Merge branch 'release/0.1.0'

CHANGES:

- Added: two *new* tools -- metadata generator and BIDS clear
- Fixed: multiple bugfixes
- Added: Aesthetic improvements

.dockerignore

@@ -0,0 +1 @@
+sandbox

Dockerfile

@@ -12,17 +12,17 @@ COPY manifest.json ${FLYWHEEL}/manifest.json
 ENTRYPOINT ["/flywheel/v0/fw_heudiconv_run.py"]
 
 # Copy over python scripts that generate the BIDS hierarchy
-RUN apt-get -y update
-RUN apt-get install -y zip
-RUN pip install --no-cache heudiconv flywheel-sdk pandas
+RUN apt-get -y update && apt-get install -y curl
+RUN curl -sL https://deb.nodesource.com/setup_10.x | bash
+RUN apt-get -y update && apt-get install -y zip nodejs
+RUN npm install -g bids-validator
+RUN pip install --no-cache heudiconv nipype flywheel-sdk pandas
+
 COPY . /src
+
 RUN cd /src \
     && pip install . \
-    && pip install --no-cache --no-deps heudiconv \
-    && pip install --no-cache flywheel-sdk \
-    && pip install --no-cache nipype \
-    && rm -rf /src \
-    && apt-get install -y --no-install-recommends zip
+    && rm -rf /src
 
 COPY fw_heudiconv_run.py /flywheel/v0/fw_heudiconv_run.py
 RUN chmod +x ${FLYWHEEL}/*

fw_heudiconv/cli/clear.py

@@ -0,0 +1,170 @@
+import argparse
+import flywheel
+import logging
+import warnings
+import sys
+
+with warnings.catch_warnings():
+    warnings.simplefilter('ignore')
+    from fw_heudiconv.cli.export import get_nested
+
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger('fw-heudiconv-clearer')
+
+
+def clear_bids(client, project_label, session_labels=None, subject_labels=None, dry_run=False, file_types = ['.nii', '.bval', '.bvec']):
+
+    logger.info("Querying Flywheel server...")
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        project_obj = client.projects.find_first('label="{}"'.format(project_label))
+
+    if project_obj is None:
+        logger.error("Project not found! Maybe check spelling...?")
+        return 1
+
+    logger.debug('\tFound project: \n\t\t%s (%s)', project_obj['label'], project_obj.id)
+    sessions = client.get_project_sessions(project_obj.id)
+
+    # filters
+    if subject_labels:
+        sessions = [s for s in sessions if s.subject['label'] in subject_labels]
+    if session_labels:
+        sessions = [s for s in sessions if s.label in session_labels]
+
+    if not sessions:
+        logger.error("No sessions found!")
+        return 1
+
+    logger.info('\tFound subjects:\n\t\t%s',
+                 "\n\t\t".join(set(['%s (%s)' % (ses.subject.label, ses.subject.id) for ses in sessions])))
+
+    logger.info('\tFound sessions:\n\t\t%s',
+                 "\n\t\t".join(['%s (%s)' % (ses['label'], ses.id) for ses in sessions]))
+
+    file_list = []
+    for ses in sessions:
+
+        acquisitions = ses.acquisitions()
+
+        for acq in acquisitions:
+
+            files = [f.to_dict() for f in acq.files if any([x in f.name for x in file_types])]
+
+            files = [f for f in files if get_nested(f, 'info', 'BIDS') != 'NA' and get_nested(f, 'info', 'BIDS') is not None and get_nested(f, 'info', 'BIDS', 'Filename') != '']
+
+            if files:
+                file_list.append({acq.id: files})
+
+    fnames = []
+    for x in file_list:
+        for k, v in x.items():
+            for u in v:
+                name = get_nested(u, 'info', 'BIDS', 'Filename')
+                if name is not None:
+                    fnames.append(name)
+
+    if file_list:
+        logger.debug("This will remove BIDS data from %d files:\n\t%s" % (len(file_list), "\n\t".join([x for x in fnames])))
+
+
+        if not dry_run:
+            logger.info('\t\t=======: Removing BIDS data :=======\n')
+
+            for acq_files in file_list:
+
+                for k, v in acq_files.items():
+                    acq = client.get(k)
+
+                    for fi in v:
+
+                        BIDS = get_nested(fi, 'info', 'BIDS')
+                        new_bids = {k:'' for k,v in BIDS.items()}
+                        acq.update_file_info(fi['name'], {'BIDS': new_bids})
+
+        else:
+            logger.info("Disable `dry_run` mode to apply these changes and remove the BIDS information.")
+
+    else:
+        logger.info("No BIDS data to remove! (That was easy...)")
+
+    return 0
+
+
+def get_parser():
+
+    parser = argparse.ArgumentParser(
+        description="Go nuclear: clear BIDS data from Flywheel")
+    parser.add_argument(
+        "--project",
+        help="The project in flywheel",
+        nargs="+",
+        required=True
+    )
+    parser.add_argument(
+        "--subject",
+        help="The subject label(s)",
+        nargs="+",
+        default=None
+    )
+    parser.add_argument(
+        "--session",
+        help="The session label(s)",
+        nargs="+",
+        default=None
+    )
+    parser.add_argument(
+        "--verbose",
+        help="Print ongoing messages of progress",
+        action='store_true',
+        default=False
+    )
+    parser.add_argument(
+        "--dry-run",
+        help="Don't apply changes",
+        action='store_true',
+        default=False
+    )
+    parser.add_argument(
+        "--api-key",
+        help="API Key",
+        action='store',
+        default=None
+    )
+
+    return parser
+
+
+def main():
+
+    logger.info("{:=^70}\n".format(": fw-heudiconv clearer starting up :"))
+    parser = get_parser()
+    args = parser.parse_args()
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        if args.api_key:
+            fw = flywheel.Client(args.api_key)
+        else:
+            fw = flywheel.Client()
+    assert fw, "Your Flywheel CLI credentials aren't set!"
+
+    # Print a lot if requested
+    if args.verbose:
+        logger.setLevel(logging.DEBUG)
+
+    project_label = ' '.join(args.project)
+    status = clear_bids(client=fw,
+                    project_label=project_label,
+                    session_labels=args.session,
+                    subject_labels=args.subject,
+                    dry_run=args.dry_run)
+
+    logger.info("Done!")
+    logger.info("{:=^70}".format(": Exiting fw-heudiconv clearer :"))
+    sys.exit(status)
+
+if __name__ == '__main__':
+    main()

