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Merge pull request #134 from gkiar/gk-dev
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Added importer for 0.4 and 0.4.5. descriptors to 0.5
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@glatard
glatard committed Sep 12, 2017
2 parents edc724b + 65f12b0 commit e0aaf74
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Showing 5 changed files with 336 additions and 26 deletions.
93 changes: 78 additions & 15 deletions tools/python/boutiques/importer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,37 +26,94 @@

from argparse import ArgumentParser
from jsonschema import ValidationError
from boutiques.validator import validate_json
import json
import os


class Importer():

def __init__(self,app_dir,output_file):
self.app_dir = app_dir
path, fil = os.path.split(__file__)
self.template_file = os.path.join(path, "bids-app-template", "template.json")
def __init__(self, output_file):
self.output_file = output_file

def upgrade_04(self, input_file):
"""
Differences between 0.4 and current (0.5):
-schema version (obv)
-singularity should now be represented same as docker
-walltime should be part of suggested_resources structure
I.e.
"schema-version": "0.4",
...... becomes.....
"schema-version": "0.5",
I.e.
"container-image": {
"type": "singularity",
"url": "shub://gkiar/ndmg-cbrain:master"
},
...... becomes.....
"container-image": {
"type": "singularity",
"image": "gkiar/ndmg-cbrain:master",
"index": "shub://",
},
I.e.
"walltime-estimate": 3600,
...... becomes.....
"suggested-resources": {
"walltime-estimate": 3600
},
"""
with open(input_file, 'r') as fhandle:
descriptor = json.load(fhandle)

descriptor["schema-version"] = "0.5"

if "container-image" in descriptor.keys():
if "singularity" == descriptor["container-image"]["type"]:
url = descriptor["container-image"]["url"]
img = url.split("://")
if len(img) == 1:
descriptor["container-image"]["image"] = img[0]
elif len(img) == 2:
descriptor["container-image"]["image"] = img[1]
descriptor["container-image"]["index"] = img[0] + "://"
del descriptor["container-image"]["url"]

def get_entry_point(self):
if "walltime-estimate" in descriptor.keys():
descriptor["suggested-resources"] = {"walltime-estimate": descriptor["walltime-estimate"]}
del descriptor["walltime-estimate"]

with open(self.output_file, 'w') as fhandle:
fhandle.write(json.dumps(descriptor, indent=4))
validate_json(self.output_file)

def get_entry_point(self, app_dir):
entrypoint = None
with open(os.path.join(self.app_dir,"Dockerfile")) as f:
with open(os.path.join(app_dir,"Dockerfile")) as f:
content = f.readlines()
for line in content:
split = line.split()
if len(split) >=2 and split[0] == "ENTRYPOINT":
entrypoint = split[1].strip("[]\"")
return entrypoint

def import_bids(self):
with open(self.template_file) as f:
def import_bids(self, app_dir):
path, fil = os.path.split(__file__)
template_file = os.path.join(path, "bids-app-template", "template.json")

with open(template_file) as f:
template_string = f.read()

errors = []
app_name = os.path.basename(os.path.abspath(self.app_dir))
with open(os.path.join(self.app_dir,"version"),"r") as f:
app_name = os.path.basename(os.path.abspath(app_dir))
with open(os.path.join(app_dir,"version"),"r") as f:
version = f.read().strip()
git_repo = "https://github.com/BIDS-Apps/"+app_name
entrypoint = self.get_entry_point()
entrypoint = self.get_entry_point(app_dir)
container_image = "bids/"+app_name
analysis_types = "participant\", \"group\", \"session"

Expand All @@ -81,12 +138,18 @@ def main(args=None):

# Arguments parsing
parser = ArgumentParser()
parser.add_argument("bids_app_dir", help="Root directory of the BIDS app to import.")
parser.add_argument("importing", help="Type of import we are performing",
choices=['bids', '0.4'])
parser.add_argument("output_file", help="File where the Boutiques descriptor will be written.")
parser.add_argument("--input_file", help="File for existing Boutiques descriptor of older version")
parser.add_argument("--bids_app_dir", help="Root directory of the BIDS app to import.")
results = parser.parse_args() if args is None else parser.parse_args(args)

importer = Importer(results.bids_app_dir,results.output_file)
importer.import_bids()

importer = Importer(results.output_file)
if results.importing == '0.4':
importer.upgrade_04(results.input_file)
elif results.importing == 'bids':
importer.import_bids(results.bids_app_dir)

