From 35e6df6f7ec8e927f02acf9ae6f1408717914f6e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 22 Nov 2018 21:31:32 +0000
Subject: [PATCH] CI: Auto-zenodo deposit on releases
---
.ci/zenodo.py | 92 +++++++++++++++++++++++++++++++++++++
.ci/zenodo_deposit.sh | 26 +++++++++++
.ci/zenodo_meta.json.jinja2 | 19 ++++++++
.gitlab-ci.yml | 23 ++++++++++
4 files changed, 160 insertions(+)
create mode 100644 .ci/zenodo.py
create mode 100644 .ci/zenodo_deposit.sh
create mode 100644 .ci/zenodo_meta.json.jinja2
diff --git a/.ci/zenodo.py b/.ci/zenodo.py
new file mode 100644
index 000000000..116645ecf
--- /dev/null
+++ b/.ci/zenodo.py
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+#
+# Deposit a new version of something on zenodo.
+#
+# It is assumed that a deposit already exists on zenodo - you must
+# specify the deposit ID of that original deposit.
+#
+# http://developers.zenodo.org/#rest-api
+
+
+import os.path as op
+import sys
+import json
+
+import jinja2 as j2
+import requests
+
+
+def deposit(zenodo_url, access_token, dep_id, upload_file, meta):
+
+ urlbase = '{}/api/deposit/depositions'.format(zenodo_url)
+ headers = {'Content-Type': 'application/json'}
+ params = {'access_token' : access_token}
+
+ # Create a new deposit
+ url = '{}/{}/actions/newversion'.format(urlbase, dep_id)
+ print('Creating new deposit: {}'.format(url))
+ r = requests.post(url, params=params)
+ if r.status_code != 201:
+ raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+ newurl = r.json()['links']['latest_draft']
+ dep_id = newurl.split('/')[-1]
+
+ print("New deposition ID: {}".format(dep_id))
+
+ # Upload the file
+ data = {'filename': op.basename(upload_file)}
+ files = {'file': open(upload_file, 'rb')}
+ url = '{}/{}/files'.format(urlbase, dep_id)
+ print('Uploading file: {}'.format(url))
+ r = requests.post(url, params=params, data=data, files=files)
+
+ if r.status_code != 201:
+ raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+ # Upload the metadata
+
+ url = '{}/{}?access_token={}'.format(urlbase, dep_id, access_token)
+ print('Uploading metadata: {}'.format(url))
+ r = requests.put(url, data=json.dumps(meta), headers=headers)
+
+ if r.status_code != 200:
+ print(r.json())
+ raise RuntimeError('PUT {} failed: {}'.format(url, r.status_code))
+
+ # Publish
+ url = '{}/{}/actions/publish'.format(urlbase, dep_id)
+ print('Publishing: {}'.format(url))
+ r = requests.post(url, params=params)
+
+ if r.status_code != 202:
+ raise RuntimeError('POST {} failed: {}'.format(url, r.status_code))
+
+
+def make_meta(templatefile, version, date):
+ with open(templatefile, 'rt') as f:
+ template = f.read()
+
+ template = j2.Template(template)
+
+ env = {
+ 'VERSION' : version,
+ 'DATE' : date,
+ }
+
+ return json.loads(template.render(**env))
+
+
+if __name__ == '__main__':
+
+ zurl = sys.argv[1]
+ tkn = sys.argv[2]
+ depid = sys.argv[3]
+ upfile = sys.argv[4]
+ metafile = sys.argv[5]
+ version = sys.argv[6]
+ date = sys.argv[7]
+
+ meta = make_meta(metafile, version, date)
+
+ deposit(zurl, tkn, depid, upfile, meta)
diff --git a/.ci/zenodo_deposit.sh b/.ci/zenodo_deposit.sh
new file mode 100644
index 000000000..32856bb59
--- /dev/null
+++ b/.ci/zenodo_deposit.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+tmp=`dirname $0`
+pushd $tmp > /dev/null
+thisdir=`pwd`
+popd > /dev/null
+
+zenodo_url=$1
+zenodo_tkn=$2
+zenodo_depid=$3
+
+version=`python setup.py -V`
+upfile=`pwd`/dist/fslpy-"$version".tar.gz
+metafile=`pwd`/.ci/zenodo_meta.json.jinja2
+date=`date +"%Y-%m-%d"`
+
+pip install --retries 10 requests jinja2
+
+python "$thisdir"/zenodo.py \
+ "$zenodo_url" \
+ "$zenodo_tkn" \
+ "$zenodo_depid" \
+ "$upfile" \
+ "$metafile" \
+ "$version" \
+ "$date"
diff --git a/.ci/zenodo_meta.json.jinja2 b/.ci/zenodo_meta.json.jinja2
new file mode 100644
index 000000000..0da8ea8ea
--- /dev/null
+++ b/.ci/zenodo_meta.json.jinja2
@@ -0,0 +1,19 @@
+{
+ "metadata" : {
+ "title" : "fslpy",
+ "upload_type" : "software",
+ "version" : "{{VERSION}}",
+ "publication_date" : "{{DATE}}",
+ "description" : "<p>The fslpy project is a <a href=\"https://fsl.fmrib.ox.ac.uk/fsl/fslwiki\">FSL</a> programming library written in Python. It is used by <a href=\"http://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/\">FSLeyes</a>.</p>\n\n<p>The fslpy library is developed at the Wellcome Centre for Integrative Neuroimaging (FMRIB), at the University of Oxford. It is hosted at <a href=\"https://git.fmrib.ox.ac.uk/fsl/fslpy/\">https://git.fmrib.ox.ac.uk/fsl/fslpy/</a>.</p>",
+ "keywords" : ["python", "mri", "neuroimaging", "neuroscience"],
+ "access_right" : "open",
+ "license" : "Apache-2.0",
+ "creators" : [
+ { "name" : "McCarthy, Paul" },
+ { "name" : "Cottaar, Michiel" },
+ { "name" : "Webster, Matthew" },
+ { "name" : "Fitzgibbon, Sean" },
+ { "name" : "Craig, Martin" }
+ ]
+ }
+}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 804ea4d68..5a7ceb6c1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -77,6 +77,12 @@ stages:
# - TWINE_PASSWORD: - Password to use when uploading to pypi
#
# - TWINE_REPOSITORY_URL: - Pypi repository to upload to
+#
+# - ZENODO_URL: - Zenodo URL to deposit release file to.
+#
+# - ZENODO_TOKEN: - Zenodo access token.
+#
+# - ZENODO_DEPOSIT_ID: - Deposit ID of previous Zenodo deposit.
###############################################################################
@@ -263,3 +269,20 @@ deploy-pypi:
script:
- bash ./.ci/deploy_pypi.sh
+
+
+deploy-zenodo
+ <<: *only_releases
+ <<: *setup_ssh
+ stage: deploy
+ when: manual
+ image: python3.6
+
+ tags:
+ - docker
+
+ dependencies:
+ - build-pypi-dist
+
+ script:
+ - bash ./.ci/zenodo_deposit.sh "$ZENODO_URL" "$ZENODO_TOKEN" "$ZENODO_DEPOSIT_ID"
--
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