Merge pull request #774 from DaNish808/cmd-tool-returns-0-761

bring back correct exit code on validation w/ errors

bids-validator/cli.js

@@ -5,16 +5,30 @@ var colors = require('colors/safe')
 var fs = require('fs')
 const remoteFiles = require('./utils/files/remoteFiles')
 
+const exitProcess = issues => {
+  if (
+    issues === 'Invalid' ||
+    (issues.errors && issues.errors.length >= 1) ||
+    (issues.config && issues.config.length >= 1)
+  ) {
+    process.exit(1)
+  } else {
+    process.exit(0)
+  }
+}
+
 module.exports = function(dir, options) {
   if (fs.existsSync(dir)) {
     if (options.json) {
       validate.BIDS(dir, options, function(issues, summary) {
         console.log(JSON.stringify({ issues, summary }))
+        exitProcess(issues)
       })
     } else {
       validate.BIDS(dir, options, function(issues, summary) {
         console.log(validate.consoleFormat.issues(issues, options) + '\n')
         console.log(validate.consoleFormat.summary(summary, options))
+        exitProcess(issues)
       })
     }
   } else {

bids-validator/tests/cli.spec.js

@@ -3,6 +3,8 @@ const { spawn } = require('child_process')
 const dir = process.cwd()
 const data_dir = dir + '/bids-validator/tests/data/'
 const test_data = data_dir + 'valid_headers/'
+const data_with_errors = data_dir + 'empty_files'
+const data_without_errors = data_dir + 'valid_dataset'
 
 const cli_path = './bids-validator/bin/bids-validator'
 
@@ -55,6 +57,40 @@ describe('CLI', () => {
     })
   })
 
+  it('without errors should exit with code 0', done => {
+    const command = spawn(cli_path, [data_without_errors, '--json'])
+    command.on('exit', code => {
+      assert.equal(code, 0)
+      done()
+    })
+  })
+
+  it('with errors should not exit with code 0', done => {
+    const command = spawn(cli_path, [data_with_errors])
+    command.on('exit', code => {
+      assert.notEqual(code, 0)
+      done()
+    })
+  })
+
+  it('with errors should not exit with code 0 with --json argument', done => {
+    const command = spawn(cli_path, [data_with_errors, '--json'])
+    let commandOutput = []
+    let output = {}
+    command.stdout.on('data', data => {
+      const dataLines = data.toString().split('\n')
+      commandOutput = commandOutput.concat(dataLines)
+    })
+    command.stderr.on('end', () => {
+      output = JSON.parse(commandOutput.join(''))
+    })
+    command.on('exit', code => {
+      assert(output.issues.errors.length > 0)
+      assert.notEqual(code, 0)
+      done()
+    })
+  })
+
   it('should print valid json when the --json argument is provided', done => {
     const command = spawn(cli_path, [test_data, '--json'])
     let commandOutput = ''

bids-validator/tests/data/valid_dataset/dataset_description.json

@@ -0,0 +1,6 @@
+{
+	"Name": "Synthetic dataset for inclusion in BIDS-examples",
+	"BIDSVersion": "1.0.2",
+	"License": "PD",
+	"Authors": ["Markiewicz, C. J."]
+}

bids-validator/tests/data/valid_dataset/participants.tsv

@@ -0,0 +1,6 @@
+participant_id	age	sex
+sub-01	34	F
+sub-02	38	M
+sub-03	22	M
+sub-04	21	F
+sub-05	42	M

bids-validator/tests/data/valid_dataset/sub-01/ses-01/sub-01_ses-01_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-01_ses-01_T1w.nii.gz	1880-01-10T05:17:54
+func/sub-01_ses-01_task-nback_run-01_bold.nii.gz	1880-01-10T05:22:54
+func/sub-01_ses-01_task-nback_run-02_bold.nii.gz	1880-01-10T05:37:54
+func/sub-01_ses-01_task-rest_bold.nii.gz	1880-01-10T05:52:54

bids-validator/tests/data/valid_dataset/sub-01/ses-02/sub-01_ses-02_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-01_ses-02_T1w.nii.gz	1802-06-04T22:54:25
+func/sub-01_ses-02_task-nback_run-01_bold.nii.gz	1802-06-04T22:59:25
+func/sub-01_ses-02_task-nback_run-02_bold.nii.gz	1802-06-04T23:14:25
+func/sub-01_ses-02_task-rest_bold.nii.gz	1802-06-04T23:29:25