# Execute program
if __name__ == "__main__":
Expand Down
235 changes: 235 additions & 0 deletions tools/python/boutiques/schema/examples/upgrade04.json
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@@ -0,0 +1,235 @@
{
"name": "ndmg",
"tool-version": "v0.0.50s",
"description": "dwi connectome estimation pipeline",
"command-line": "ndmg_pipeline [DTI] [BVAL] [BVEC] [MPRAGE] [ATLAS] [MASK] [OUTDIR] [DESIKAN] [JHU] [TALAIRACH] [AAL] [HARVARDOXFORD] [CPAC200] [CLEAN]",
"container-image": {
"type": "singularity",
"url": "shub://gkiar/ndmg-cbrain:master"
},
"schema-version": "0.4",
"walltime-estimate": 3600,
"groups": [
{
"id": "parcellation_group",
"name": "Group of all used parcellations",
"members": [
"desikan",
"jhu",
"talairach",
"aal",
"harvardoxford",
"cpac200"
],
"one-is-required": true
}
],
"inputs": [
{
"id": "dti_file",
"name": "Diffusion Tensor Image",
"type": "File",
"value-key": "[DTI]",
"optional": false
},
{
"id": "bval_file",
"name": "B-values file",
"type": "File",
"value-key": "[BVAL]",
"optional": false
},
{
"id": "bvec_file",
"name": "Gradient vectors file",
"type": "File",
"value-key": "[BVEC]",
"optional": false
},
{
"id": "mprage_file",
"name": "Structural scan file",
"type": "File",
"value-key": "[MPRAGE]",
"optional": false
},
{
"id": "atlas",
"name": "Atlas image (MNI152)",
"type": "String",
"value-key": "[ATLAS]",
"optional": false,
"value-choices": [
"/ndmg_atlases/atlas/MNI152_T1_1mm.nii.gz"
]
},
{
"id": "mask",
"name": "Atlas brain mask",
"type": "String",
"value-key": "[MASK]",
"optional": false,
"value-choices": [
"/ndmg_atlases/atlas/MNI152_T1_1mm_brain_mask.nii.gz"
]
},
{
"id": "outdir",
"name": "Output directory",
"type": "String",
"value-key": "[OUTDIR]",
"optional": false
},
{
"id": "desikan",
"name": "Desikan parcellation",
"type": "String",
"value-key": "[DESIKAN]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/desikan.nii.gz"
]
},
{
"id": "jhu",
"name": "JHU parcellation",
"type": "String",
"value-key": "[JHU]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/JHU.nii.gz"
]
},
{
"id": "talairach",
"name": "Talairach parcellation",
"type": "String",
"value-key": "[TALAIRACH]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/Talairach.nii.gz"
]
},
{
"id": "aal",
"name": "AAL parcellation",
"type": "String",
"value-key": "[AAL]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/AAL.nii.gz"
]
},
{
"id": "harvardoxford",
"name": "Harvard-Oxford parcellation",
"type": "String",
"value-key": "[HARVARDOXFORD]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/HarvardOxford.nii.gz"
]
},
{
"id": "cpac200",
"name": "CPAC200 parcellation",
"type": "String",
"value-key": "[CPAC200]",
"optional": true,
"value-choices": [
"/ndmg_atlases/labels/CPAC200.nii.gz"
]
},
{
"id": "clean",
"name": "Clean-up flag",
"type": "Flag",
"value-key": "[CLEAN]",
"optional": true,
"command-line-flag": "-c"
}
],
"output-files": [
{
"id": "aligned_dti",
"name": "Aligned DTI volume",
"path-template": "[OUTDIR]/reg_dti/[DTI]_aligned.nii.gz",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "tensors",
"name": "Tensor maps",
"path-template": "[OUTDIR]/tensors/[DTI]_tensors.npz",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "fibers",
"name": "Fiber streamlines",
"path-template": "[OUTDIR]/fibers/[DTI]_fibers.npz",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "desikan_graph",
"name": "Desikan graph",
"path-template": "[OUTDIR]/graphs/desikan/[DTI]_desikan.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "jhu_graph",
"name": "JHU graph",
"path-template": "[OUTDIR]/graphs/JHU/[DTI]_JHU.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "talairach_graph",
"name": "Talairach graph",
"path-template": "[OUTDIR]/graphs/Talairach/[DTI]_Talairach.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "aal_graph",
"name": "AAL graph",
"path-template": "[OUTDIR]/graphs/AAL/[DTI]_AAL.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "harvardoxford_graph",
"name": "Harvard-Oxford graph",
"path-template": "[OUTDIR]/graphs/HarvardOxford/[DTI]_HarvardOxford.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
},
{
"id": "cpac200_graph",
"name": "CPAC200 graph",
"path-template": "[OUTDIR]/graphs/CPAC200/[DTI]_CPAC200.gpickle",
"path-template-stripped-extensions": [
".nii", ".nii.gz"
],
"optional": true
}
]
}

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