diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index abc50b24075ff92f18832462441b969f54908035..dee8fbf0798b04a1c754d6a3adb8b5899ffccdac 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,6 +17,11 @@ install_py37:
- eossr-codemeta2zenodo --help
- eossr-codemeta2zenodo --input_codemeta_file ./codemeta.json
- cat .zenodo.json
+ - echo "testing all entry points and bash scripts"
+ - eossr-upload_new_deposit -h
+ - eossr-upload_new_version_deposit -h
+ - eossr-check_connection_zenodo -h
+ - which parse_last_release_git.sh
only:
- branches
diff --git a/eossr/api/apizenodo.py b/eossr/api/apizenodo.py
index 7eea1f13bca82099fd5521a3e58e010f45f39a3e..36b0ef88592c5391094119715afd0f6fc567cad5 100644
--- a/eossr/api/apizenodo.py
+++ b/eossr/api/apizenodo.py
@@ -313,7 +313,7 @@ class ZenodoAPI:
else:
pass
- def test_upload_to_zenodo(self):
+ def check_upload_to_zenodo(self):
"""
`Tests` the different stages of the GitLab-Zenodo connection and that the status_code returned by every
stage is the correct one.
diff --git a/eossr/scripts/check_connection_zenodo.py b/eossr/scripts/check_connection_zenodo.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9ef240f8d689459a839887e40c69ba003827ffa
--- /dev/null
+++ b/eossr/scripts/check_connection_zenodo.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import argparse
+from distutils.util import strtobool
+from eossr.api.apizenodo import ZenodoAPI
+
+
+def main():
+ # Required arguments
+ parser = argparse.ArgumentParser(description="Test the connection to zenodo and all the stages of a new upload.")
+
+ parser.add_argument('--token', '-t', type=str,
+ dest='zenodo_token',
+ help='Personal access token to (sandbox)Zenodo',
+ required=True)
+
+ parser.add_argument('--sandbox', '-s', action='store',
+ type=lambda x: bool(strtobool(x)),
+ dest='sandbox_flag',
+ help='Set the Zenodo environment.'
+ 'If True connects with Zenodo. If False with Sandbox Zenodo',
+ default=False)
+
+ parser.add_argument('--project_dir', '-p', action='store',
+ dest='project_dir',
+ help='Path to the root directory of the directory to be uploaded. '
+ 'DEFAULT; assumed to be on it, i.e., "./"',
+ default='./'
+ )
+
+ args = parser.parse_args()
+
+ zenodo = ZenodoAPI(access_token=args.zenodo_token,
+ sandbox=args.sandbox_flag,
+ proj_root_dir=args.project_dir
+ )
+
+ zenodo.test_upload_to_zenodo()
+
+
+if __name__ == '__main__':
+ main()
diff --git a/eossr/scripts/eossr_upload_new_deposit.py b/eossr/scripts/eossr_upload_new_deposit.py
new file mode 100644
index 0000000000000000000000000000000000000000..a36385d2585c5b731ae490b400222aeccbf7d6c5
--- /dev/null
+++ b/eossr/scripts/eossr_upload_new_deposit.py
@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+
+import os
+import json
+import argparse
+from pathlib import Path
+from distutils.util import strtobool
+from eossr.api.apizenodo import ZenodoAPI
+from eossr.metadata.codemeta2zenodo import parse_codemeta_and_write_zenodo_metadata_file
+
+
+def create_zenodo_metadata(metadata_filename, repo_root_dir='./'):
+ """
+ Checks for a zenodo metadata file, otherwise it looks for a codemeta.json file to create a the .zenodo.json file
+
+ :param metadata_filename: str
+ path and name to the zenodo metadata json file
+ NOT TO BE CHANGED. The file must be named `.zenodo.json` and be stored in the root directory of the library.