fw_heudiconv/cli/curate.py

@@ -4,15 +4,16 @@
 import argparse
 import warnings
 import flywheel
+import pprint
 from collections import defaultdict
 from ..convert import apply_heuristic, confirm_intentions, confirm_bids_namespace
 from ..query import get_seq_info
 from heudiconv import utils
-from heudiconv import heuristics
 import logging
 
 logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger('fwHeuDiConv-curator')
+logger = logging.getLogger('fw-heudiconv-curator')
+
 
 def pretty_string_seqinfo(seqinfo):
     tr = seqinfo.TR if seqinfo.TR is not None else -1.0
@@ -86,6 +87,7 @@ def convert_to_bids(client, project_label, heuristic_path, subject_labels=None,
     logger.info("Applying heuristic to query results...")
     to_rename = heuristic.infotodict(seq_infos)
 
+    print(to_rename)
     if not to_rename:
         logger.debug("No changes to apply!")
         sys.exit(1)
@@ -94,7 +96,7 @@ def convert_to_bids(client, project_label, heuristic_path, subject_labels=None,
     if hasattr(heuristic, "IntendedFor"):
         logger.info("Processing IntendedFor fields based on heuristic file")
         intention_map.update(heuristic.IntendedFor)
-        logger.debug("Intention map: %s", intention_map)
+        logger.debug("Intention map: %s", pprint.pformat([(k[0], v) for k, v in dict(intention_map).items()]))
 
     metadata_extras = defaultdict(list)
     if hasattr(heuristic, "MetadataExtras"):
@@ -123,18 +125,17 @@ def convert_to_bids(client, project_label, heuristic_path, subject_labels=None,
             apply_heuristic(client, key, value, dry_run, intention_map[key],
                             metadata_extras[key], subject_rename, session_rename, seqitem+1)
 
-    if not dry_run:
-        for ses in sessions:
-            confirm_intentions(client, ses)
+    for ses in sessions:
+        confirm_intentions(client, ses, dry_run)
+
 
 def get_parser():
 
     parser = argparse.ArgumentParser(
-        description="Use a heudiconv heuristic to curate bids on flywheel")
+        description="Use a heudiconv heuristic to curate data into BIDS on flywheel")
     parser.add_argument(
         "--project",
         help="The project in flywheel",
-        nargs="+",
         required=True
     )
     parser.add_argument(
@@ -161,35 +162,51 @@ def get_parser():
         default=False
     )
     parser.add_argument(
-        "--dry_run",
+        "--dry-run",
         help="Don't apply changes",
         action='store_true',
         default=False
     )
+    parser.add_argument(
+        "--api-key",
+        help="API Key",
+        action='store',
+        default=None
+    )
 
     return parser
 
 
 def main():
+
+    logger.info("{:=^70}\n".format(": fw-heudiconv curator starting up :"))
+
+    parser = get_parser()
+    args = parser.parse_args()
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
-        fw = flywheel.Client()
+        if args.api_key:
+            fw = flywheel.Flywheel(args.api_key)
+        else:
+            fw = flywheel.Client()
     assert fw, "Your Flywheel CLI credentials aren't set!"
-    parser = get_parser()
-    args = parser.parse_args()
 
     # Print a lot if requested
     if args.verbose:
         logger.setLevel(logging.DEBUG)
 
-    project_label = ' '.join(args.project)
     convert_to_bids(client=fw,
-                    project_label=project_label,
+                    project_label=args.project,
                     heuristic_path=args.heuristic,
                     session_labels=args.session,
                     subject_labels=args.subject,
                     dry_run=args.dry_run)
 
+    logger.info("Done!")
+    logger.info("{:=^70}".format(": Exiting fw-heudiconv curator :"))
+    sys.exit()
+
 
 if __name__ == '__main__':
     main()