjun Sridhar", email = "arjun.sridhar@alleninstitute.org" },
 ]
 dependencies = [
-    "np_session>=0.6.4",
-    "np-tools>=0.1.21",
-    "np-config>=0.4.24",
+    "np_session>=0.6.44",
+    "np-tools>=0.1.23",
+    "np-config>=0.4.33",
     "requests>=2.31.0",
     "npc-session>=0.1.34",
     "polars>=0.20.16",
+    "npc-lims>=0.1.168",
+    "npc-ephys>=0.1.28",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 readme = "README.md"
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -73,7 +81,8 @@ Source = "https://github.com/AllenInstitute/np_codeocean"
 Issues = "https://github.com/AllenInstitute/np_codeocean/issues"
 
 [project.scripts]
-upload = "np_codeocean.upload:main"
+upload_dr_behavior = "np_codeocean.scripts.upload_dynamic_routing_behavior:main"
+upload_dr_ecephys = "np_codeocean.scripts.upload_dynamic_routing_ecephys:main"
 upload_sessions = "np_codeocean.scripts.upload_sessions:main"
 
 [project.optional-dependencies]
@@ -81,6 +90,14 @@ dev = [
     "bump>=1.3.2",
     "pdm>=2.4.9",
 ]
+dynamic-routing-metadata = [
+    "np-aind-metadata>=0.1.17",
+    "npc-lims>=0.1.154",
+    "npc-sessions>=0.0.253",
+    "aind-data-transfer-models>=0.13.1",
+    "aind-codeocean-pipeline-monitor[full]>=0.5.0",
+    "aind-metadata-mapper==0.18.2",
+]
 
 [build-system]
 requires = [

np_codeocean-0.3.0/src/np_codeocean/__init__.py

@@ -0,0 +1,2 @@
+from np_codeocean.utils import *
+from np_codeocean.np_session_utils import *

