Merge pull request #1 from CCBR/dev

updated parkit with parkit_e2e and slurm support

.custom-codespell-dictionary.txt

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+DNE

.gitignore

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 **/site/*
-**.koparde*
+**/.koparde*
+**/*.pyc
+**/.prettierrc
+**/*.tmp
+**/createtar.*.err
+**/createtar.*.out
+**/deposittar.*.err
+**/deposittar.*.out
+**/createmetadata.*.out
+**/createmetadata.*.err
+**/createemptycollection.*.err
+**/createemptycollection.*.out

.pre-commit-config.yaml

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+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      #    - id: check-added-large-files
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        args: ["--ignore-words=.custom-codespell-dictionary.txt"]
+  # https://github.com/codespell-project/codespell/issues/1498
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  # R formatting
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    hooks:
+      - id: style-files
+  # general linting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+  # enforce commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff

.prettierignore

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+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
+_extensions

CHANGELOG.md

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+## v1.0
+
+### Features/Bugs
+
+- `parkit` added... built using python
+- `parkit_e2e` added ... uses `parkit` and "slurm"

README.md

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+## parkit
+
+**Park** an **arc**hived project tool**kit**!
+
+> DISCLAIMERS:
+>
+> - works only on [BIOWULF](https://hpc.nih.gov/) or HELIX
+> - moves files to [HPC-DME](https://hpcdmeweb.nci.nih.gov/login)
+
+### Usage:
+
+```bash
+./parkit --help
+usage: parkit [-h] {createtar,createmetadata,createemptycollection,deposittar} ...
+
+parkit subcommands to park data in HPCDME
+
+positional arguments:
+  {createtar,createmetadata,createemptycollection,deposittar}
+                        Subcommand to run
+    createtar           create tarball(and its filelist) from a project folder.
+    createmetadata      create the metadata.json file required for a tarball (and its filelist)
+    createemptycollection
+                        creates empty project and analysis collections
+    deposittar          deposit tarball(and filelist) into vault
+
+options:
+  -h, --help            show this help message and exit
+```
+
+### Example:
+
+- Say you want to archive `/data/CCBR/projects/CCBR-12345` folder to `/CCBR_Archive/GRIDFTP/CCBR-12345` collection on HPC-DME
+- you can run the following commands sequentially to do this:
+
+```bash
+# create the tarball
+./parkit createtar --folder /data/CCBR/projects/ccbr_12345
+
+# create an empty collection on HPC-DME
+./parkit createemptycollection --dest /CCBR_Archive/GRIDFTP/CCBR-12345 --projectdesc "testing" --projecttitle "test project 1"
+
+# create required metadata
+./parkit createmetadata --tarball /data/CCBR/projects/ccbr_12345.tar --dest /CCBR_Archive/GRIDFTP/CCBR-12345
+
+# deposit the tar into HPC-DME
+./parkit deposittar --tarball /data/CCBR/projects/ccbr_12345.tar --dest /CCBR_Archive/GRIDFTP/CCBR-12345
+
+# bunch of extra files are created in the process
+ls /data/CCBR/projects/ccbr_12345.tar*
+/data/CCBR/projects/ccbr_12345.tar           /data/CCBR/projects/ccbr_12345.tar.filelist.md5            /data/CCBR/projects/ccbr_12345.tar.md5
+/data/CCBR/projects/ccbr_12345.tar.filelist  /data/CCBR/projects/ccbr_12345.tar.filelist.metadata.json  /data/CCBR/projects/ccbr_12345.tar.metadata.json
+
+# these extra files can now be deleted
+rm -f /data/CCBR/projects/ccbr_12345.tar*
+
+# you can also deleted the recently parked project folder
+rm -rf /data/CCBR/projects/ccbr_12345
+
+# Done!
+```

VERSION

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+1.0.0

bin/parkit

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+redirect