+
+ :param repo_root_dir: str
+ Path to the project root directory to be uploaded
+ """
+ # root_dir = find_root_directory()
+ root_dir = Path(repo_root_dir)
+ print(f'working dir : {root_dir}') # DEBUG
+
+ files_json = [file for file in os.listdir(root_dir) if file.endswith('.json')]
+ print(f'JSON files found: \n{files_json}')
+
+ zenodo_metadata_filename = metadata_filename
+ codemeta_file = 'codemeta.json'
+
+ if codemeta_file in files_json and zenodo_metadata_filename not in files_json:
+ print(f"\nCreating {zenodo_metadata_filename} automatically on the CI pipeline.\n")
+ parse_codemeta_and_write_zenodo_metadata_file(codemeta_file, zenodo_metadata_filename)
+
+ elif os.path.isfile(zenodo_metadata_filename):
+ print(f"\n{zenodo_metadata_filename} metadata file found in the root directory of the library ! \n")
+ pass
+
+ else:
+ print(f"\n{codemeta_file} not found, thus any zenodo_metadata file `{zenodo_metadata_filename}` was"
+ f" created during the CI pipeline."
+ f"Please provide one so that the CI can run correctly (examples in the 'codemeta_utils' directory)")
+ exit(-1)
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Upload new deposit entry to Zenodo")
+
+ parser.add_argument('--token', '-t', type=str,
+ dest='zenodo_token',
+ help='Personal access token to (sandbox)Zenodo',
+ required=True)
+
+ parser.add_argument('--sandbox', '-s', action='store',
+ type=lambda x: bool(strtobool(x)),
+ dest='sandbox_flag',
+ help='Set the Zenodo environment.'
+ 'If True connects with Zenodo. If False with Sanbox Zenodo',
+ default=False)
+
+ parser.add_argument('--input-dir', '-i', type=str,
+ dest='input_directory',
+ help='Path to the directory containing the files to upload.'
+ 'ALL files will be uploaded.',
+ required=True)
+
+ args = parser.parse_args()
+
+ zenodo = ZenodoAPI(
+ access_token=args.zenodo_token,
+ sandbox=args.sandbox_flag # True for sandbox.zenodo.org !! False for zenodo.org
+ )
+
+ # 1 - create empty deposit
+ new_entry = zenodo.create_new_entry()
+
+ if new_entry.status_code < 399:
+ deposition_id = new_entry.json()['id']
+ doi = new_entry.json()['metadata']['prereserve_doi']['doi']
+ print(f" * Status {new_entry.status_code}. New entry to Zenodo created ! Deposition id {deposition_id}")
+ else:
+ print(f" ! ERROR; the NEW entry COULD NOT be created.")
+ print(new_entry.json())
+
+ # 2 - upload files
+ for file in os.listdir(args.input_directory):
+ full_path_file = args.input_directory + '/' + file
+
+ new_upload = zenodo.upload_file_entry(
+ deposition_id,
+ name_file=file,
+ path_file=full_path_file
+ )
+
+ print(f" * File {file} correctly uploaded !\n", new_upload)
+
+ # 3 - Create the zenodo metadata file from a codemeta.json file
+ zenodo_metadata_filename = '.zenodo.json'
+ create_zenodo_metadata(zenodo_metadata_filename)
+
+ # And upload the repository metadata
+ with open(zenodo_metadata_filename) as json_file:
+ entry_metadata = json.load(json_file)
+
+ # entry_info['metadata']['doi'] = doi # In the new version of the API the doi is updated automatically.
+ update_entry = zenodo.update_metadata_entry(
+ deposition_id,
+ json_metadata=entry_metadata
+ )
+
+ if update_entry.status_code < 399:
+ print(f" * Status {update_entry.status_code}. Repository information correctly uploaded !")
+ else:
+ print(f" ! Repository information NOT correctly uploaded ! Status {update_entry.status_code}\n",
+ update_entry.json())
+
+ # 4 - publish entry
+ publish = zenodo.publish_entry(deposition_id)
+
+ if publish.status_code == 204:
+ print(" * New deposit correctly published !\n")
+ print(f" * The new doi should look like 10.5281/{deposition_id}. However please")
+ print(f" ** Check the upload at {zenodo.zenodo_api_url[:-4]}/deposit/{deposition_id} **")
+ else:
+ print(f" ! New deposit NOT correctly published ! Status {publish.status_code}\n",
+ publish.json())
+
+
+if __name__ == '__main__':
+ main()
diff --git a/eossr/scripts/eossr_upload_new_version_deposit.py b/eossr/scripts/eossr_upload_new_version_deposit.py
new file mode 100644
index 0000000000000000000000000000000000000000..a696ab696b27bfdd7213d74514271234ad01aff6
--- /dev/null
+++ b/eossr/scripts/eossr_upload_new_version_deposit.py
@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+
+
+import os
+import json
+import argparse
+from pathlib import Path
+from distutils.util import strtobool
+from eossr.api.apizenodo import ZenodoAPI
+from eossr.metadata.codemeta2zenodo import parse_codemeta_and_write_zenodo_metadata_file
+
+
+def create_zenodo_metadata(metadata_filename, repo_root_dir='./'):
+ """
+ Checks for a zenodo metadata file, otherwise it looks for a codemeta.json file to create a the .zenodo.json file
+
+ param metadata_filename: str
+ path and name to the zenodo metada json file
+ NOT TO BE CHANGED. The file must be named `.zenodo.json` and be stored in the root directory of the library.