np_codeocean-0.3.0/src/np_codeocean/np_session_utils.py

@@ -0,0 +1,367 @@
+from __future__ import annotations
+
+import dataclasses
+import datetime
+import doctest
+import pathlib
+from collections.abc import Iterable
+import shutil
+
+import aind_data_transfer_models.core
+import np_config
+import np_logging
+import np_session
+import np_tools
+
+import np_codeocean.utils as utils
+
+logger = np_logging.get_logger(__name__)
+
+@dataclasses.dataclass
+class CodeOceanUpload:
+    """Objects required for uploading a Mindscope Neuropixels session to CodeOcean.
+        Paths are symlinks to files on np-exp.
+    """
+    session: np_session.Session
+    """Session object that the paths belong to."""
+    
+    platform: utils.AINDPlatform
+    """The 'platform' in the Neural Dynamics data schema language (effectively the rig
+    type, which determines the processing pipeline the data follows).
+     
+    Our rules are:
+    - if it ran in a behavior box: `behavior`
+    - anything else: `ecephys`
+    
+    This means there will be behavior-only sessions that ran on NP-rigs
+    without ephys data (habs, opto experiments etc.), that will be uploaded as
+    `ecephys` platform data.
+    """
+
+    behavior: pathlib.Path | None
+    """Directory of symlinks to files in top-level of session folder on np-exp,
+    plus all files in `exp` and `qc` subfolders, if present. Excludes behavior video files
+    and video info jsons."""
+    
+    behavior_videos: pathlib.Path | None    
+    """Directory of symlinks to behavior video files and video info jsons in
+    top-level of session folder on np-exp."""
+    
+    ephys: pathlib.Path | None
+    """Directory of symlinks to raw ephys data files on np-exp, with only one
+    `recording` per `Record Node` folder."""
+
+    aind_metadata: pathlib.Path | None
+    """Directory of symlinks to aind metadata json files in top-level of session folder 
+    on np-exp."""
+
+    job: pathlib.Path
+    """File containing job parameters for `aind-data-transfer`"""
+
+    force_cloud_sync: bool = False
+    """If True, re-upload and re-make raw asset even if data exists on S3."""
+
+    @property
+    def project_name(self) -> str:
+        if isinstance(self.session, np_session.PipelineSession):
+            return "OpenScope"
+        return "Dynamic Routing"
+
+    @property
+    def root(self) -> pathlib.Path:
+        for attr in (self.behavior, self.behavior_videos, self.ephys, self.aind_metadata):
+            if attr is not None:
+                return attr.parent
+        raise ValueError(f"No upload directories assigned to {self!r}")
+
+def create_aind_metadata_symlinks(upload: CodeOceanUpload) -> bool:
+    """
+    Create symlinks in `dest` pointing to aind metadata json files from the root directory
+    on np-exp. Returns True if any metadata files are found in np-exp and the `aind_metadata`
+    folder is created.
+    """
+    has_metadata_files = False
+    for src in upload.session.npexp_path.glob('*'):
+        if src.stem in utils.AIND_METADATA_NAMES:
+            np_tools.symlink(src, upload.aind_metadata / src.name)
+            has_metadata_files = True
+    if has_metadata_files:
+        logger.debug(f'Finished creating symlinks to aind metadata files in {upload.session.npexp_path}')
+    else:
+        logger.debug(f'No metadata files found in {upload.session.npexp_path}; No symlinks for metadata were made')
+    return has_metadata_files
+
+
+def create_ephys_symlinks(session: np_session.Session, dest: pathlib.Path, 
+                          recording_dirs: Iterable[str] | None = None) -> None:
+    """Create symlinks in `dest` pointing to raw ephys data files on np-exp, with only one
+    `recording` per `Record Node` folder (the largest, if multiple found).
+    
+    Relative paths are preserved, so `dest` will essentially be a merge of
+    _probeABC / _probeDEF folders.
+    
+    Top-level items other than `Record Node *` folders are excluded.
+    """
+    root_path = session.npexp_path
+    if isinstance(session, np_session.PipelineSession) and session.lims_path is not None:
+        # if ephys has been uploaded to lims, use lims path, as large raw data may have
+        # been deleted from np-exp
+        if any(
+            np_tools.get_filtered_ephys_paths_relative_to_record_node_parents(
