add repo templates, fix s3 export

docker/dicom_indexer/indexer/index_dicom.py

@@ -426,19 +426,21 @@ def export_to_s3(
     # TODO: check if we can reuse a single bucket (or per study) with fileprefix
     # git-annex initremote remotename ...
     remote_name = s3_url.hostname
-    bucket_name, path = pathlib.Path(s3_url.path).parts
-    ds.repo.initremote(
+    _, bucket_name, *fileprefix = pathlib.Path(s3_url.path).parts
+    fileprefix.append(session_metas['StudyInstanceUID']+'/')
+    ds.repo.init_remote(
         remote_name,
         S3_REMOTE_DEFAULT_PARAMETERS
         + [
             f"host={s3_url.hostname}",
             f"bucket={bucket_name}",
-            f"fileprefix={'/'.join(path)}",
+            f"fileprefix={'/'.join(fileprefix)}",
         ],
     )
     ds.repo.set_preferred_content(
-        remote_name,
-        "include=**.{7z,tar.gz,zip}",
+        "wanted",
+        "include=*7z or include=*.tar.gz or include=*zip",
+        remote=remote_name,
     )
 
     ds.push(to=remote_name)

docker/dicom_indexer/indexer/repo_templates/bids/.all-contributorsrc

@@ -0,0 +1,5 @@
+{
+  "files": [
+    "README"
+  ]
+}

docker/dicom_indexer/indexer/repo_templates/bids/.bidsignore

@@ -0,0 +1,3 @@
+**/anat/*localizer*
+**/anat/*scout*
+**/*__dup*

docker/dicom_indexer/indexer/repo_templates/bids/.derivatives

@@ -0,0 +1 @@
+qc/mriqc

docker/dicom_indexer/indexer/repo_templates/bids/.gitattributes

@@ -0,0 +1,13 @@
+**/.git* annex.largefiles=nothing
+* annex.largefiles=(largerthan=100kb)
+*.yml  annex.largefiles=nothing
+*.json annex.largefiles=nothing
+*.txt annex.largefiles=nothing
+*.tsv annex.largefiles=nothing
+*.nii.gz annex.largefiles=anything
+*.tgz annex.largefiles=anything
+*_scans.tsv annex.largefiles=anything
+# annex event files as they contain subjects behavioral responses
+sub-*/**/*_events.tsv annex.largefiles=anything
+*.bk2 annex.largefiles=anything
+.bidsignore annex.largefiles=nothing

docker/dicom_indexer/indexer/repo_templates/bids/.gitignore

@@ -0,0 +1,2 @@
+.pybids_cache/**
+.heudiconv

docker/dicom_indexer/indexer/repo_templates/bids/.gitlab-ci.yml

@@ -0,0 +1,4 @@
+include:
+  - project: 'unf/ni-dataops'
+    file:
+      - 'ci-pipelines/bids/bids_repo.yml'

docker/dicom_indexer/indexer/repo_templates/bids/README

@@ -0,0 +1,6 @@
+# xyz dataset
+
+## Contributors
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->

docker/dicom_indexer/indexer/repo_templates/dicom_study/.gitattributes

@@ -0,0 +1,12 @@
+**/.git* annex.largefiles=nothing
+* annex.largefiles=(largerthan=100kb)
+*.yml  annex.largefiles=nothing
+*.json annex.largefiles=nothing
+*.txt annex.largefiles=nothing
+*.tsv annex.largefiles=nothing
+*.nii.gz annex.largefiles=anything
+*.tgz annex.largefiles=anything
+*_scans.tsv annex.largefiles=anything
+# annex event files as they contain subjects behavioral responses
+sub-*/**/*_events.tsv annex.largefiles=anything
+*.bk2 annex.largefiles=anything

docker/dicom_indexer/indexer/repo_templates/dicom_study/.gitlab-ci.yml

@@ -0,0 +1,6 @@
+
+include:
+  - local: /ci-env.yml
+  - project: 'unf/ni-dataops'
+    file:
+      - 'ci-pipelines/sources/dicoms_study.yml'