bids-validator/tests/data/valid_dataset/sub-01/sub-01_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	systolic_blood_pressure
+ses-01	112
+ses-02	113

bids-validator/tests/data/valid_dataset/sub-02/ses-01/sub-02_ses-01_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-02_ses-01_T1w.nii.gz	1874-04-12T01:43:17
+func/sub-02_ses-01_task-nback_run-01_bold.nii.gz	1874-04-12T01:48:17
+func/sub-02_ses-01_task-nback_run-02_bold.nii.gz	1874-04-12T02:03:17
+func/sub-02_ses-01_task-rest_bold.nii.gz	1874-04-12T02:18:17

bids-validator/tests/data/valid_dataset/sub-02/ses-02/sub-02_ses-02_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-02_ses-02_T1w.nii.gz	1814-09-10T07:05:33
+func/sub-02_ses-02_task-nback_run-01_bold.nii.gz	1814-09-10T07:10:33
+func/sub-02_ses-02_task-nback_run-02_bold.nii.gz	1814-09-10T07:25:33
+func/sub-02_ses-02_task-rest_bold.nii.gz	1814-09-10T07:40:33

bids-validator/tests/data/valid_dataset/sub-02/sub-02_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	systolic_blood_pressure
+ses-01	114
+ses-02	115

bids-validator/tests/data/valid_dataset/sub-03/ses-01/sub-03_ses-01_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-03_ses-01_T1w.nii.gz	1852-10-11T23:35:34
+func/sub-03_ses-01_task-nback_run-01_bold.nii.gz	1852-10-11T23:40:34
+func/sub-03_ses-01_task-nback_run-02_bold.nii.gz	1852-10-11T23:55:34
+func/sub-03_ses-01_task-rest_bold.nii.gz	1852-10-12T00:10:34

bids-validator/tests/data/valid_dataset/sub-03/ses-02/sub-03_ses-02_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-03_ses-02_T1w.nii.gz	1843-04-22T00:23:54
+func/sub-03_ses-02_task-nback_run-01_bold.nii.gz	1843-04-22T00:28:54
+func/sub-03_ses-02_task-nback_run-02_bold.nii.gz	1843-04-22T00:43:54
+func/sub-03_ses-02_task-rest_bold.nii.gz	1843-04-22T00:58:54

bids-validator/tests/data/valid_dataset/sub-03/sub-03_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	systolic_blood_pressure
+ses-01	112
+ses-02	115

bids-validator/tests/data/valid_dataset/sub-04/ses-01/sub-04_ses-01_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-04_ses-01_T1w.nii.gz	1800-05-21T11:18:59
+func/sub-04_ses-01_task-nback_run-01_bold.nii.gz	1800-05-21T11:23:59
+func/sub-04_ses-01_task-nback_run-02_bold.nii.gz	1800-05-21T11:38:59
+func/sub-04_ses-01_task-rest_bold.nii.gz	1800-05-21T11:53:59

bids-validator/tests/data/valid_dataset/sub-04/ses-02/sub-04_ses-02_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-04_ses-02_T1w.nii.gz	1847-10-17T10:15:19
+func/sub-04_ses-02_task-nback_run-01_bold.nii.gz	1847-10-17T10:20:19
+func/sub-04_ses-02_task-nback_run-02_bold.nii.gz	1847-10-17T10:35:19
+func/sub-04_ses-02_task-rest_bold.nii.gz	1847-10-17T10:50:19

bids-validator/tests/data/valid_dataset/sub-04/sub-04_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	systolic_blood_pressure
+ses-01	111
+ses-02	115

bids-validator/tests/data/valid_dataset/sub-05/ses-01/sub-05_ses-01_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-05_ses-01_T1w.nii.gz	1899-07-07T16:04:21
+func/sub-05_ses-01_task-nback_run-01_bold.nii.gz	1899-07-07T16:09:21
+func/sub-05_ses-01_task-nback_run-02_bold.nii.gz	1899-07-07T16:24:21
+func/sub-05_ses-01_task-rest_bold.nii.gz	1899-07-07T16:39:21

bids-validator/tests/data/valid_dataset/sub-05/ses-02/sub-05_ses-02_scans.tsv

@@ -0,0 +1,5 @@
+filename	acq_time
+anat/sub-05_ses-02_T1w.nii.gz	1868-01-31T20:57:43
+func/sub-05_ses-02_task-nback_run-01_bold.nii.gz	1868-01-31T21:02:43
+func/sub-05_ses-02_task-nback_run-02_bold.nii.gz	1868-01-31T21:17:43
+func/sub-05_ses-02_task-rest_bold.nii.gz	1868-01-31T21:32:43