+                session.npexp_path, specific_recording_dir_names=recording_dirs
+            )
+        ):
+            root_path = session.lims_path
+    logger.info(f'Creating symlinks to raw ephys data files in {root_path}...')
+    for abs_path, rel_path in np_tools.get_filtered_ephys_paths_relative_to_record_node_parents(
+        root_path, specific_recording_dir_names=recording_dirs
+        ):
+        if not abs_path.is_dir():
+            np_tools.symlink(abs_path, dest / rel_path)
+    logger.debug(f'Finished creating symlinks to raw ephys data files in {root_path}')
+    utils.cleanup_ephys_symlinks(dest)
+
+
+def create_behavior_symlinks(session: np_session.Session, dest: pathlib.Path | None) -> None:
+    """Create symlinks in `dest` pointing to files in top-level of session
+    folder on np-exp, plus all files in `exp` subfolder, if present.
+    """
+    if dest is None: 
+        logger.debug(f"No behavior folder supplied for {session}")
+        return
+    subfolder_names = ('exp', 'qc')
+    logger.info(f'Creating symlinks in {dest} to files in {session.npexp_path}...')
+    for src in session.npexp_path.glob('*'):
+        if not src.is_dir() and not utils.is_behavior_video_file(src):
+            np_tools.symlink(src, dest / src.relative_to(session.npexp_path))
+    logger.debug(f'Finished creating symlinks to top-level files in {session.npexp_path}')
+
+    for name in subfolder_names:
+        subfolder = session.npexp_path / name
+        if not subfolder.exists():
+            continue
+        for src in subfolder.rglob('*'):
+            if not src.is_dir():
+                np_tools.symlink(src, dest / src.relative_to(session.npexp_path))
+        logger.debug(f'Finished creating symlinks to {name!r} files')
+
+
+def create_behavior_videos_symlinks(session: np_session.Session, dest: pathlib.Path | None) -> None:
+    """Create symlinks in `dest` pointing to MVR video files and info jsons in top-level of session
+    folder on np-exp.
+    """
+    if dest is None: 
+        logger.debug(f"No behavior_videos folder supplied for {session}")
+        return
+    logger.info(f'Creating symlinks in {dest} to files in {session.npexp_path}...')
+    for src in session.npexp_path.glob('*'):
+        if utils.is_behavior_video_file(src):
+            np_tools.symlink(src, dest / src.relative_to(session.npexp_path))
+    logger.debug(f'Finished creating symlinks to behavior video files in {session.npexp_path}')
+
+
+def get_surface_channel_start_time(session: np_session.Session) -> datetime.datetime:
+    """
+    >>> session = np_session.Session("//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_690706_20231129_surface_channels")
+    >>> get_surface_channel_start_time(session)
+    datetime.datetime(2023, 11, 29, 14, 56, 25, 219000)
+    """
+    sync_messages_paths = tuple(session.npexp_path.glob('*/*/*/sync_messages.txt'))
+    if not sync_messages_paths:
+        raise ValueError(f'No sync messages txt found for surface channel session {session}')
+    sync_messages_path = sync_messages_paths[0]
+
+    with open(sync_messages_path, 'r') as f:
+        software_time_line = f.readlines()[0]
+
+    timestamp_value = float(software_time_line[software_time_line.index(':')+2:].strip())
+    timestamp = datetime.datetime.fromtimestamp(timestamp_value / 1e3)
+    return timestamp
+
+
+def get_upload_csv_for_session(upload: CodeOceanUpload) -> dict[str, str | int | bool]:
+    """
+    >>> path = "//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_690706_20231129_surface_channels"
+    >>> utils.is_surface_channel_recording(path)
+    True
+    >>> upload = create_codeocean_upload(path)
+    >>> ephys_upload_csv = get_upload_csv_for_session(upload)
+    >>> ephys_upload_csv['modality0.source']
+    '//allen/programs/mindscope/workgroups/np-exp/codeocean/DRpilot_690706_20231129_surface_channels/ephys'
+    >>> ephys_upload_csv.keys()
+    dict_keys(['project_name', 'platform', 'subject-id', 'force_cloud_sync', 'modality0', 'modality0.source', 'acq-datetime'])
+    """
+    params = {
+        'project_name': upload.project_name,
+        'platform': upload.platform,
+        'subject-id': str(upload.session.mouse),
+        'force_cloud_sync': upload.force_cloud_sync,
+    }
+    idx = 0
+    for modality_name, attr_name in {
