Merge pull request miykael#149 from effigies/fix/datalad_command

djarecka · web-flow · commit be1ea720b525 · 2020-03-05T17:19:41.000-05:00
FIX: Datalad command
diff --git a/Dockerfile b/Dockerfile
@@ -138,6 +138,7 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     &&   pip install --no-cache-dir  \
              https://github.com/nipy/nipype/tarball/master \
              https://github.com/INCF/pybids/tarball/0.7.1 \
+             niflow-nipype1-workflows \
              nilearn \
              datalad[full] \
              nipy \
diff --git a/notebooks/basic_data_input.ipynb b/notebooks/basic_data_input.ipynb
@@ -651,7 +651,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!datalad get -r -J 4 /data/ds000114/derivatives/freesurfer/sub-01"
+    "!datalad get -r -J 4 -d /data/ds000114 /data/ds000114/derivatives/freesurfer/sub-01"
    ]
   },
   {
diff --git a/notebooks/example_normalize.ipynb b/notebooks/example_normalize.ipynb
@@ -27,7 +27,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"
+    "datalad get -J 4 -d /data/ds000114 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"
    ]
   },
   {
diff --git a/notebooks/example_preprocessing.ipynb b/notebooks/example_preprocessing.ipynb
@@ -32,8 +32,9 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
-    "                /data/ds000114/sub-*/ses-test/func/*fingerfootlips*"
+    "datalad get -J 4 -d /data/ds000114 \\\n",
+    "    /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
+    "    /data/ds000114/sub-*/ses-test/func/*fingerfootlips*"
    ]
   },
   {
diff --git a/notebooks/handson_preprocessing.ipynb b/notebooks/handson_preprocessing.ipynb
@@ -29,8 +29,9 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J 4 /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",
-    "                /data/ds000114/sub-0[234789]/ses-test/func/*fingerfootlips*"
+    "datalad get -J 4 -d /data/ds000114 \\\n",
+    "    /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",
+    "    /data/ds000114/sub-0[234789]/ses-test/func/*fingerfootlips*"
    ]
   },
   {
diff --git a/notebooks/introduction_dataset.ipynb b/notebooks/introduction_dataset.ipynb
@@ -68,9 +68,9 @@
    "source": [
     "%%bash\n",
     "cd /data/ds000114\n",
-    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
-    "                /data/ds000114/sub-01/ses-test/anat \\\n",
-    "                /data/ds000114/sub-*/ses-test/func/*fingerfootlips*"
+    "datalad get -J 4 derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
+    "                 sub-01/ses-test/anat \\\n",
+    "                 sub-*/ses-test/func/*fingerfootlips*"
    ]
   },
   {
@@ -121,7 +121,7 @@
    "source": [
     "%%bash\n",
     "cd /data/ds000114\n",
-    "datalad get /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-linebisection_events.tsv"
+    "datalad get sub-01/ses-test/func/sub-01_ses-test_task-linebisection_events.tsv"
    ]
   },
   {

Original file line number	Diff line number	Diff line change
`@@ -651,7 +651,7 @@`
`651`	`651`	`"metadata": {},`
`652`	`652`	`"outputs": [],`
`653`	`653`	`"source": [`
`654`		`- "!datalad get -r -J 4 /data/ds000114/derivatives/freesurfer/sub-01"`
	`654`	`+ "!datalad get -r -J 4 -d /data/ds000114 /data/ds000114/derivatives/freesurfer/sub-01"`
`655`	`655`	`]`
`656`	`656`	`},`
`657`	`657`	`{`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@`
`27`	`27`	`"outputs": [],`
`28`	`28`	`"source": [`
`29`	`29`	`"%%bash\n",`
`30`		`- "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"`
	`30`	`+ "datalad get -J 4 -d /data/ds000114 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"`
`31`	`31`	`]`
`32`	`32`	`},`
`33`	`33`	`{`
Original file line number	Diff line number	Diff line change
`@@ -32,8 +32,9 @@`
`32`	`32`	`"outputs": [],`
`33`	`33`	`"source": [`
`34`	`34`	`"%%bash\n",`
`35`		`- "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-/anat/preproc.nii.gz \\\n",`
`36`		`- " /data/ds000114/sub-/ses-test/func/fingerfootlips*"`
	`35`	`+ "datalad get -J 4 -d /data/ds000114 \\\n",`
	`36`	`+ " /data/ds000114/derivatives/fmriprep/sub-/anat/preproc.nii.gz \\\n",`
	`37`	`+ " /data/ds000114/sub-/ses-test/func/fingerfootlips*"`
`37`	`38`	`]`
`38`	`39`	`},`
`39`	`40`	`{`
Original file line number	Diff line number	Diff line change
`@@ -29,8 +29,9 @@`
`29`	`29`	`"outputs": [],`
`30`	`30`	`"source": [`
`31`	`31`	`"%%bash\n",`
`32`		`- "datalad get -J 4 /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",`
`33`		`- " /data/ds000114/sub-0[234789]/ses-test/func/fingerfootlips"`
	`32`	`+ "datalad get -J 4 -d /data/ds000114 \\\n",`
	`33`	`+ " /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",`
	`34`	`+ " /data/ds000114/sub-0[234789]/ses-test/func/fingerfootlips"`
`34`	`35`	`]`
`35`	`36`	`},`
`36`	`37`	`{`
Original file line number	Diff line number	Diff line change
`@@ -68,9 +68,9 @@`
`68`	`68`	`"source": [`
`69`	`69`	`"%%bash\n",`
`70`	`70`	`"cd /data/ds000114\n",`
`71`		`- "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-/anat/preproc.nii.gz \\\n",`
`72`		`- " /data/ds000114/sub-01/ses-test/anat \\\n",`
`73`		`- " /data/ds000114/sub-/ses-test/func/fingerfootlips*"`
	`71`	`+ "datalad get -J 4 derivatives/fmriprep/sub-/anat/preproc.nii.gz \\\n",`
	`72`	`+ " sub-01/ses-test/anat \\\n",`
	`73`	`+ " sub-/ses-test/func/fingerfootlips*"`
`74`	`74`	`]`
`75`	`75`	`},`
`76`	`76`	`{`
`@@ -121,7 +121,7 @@`
`121`	`121`	`"source": [`
`122`	`122`	`"%%bash\n",`
`123`	`123`	`"cd /data/ds000114\n",`
`124`		`- "datalad get /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-linebisection_events.tsv"`
	`124`	`+ "datalad get sub-01/ses-test/func/sub-01_ses-test_task-linebisection_events.tsv"`
`125`	`125`	`]`
`126`	`126`	`},`
`127`	`127`	`{`