bids-validator/tests/data/valid_dataset/sub-05/sub-05_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	systolic_blood_pressure
+ses-01	114
+ses-02	110

bids-validator/tests/data/valid_dataset/task-nback_bold.json

@@ -0,0 +1,4 @@
+{
+    "TaskName": "N-Back",
+    "RepetitionTime": 2.5
+}

bids-validator/tests/data/valid_dataset/task-nback_events.tsv

@@ -0,0 +1,43 @@
+onset	duration	trial_type	weight
+2.016	1	scene_nontarget_nbackparam	-0.5
+4.0169999999999995	1	scene_target_nbackparam	-0.5
+6.018	1	scene_target_nbackparam	-0.5
+8.019	1	scene_nontarget_nbackparam	-0.5
+10.02	1	scene_dist_rtparam	0.348
+12.02	1	scene_nontarget_nbackparam	-0.5
+14.005	1	scene_nontarget_nbackparam	-0.5
+16.005	1	scene_dist_rtparam	-0.122
+18.006	1	scene_nontarget_nbackparam	-0.5
+20.007	1	scene_dist_rtparam	0.10400000000000001
+24.025	1	faces_nontarget_rtparam	0.026000000000000002
+26.01	1	faces_nontarget_rtparam	-0.09699999999999999
+28.01	1	faces_nontarget_rtparam	-0.024
+30.011	1	faces_nontarget_rtparam	0.049
+32.012	1	faces_nontarget_rtparam	0.019
+34.013000000000005	1	faces_dist_nbackparam	-0.455
+36.014	1	faces_target_rtparam	-0.07400000000000001
+38.014	1	faces_nontarget_rtparam	-0.062
+40.015	1	faces_nontarget_rtparam	0.01
+42.016000000000005	1	faces_dist_nbackparam	-0.455
+68.01	1	scene_nontarget_nbackparam	0.5
+70.01100000000001	1	scene_nontarget_nbackparam	0.5
+72.012	1	scene_nontarget_nbackparam	0.5
+74.013	1	scene_nontarget_nbackparam	0.5
+76.013	1	scene_dist_rtparam	0.136
+78.014	1	scene_target_nbackparam	0.5
+80.015	1	scene_nontarget_nbackparam	0.5
+82.016	1	scene_nontarget_nbackparam	0.5
+84.01700000000001	1	scene_nontarget_nbackparam	0.5
+86.01799999999999	1	scene_target_nbackparam	0.5
+90.01899999999999	1	faces_nontarget_rtparam	-0.175
+92.02	1	faces_nontarget_rtparam	-0.195
+94.021	1	faces_dist_nbackparam	0.545
+96.022	1	faces_dist_nbackparam	0.545
+98.022	1	faces_target_rtparam	-0.068
+100.023	1	faces_nontarget_rtparam	0.018000000000000002
+102.024	1	faces_nontarget_rtparam	-0.019
+104.025	1	faces_target_rtparam	0.156
+106.009	1	faces_nontarget_rtparam	-0.035
+108.01	1	faces_target_rtparam	-0.057
+154.012	1	scene_nontarget_nbackparam	-0.5
+156.013	1	scene_nontarget_nbackparam	-0.5

bids-validator/tests/data/valid_dataset/task-nback_physio.json

@@ -0,0 +1,5 @@
+{
+    "SamplingFrequency": 10.0,
+    "StartTime": 0.0,
+    "Columns": ["respiratory", "cardiac"]
+}

bids-validator/tests/data/valid_dataset/task-nback_stim.json

@@ -0,0 +1,5 @@
+{
+    "SamplingFrequency": 2.0,
+    "StartTime": 0.0,
+    "Columns": ["stimA", "stimB"]
+}

bids-validator/tests/data/valid_dataset/task-rest_bold.json

@@ -0,0 +1,4 @@
+{
+    "TaskName": "Rest",
+    "RepetitionTime": 2.5
+}

bids-validator/tests/data/valid_dataset/task-rest_physio.json

@@ -0,0 +1,5 @@
+{
+    "SamplingFrequency": 10.0,
+    "StartTime": 0.0,
+    "Columns": ["respiratory", "cardiac"]
+}