+        'ecephys': 'ephys',
+        'behavior': 'behavior',
+        'behavior-videos': 'behavior_videos',
+    }.items():
+        if getattr(upload, attr_name) is not None:
+            params[f'modality{idx}'] = modality_name
+            params[f'modality{idx}.source'] = np_config.normalize_path(getattr(upload, attr_name)).as_posix()
+            idx += 1
+    
+    if upload.aind_metadata:
+        params['metadata_dir'] = upload.aind_metadata.as_posix()
+            
+    if utils.is_surface_channel_recording(upload.session.npexp_path.as_posix()):
+        date = datetime.datetime(upload.session.date.year, upload.session.date.month, upload.session.date.day)
+        session_date_time = date.combine(upload.session.date, get_surface_channel_start_time(upload.session).time())
+        params['acq-datetime'] = f'{session_date_time.strftime(utils.ACQ_DATETIME_FORMAT)}'
+    else:
+        params['acq-datetime'] = f'{upload.session.start.strftime(utils.ACQ_DATETIME_FORMAT)}'
+    
+    return params # type: ignore
+
+
+def is_ephys_session(session: np_session.Session) -> bool:
+    return bool(next(session.npexp_path.rglob('settings*.xml'), None))
+
+def get_np_session(session_path_or_folder_name: str) -> np_session.Session:
+    """Accommodates surface channel folders, and updates the returned instance's
+    npexp_path accordingly"""
+    is_surface_channel_recording = utils.is_surface_channel_recording(session_path_or_folder_name)
+    session = np_session.Session(session_path_or_folder_name)
+    if is_surface_channel_recording and not utils.is_surface_channel_recording(session.npexp_path.name):
+        # manually assign surface channel path which was lost when creating
+        # session object
+        session = np_session.Session(session.npexp_path.parent / f'{session.folder}_surface_channels')
+        if 'surface_channels' not in session.npexp_path.name or not session.npexp_path.exists():
+            raise FileNotFoundError(f"Surface channel path {session.npexp_path} does not exist, or does not exist in expected folder (ie np-exp)")
+    return session
+
+def create_codeocean_upload(
+    session_path_or_folder_name: str,
+    recording_dirs: Iterable[str] | None = None,
+    force_cloud_sync: bool = False,
+    codeocean_root: pathlib.Path = np_session.NPEXP_PATH / 'codeocean',
+) -> CodeOceanUpload:
+    """Create directories of symlinks to np-exp files with correct structure
+    for upload to CodeOcean.
+    
+    - only one `recording` per `Record Node` folder (largest if multiple found)
+    - job file for feeding into `aind-data-transfer`
+    
+    >>> upload = create_codeocean_upload("//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_690706_20231129_surface_channels")
+    >>> upload.behavior is None
+    True
+    >>> upload.ephys.exists()
+    True
+    """
+    platform: utils.AINDPlatform = 'ecephys' # all session-type uploads with a folder of data are ecephys platform; behavior platform is for behavior-box sessions
+
+    session = get_np_session(str(session_path_or_folder_name))
+    if utils.is_surface_channel_recording(str(session_path_or_folder_name)):
+        root = codeocean_root / f'{session.folder}_surface_channels'
+        behavior = None
+        behavior_videos = None
+    else:
+        root = codeocean_root / session.folder
+        behavior = np_config.normalize_path(root / 'behavior')
+        behavior_videos = behavior.with_name('behavior-videos')
+
+    logger.debug(f'Created directory {root} for CodeOcean upload')
+
+    logger.info('Attempting to create sub directory for AIND metadata jsons..')
+    metadata_path = get_aind_metadata_path(root)
+    
+    return CodeOceanUpload(
+        session = session, 
+        behavior = behavior,
+        behavior_videos = behavior_videos,
+        ephys = np_config.normalize_path(root / 'ephys') if is_ephys_session(session) else None,
+        aind_metadata = metadata_path if has_metadata(session) else None,
+        job = np_config.normalize_path(root / 'upload.csv'),
+        force_cloud_sync=force_cloud_sync,
+        platform=platform,
+    )
+
+def has_metadata(session: np_session.Session) -> bool:
+    return any(
+        (session.npexp_path / name).exists()
+        for name in utils.AIND_METADATA_NAMES
+    )
+    
