bugfixes and docker ignore added

.dockerignore

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

Dockerfile

@@ -12,19 +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 curl nodejs
-RUN curl -L https://www.npmjs.com/install.sh | sh
+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 flywheel-sdk pandas fw-heudiconv
+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/meta.py

@@ -62,7 +62,7 @@ def initialise_dataset(client, project_label, subject_labels=None, session_label
 def attach_to_object(object, file, dry_run):
 
     if dry_run:
-        logger.info("{}\t-->\t{}".format(file.ljust(20), ))
+        logger.info("{}\t-->\t{}".format(file.ljust(20), object.label))
         return 0
     my_file = Path(file)
     if my_file.is_file():

fw_heudiconv/cli/tabulate.py

@@ -88,7 +88,7 @@ def get_parser():
         default=False
     )
     parser.add_argument(
-        "--dry_run",
+        "--dry-run",
         help="Don't apply changes",
         action='store_true',
         default=False

fw_heudiconv_run.py

@@ -10,7 +10,7 @@
 # logging stuff
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger('fw-heudiconv-gear')
-logger.info("=======: fw-heudiconv gear manager starting up :=======\n".center(70))
+logger.info("{:=^70}\n".format(": fw-heudiconv gear manager starting up :"))
 
 # start up inputs
 invocation = json.loads(open('config.json').read())
@@ -63,7 +63,10 @@
 logger.info("Dry run: {}".format(dry_run))
 
 # action
-call = "fw-heudiconv-{} --dry-run --verbose --api-key {} --project {}".format(action.lower(), key, project_label, heuristic)
+call = "fw-heudiconv-{} --verbose --api-key {} --project {}".format(action.lower(), key, project_label, heuristic)
+
+if dry_run:
+    call  = call + " --dry-run"
 
 if heuristic and action.lower() == "curate":
     call = call + " --heuristic {}".format(heuristic)
@@ -81,6 +84,9 @@
 if action.lower() == "validate":
     call = call + " --flywheel --directory {}".format("/flywheel/v0/output")
 
+if action.lower() == "tabulate":
+    call = call + " --path {}".format("/flywheel/v0/output")
+
 os.system(call)
 
 if action.lower() in ["export", "tabulate"]:
@@ -98,4 +104,4 @@
             shutil.rmtree(x)
 
 logger.info("Done!")
-logger.info("=======: Exiting fw-heudiconv gear manager :=======\n".center(70))
+logger.info("{:=^70}\n".format(": Exiting fw-heudiconv gear manager :"))

manifest.json

@@ -2,7 +2,7 @@
 	"name": "fw-heudiconv",
 	"label": "Flywheel HeuDiConv",
 	"description": "HeuDiConv-style BIDS curation on Flywheel. Flywheel HeuDiConv (or fw-heudiconv, pronounced /fwuː di kɑː n(v)/) is a Python-based toolkit that leverages the flexibility and comprehensiveness of HeuDiConv to curate neuroimaging data on Flywheel into a BIDS-valid format.",
-	"version": "0.1.0_0.1.0",
+	"version": "0.2.3_0.1.0",
 	"inputs": {
 		"api-key": {
 			"base": "api-key"
@@ -16,7 +16,7 @@
 	"config": {
 		"action": {
 			"default": "Curate",
-			"description": "Curate: Apply heuristic to project. Export: Create zip of BIDS tree. Tabulate: Create a table of sequence information in a project.",
+			"description": "Curate: Apply heuristic to project. Export: Create zip of BIDS tree. Tabulate: Create a table of sequence information in a project. Clear: Clear BIDS data from project. Meta: Autogenerate BIDS metadata for project.",
 			"type": "string",
 			"enum": ["Curate", "Export", "Tabulate", "Clear", "Meta"]
 		},
@@ -51,7 +51,7 @@
 	"custom": {
 		"gear-builder": {
 			"category": "analysis",
-			"image": "pennbbl/fw-heudiconv:latest"
+			"image": "pennbbl/fw-heudiconv:0.2.0_0.1.0"
 		},
 		"flywheel":{"suite": "PennBBL"}
 	}