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bids-apps / oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI
Apache License 2.0
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Input data is not validated #9

Closed chrisgorgo closed 7 years ago

chrisgorgo commented 7 years ago

we should at least check if it's BIDS

raamana commented 7 years ago

Hey Chris,

I installed bids-validation using npm on CentOS, and it seems to not run properly on the latest downloads of ds114_test[12] - see below. Any ideas?

$ 09:32:48 miner ~ >> /home/praamana/node_modules/.bin/bids-validator /sgehome/BIDS-examples/ds114_test1/

/home/praamana/node_modules/bids-validator/validators/bids.js:115 if (path.startsWith('/sub-')) {hasSubjectDir = true;} ^ TypeError: Object /dataset_description.json has no method 'startsWith' at /home/praamana/node_modules/bids-validator/validators/bids.js:115:22 at Object.async.forEachOf.async.eachOf (/home/praamana/node_modules/bids-validator/node_modules/async/lib/async.js:233:13) at Object.BIDS.fullTest (/home/praamana/node_modules/bids-validator/validators/bids.js:110:15) at /home/praamana/node_modules/bids-validator/validators/bids.js:35:26 at Object.BIDS.quickTest (/home/praamana/node_modules/bids-validator/validators/bids.js:79:9) at /home/praamana/node_modules/bids-validator/validators/bids.js:33:18 at Object.readDir (/home/praamana/node_modules/bids-validator/utils/files.js:89:9) at Object.BIDS.start as BIDS at module.exports (/home/praamana/node_modules/bids-validator/cli.js:12:18) at Object. (/home/praamana/node_modules/bids-validator/bin/bids-validator:24:18) $ 09:33:18 miner ~ >> /home/praamana/node_modules/.bin/bids-validator /sgehome/BIDS-examples/ds114_test2

/home/praamana/node_modules/bids-validator/validators/bids.js:115 if (path.startsWith('/sub-')) {hasSubjectDir = true;} ^ TypeError: Object /dataset_description.json has no method 'startsWith' at /home/praamana/node_modules/bids-validator/validators/bids.js:115:22 at Object.async.forEachOf.async.eachOf (/home/praamana/node_modules/bids-validator/node_modules/async/lib/async.js:233:13) at Object.BIDS.fullTest (/home/praamana/node_modules/bids-validator/validators/bids.js:110:15) at /home/praamana/node_modules/bids-validator/validators/bids.js:35:26 at Object.BIDS.quickTest (/home/praamana/node_modules/bids-validator/validators/bids.js:79:9) at /home/praamana/node_modules/bids-validator/validators/bids.js:33:18 at Object.readDir (/home/praamana/node_modules/bids-validator/utils/files.js:89:9) at Object.BIDS.start as BIDS at module.exports (/home/praamana/node_modules/bids-validator/cli.js:12:18) at Object. (/home/praamana/node_modules/bids-validator/bin/bids-validator:24:18) $ 09:33:24 miner ~ >> ls /sgehome/BIDS-examples/ds114_test? /sgehome/BIDS-examples/ds114_test1: dataset_description.json dwi.bval dwi.bvec out sub-01 sub-02 task-fingerfootlips_bold.json task-fingerfootlips_events.tsv task-linebisection_bold.json

/sgehome/BIDS-examples/ds114_test2: dataset_description.json dwi.bval dwi.bvec out sub-01 sub-02 task-fingerfootlips_bold.json task-fingerfootlips_events.tsv task-linebisection_bold.json $ 09:33:33 miner ~ >>

raamana commented 7 years ago

Validation is included now.