+def get_aind_metadata_path(upload_root: pathlib.Path) -> pathlib.Path:
+    return np_config.normalize_path(upload_root / 'aind_metadata')
+
+def upload_session(
+    session_path_or_folder_name: str, 
+    recording_dirs: Iterable[str] | None = None,
+    force: bool = False,
+    dry_run: bool = False,
+    test: bool = False,
+    hpc_upload_job_email: str = utils.HPC_UPLOAD_JOB_EMAIL,
+    regenerate_symlinks: bool = True,
+    adjust_ephys_timestamps: bool = True,
+    codeocean_configs: aind_data_transfer_models.core.CodeOceanPipelineMonitorConfigs | None = None,
+) -> None:
+    codeocean_root = np_session.NPEXP_PATH / ('codeocean-dev' if test else 'codeocean')
+    logger.debug(f'{codeocean_root = }')
+    upload = create_codeocean_upload(
+        str(session_path_or_folder_name),
+        codeocean_root=codeocean_root,
+        recording_dirs=recording_dirs,
+        force_cloud_sync=force
+    )
+    if regenerate_symlinks and upload.root.exists():
+        logger.debug(f'Removing existing {upload.root = }')
+        shutil.rmtree(upload.root.as_posix(), ignore_errors=True)
+    if upload.aind_metadata:
+        create_aind_metadata_symlinks(upload)
+    if upload.ephys:
+        create_ephys_symlinks(upload.session, upload.ephys, recording_dirs=recording_dirs)
+    if upload.behavior:
+        create_behavior_symlinks(upload.session, upload.behavior)
+    if upload.behavior_videos:
+        create_behavior_videos_symlinks(upload.session, upload.behavior_videos)
+    if adjust_ephys_timestamps and upload.ephys:
+        if not upload.behavior: # includes surface channel recordings
+            logger.warning(f"Cannot adjust ephys timestamps for {upload.session} - no behavior folder supplied for upload")
+        else:
+            try:
+                utils.write_corrected_ephys_timestamps(ephys_dir=upload.ephys, behavior_dir=upload.behavior)
+            except utils.SyncFileNotFoundError:
+                raise FileNotFoundError(
+                    (
+                        f"Cannot adjust timestamps - no sync file found in {upload.behavior}. "
+                        "If the session doesn't have one, run with "
+                        "`adjust_ephys_timestamps=False` or `--no-sync` flag in CLI"
+                    )
+                ) from None
+    for path in (upload.ephys, upload.behavior, upload.behavior_videos, upload.aind_metadata):
+        if path is not None and path.exists():
+            utils.convert_symlinks_to_posix(path)
+    csv_content: dict = get_upload_csv_for_session(upload)
+    utils.write_upload_csv(csv_content, upload.job)
+    np_logging.web('np_codeocean').info(f'Submitting {upload.session} to hpc upload queue')
+    utils.put_jobs_for_hpc_upload(
+        utils.get_job_models_from_csv(upload.job, codeocean_configs=codeocean_configs),
+        upload_service_url=utils.DEV_SERVICE if test else utils.AIND_DATA_TRANSFER_SERVICE,
+        user_email=hpc_upload_job_email,
+        dry_run=dry_run,
+        save_path=upload.job.with_suffix('.json'),
+    )
+    if not dry_run:
+        logger.info(f'Finished submitting {upload.session} - check progress at {utils.DEV_SERVICE if test else utils.AIND_DATA_TRANSFER_SERVICE}')
+    
+    if (is_split_recording := 
+        recording_dirs is not None 
+        and len(tuple(recording_dirs)) > 1 
+        and isinstance(recording_dirs, str)
+    ):
+        logger.warning(f"Split recording {upload.session} will need to be sorted manually with `CONCAT=True`")
+
+if __name__ == '__main__':
+    import doctest
+
+    doctest.testmod(
+        optionflags=(doctest.IGNORE_EXCEPTION_DETAIL | doctest.NORMALIZE_WHITESPACE),
+    )

np_codeocean-0.3.0/src/np_codeocean/scripts/fix_ephys_data_on_s3.py

@@ -0,0 +1,20 @@
+import datetime
+import logging
+import pathlib
+import npc_lims
+
+import np_codeocean
+
+logging.basicConfig(
+    filename=f"logs/{pathlib.Path(__file__).stem}_{datetime.datetime.now().strftime('%Y-%d-%m_%H-%M-%S')}.log",
+    level=logging.DEBUG, 
+    format="%(asctime)s | %(name)s | %(levelname)s | %(message)s", 
+    datefmt="%Y-%m-%d %H:%M:%S",
+    )
+logger = logging.getLogger(__name__)
+
+session_id = 'ecephys_702136_2024-03-06_11-25-22'
+root = npc_lims.get_raw_data_root(session_id)
+ephys = root / 'ecephys_clipped'
+
+np_codeocean.cleanup_ephys_symlinks(ephys)