+ """
+ # root_dir = find_root_directory()
+ root_dir = Path(repo_root_dir)
+
+ files_json = [file for file in os.listdir(root_dir) if file.endswith('.json')]
+ print(f'JSON files : {files_json}')
+
+ zenodo_metadata_filename = metadata_filename
+ codemeta_file = 'codemeta.json'
+
+ if codemeta_file in files_json and zenodo_metadata_filename not in files_json:
+ print(f"\nCreating {zenodo_metadata_filename} automatically at the CI pipeline.\n")
+ parse_codemeta_and_write_zenodo_metadata_file(codemeta_file, zenodo_metadata_filename)
+
+ elif os.path.isfile(zenodo_metadata_filename):
+ print(f"\n{zenodo_metadata_filename} metadata file found in the root directory of the library ! \n")
+ pass
+
+ else:
+ print(f"\n{codemeta_file} not found, thus any zenodo_metadata file `{zenodo_metadata_filename}` was"
+ f" created during the CI pipeline."
+ f"Please provide one so that the CI can run correctly (examples in the 'codemeta_utils' directory)")
+ exit(-1)
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Upload a new version of an existing deposit to Zenodo")
+
+ parser.add_argument('--token', '-t', type=str,
+ dest='zenodo_token',
+ help='Personal access token to (sandbox)Zenodo',
+ required=True)
+
+ parser.add_argument('--sandbox', '-s', action='store',
+ type=lambda x: bool(strtobool(x)),
+ dest='sandbox_flag',
+ help='Set the Zenodo environment.'
+ 'If True connects with Zenodo. If False with Sandbox Zenodo',
+ default=False)
+
+ parser.add_argument('--input-dir', '-i', type=str,
+ dest='input_directory',
+ help='Path to the directory containing the files to upload.'
+ 'ALL files will be uploaded.',
+ required=True)
+
+ parser.add_argument('--deposit_id', '-id', type=str,
+ dest='deposit_id',
+ help='deposit_id of the deposit that is going to be updated by a new version',
+ required=True)
+
+ args = parser.parse_args()
+
+ zenodo = ZenodoAPI(
+ access_token=args.zenodo_token,
+ sandbox=args.sandbox_flag # True for sandbox.zenodo.org !! False for zenodo.org
+ )
+
+ # 1 - request a new version of an existing deposit
+ new_version = zenodo.new_version_entry(args.deposit_id)
+
+ if new_version.status_code < 399:
+ print(f" * Status {new_version.status_code}. New version of the {args.deposit_id} entry correctly created !")
+ else:
+ print(f" ! ERROR; new version of the {args.deposit_id} entry COULD NOT be created.")
+ print(new_version.json())
+
+ new_deposition_id = new_version.json()['links']['latest_draft'].rsplit('/')[-1]
+
+ # PRE-2 - If you DO NOT want to erase the old files, comment the following lines
+ old_files_ids = [file['id'] for file in new_version.json()['files']]
+ for file_id in old_files_ids:
+ zenodo.erase_file_entry(
+ new_deposition_id,
+ file_id
+ )
+
+ # 2 - Upload new version of file(s)
+ for file in os.listdir(args.input_directory):
+ full_path_file = args.input_directory + '/' + file
+
+ new_upload = zenodo.upload_file_entry(
+ new_deposition_id,
+ name_file=file,
+ path_file=full_path_file
+ )
+
+ print(f" * File {file} correctly uploaded !\n", new_upload)
+
+ # 3 - Look for a zenodo metadata file, otherwise try to create one
+ zenodo_metadata_filename = '.zenodo.json'
+ create_zenodo_metadata(zenodo_metadata_filename)
+
+ with open(zenodo_metadata_filename) as json_file:
+ update_entry_metadata = json.load(json_file)
+
+ # update_entry_info['metadata']['doi'] = doi # In the new version of the API the doi is updated automatically.
+ update_entry = zenodo.update_metadata_entry(
+ new_deposition_id,
+ json_metadata=update_entry_metadata
+ )
+
+ if update_entry.status_code < 399:
+ print(f" * Status {update_entry.status_code}. Repository information correctly uploaded !\n")
+ else:
+ print(f" ! Repository information NOT correctly uploaded ! Status {update_entry.status_code}\n",
+ update_entry.json())
+
+ # 4 - publish entry - to publish the entry, uncomment the two lone below
+ publish = zenodo.publish_entry(new_deposition_id)
+
+ if publish.status_code == 204:
+ print(" * New version of the old deposition correctly published !\n")
+ print(f" * Old deposition id {args.deposit_id}, new deposition id {new_deposition_id}")
+ print(f" * The new doi should look like 10.5281/{new_deposition_id}. However please")
+ print(f" ** Check the upload at {zenodo.zenodo_api_url[:-4]}/deposit/{new_deposition_id} **")
+ else:
+ print(f" ! New deposit NOT correctly published ! Status {publish.status_code}\n",
+ publish.json())
+
+
+if __name__ == '__main__':
+ main()
diff --git a/eossr/scripts/parse_last_release_git.sh b/eossr/scripts/parse_last_release_git.sh
new file mode 100755
index 0000000000000000000000000000000000000000..cf70750df0a454e0a90ac3b56582d3e3b906105c
--- /dev/null
+++ b/eossr/scripts/parse_last_release_git.sh
@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+REPOSITORY_NAME="$1"
+REPOSITORY_BASE_URL="$2"
+
+LAST_RELEASE=`git ls-remote --tags --refs --sort="v:refname" $REPOSITORY_BASE_URL.git | tail -n1 | sed 's/.*\///'`
+
+if [ -z "$LAST_RELEASE" ]; then
+ echo "No tag / new release found ! - Or error when parsing. Downloading last commit to the repository (master branch) ;"
+ wget -O $REPOSITORY_NAME-master.zip "$REPOSITORY_BASE_URL"/-/archive/master/"$REPOSITORY_NAME"-master.zip
+ mv $REPOSITORY_NAME-master.zip ./build
+else
+ echo "$LAST_RELEASE tag / release found !"
+ wget -O $REPOSITORY_NAME-$LAST_RELEASE.zip "$REPOSITORY_BASE_URL"/-/archive/"$LAST_RELEASE"/"$REPOSITORY_NAME"-"$LAST_RELEASE".zip
+ mv $REPOSITORY_NAME-$LAST_RELEASE.zip ./build
+fi
diff --git a/eossr/scripts/tests/test_eossr_codemeta2zenodo.py b/eossr/scripts/tests/test_scripts.py
similarity index 100%
rename from eossr/scripts/tests/test_eossr_codemeta2zenodo.py
rename to eossr/scripts/tests/test_scripts.py
diff --git a/setup.py b/setup.py
index 1a5f5f5cdc94cdb32dff4c42e07199ef74057fc3..69f6bcf68551760d53287c7792b38a57e4e2b353 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,10 @@ import re
from setuptools import setup, find_packages
entry_points = {'console_scripts': [
- 'eossr-codemeta2zenodo = eossr.scripts.eossr_codemeta2zenodo:main'
+ 'eossr-codemeta2zenodo = eossr.scripts.eossr_codemeta2zenodo:main',
+ 'eossr-upload_new_deposit = eossr.scripts.eossr_upload_new_deposit:main',
+ 'eossr-upload_new_version_deposit = eossr.scripts.eossr_upload_new_version_deposit:main',
+ 'eossr-check_connection_zenodo = eossr.scripts.check_connection_zenodo:main'
]
}
@@ -23,7 +26,7 @@ setup(
"requests"
],
packages=find_packages(),
- # scripts=[],
+ scripts=['eossr/scripts/parse_last_release_git.sh'],
tests_require=['pytest'],
author='Thomas Vuillaume & Enrique Garcia',
author_email='vuillaume<at>lapp.in2p3.fr',