added new tool request yml

.ci/parse_issue_to_yml.py

@@ -0,0 +1,64 @@
+
+
+import sys
+import subprocess
+import yaml
+
+
+def main(argv):
+    issue_body = argv[0]
+    url = extract_url(issue_body)
+    tool = format_to_tool(url)
+    tool = annotate_section_label(tool)
+    write_yml(tool)
+    cleanup()
+
+
+def extract_url(issue_body):
+    return issue_body.split('URL to the tool in the Galaxy Toolshed repository: ', 1)[1]
+
+
+def format_to_tool(url):
+    url = url.split('/')
+
+    tool = {}
+    tool['name'] = url[5]
+    tool['owner'] = url[4]
+    tool['revisions'] = url[6]
+    tool['tool_shed_url'] = url[2]
+    tool['tool_panel_section_label'] = ''
+
+    return tool
+
+
+def annotate_section_label(tool):
+    # get galaxy_eu tools. Would be nice to do with bioblend? 
+    subprocess.run(['get-tool-list', '-g', 'https://usegalaxy.eu', '-o', 'eu_tool_list.yaml'])
+
+    with open('eu_tool_list.yaml', 'r') as fp:
+        galaxy_eu_tools = yaml.safe_load(fp)
+
+    for eu_tool in galaxy_eu_tools['tools']:
+        if eu_tool['name'] == tool['name'] and eu_tool['owner'] == tool['owner']:
+            tool['tool_panel_section_label'] = eu_tool['tool_panel_section_label']
+
+    return tool
+
+
+def write_yml(tool):
+    with open(f'requests/tool_request_{tool["name"]}.yml', 'w') as fp:
+        fp.write('tools:\n')
+        fp.write(f'  - name: {tool["name"]}\n')
+        fp.write(f'    owner: {tool["owner"]}\n')
+        fp.write(f'    tool_panel_section_label: {tool["tool_panel_section_label"]}\n')
+        fp.write(f'    tool_shed_url: {tool["tool_shed_url"]}\n')
+        fp.write(f'    revisions:\n')
+        fp.write(f'    - {tool["revisions"]}\n')
+
+
+def cleanup():
+    subprocess.run(['rm', 'eu_tool_list.yaml'])
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])

.ci/parsing_requirements.txt

@@ -0,0 +1,2 @@
+pyyaml
+ephemeris

.ci/requirements.txt

@@ -1,2 +1,3 @@
 pyyaml
 bioblend
+

.github/workflows/parse_issue_to_tool_request.yml

@@ -0,0 +1,47 @@
+
+# reads a 
+
+name: parse tool request to yml
+
+# workflow triggered on new issue
+on:
+  issues:
+    types: opened
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  parse:
+    if: contains(github.event.issue.body, '/toolshed.g2.bx.psu.edu')
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      # set up python environment
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      # Install python dependencies for check_files script
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r .ci/parsing_requirements.txt
+
+      # Parse the issue into yml (autoannotate using eu section label)
+      - name: parse issue to yml
+        run: python .ci/parse_issue_to_yml.py "$ISSUE_BODY"
+        env:
+          ISSUE_BODY: ${{ toJson(github.event.issue.body) }}
+
+
+      - name: Create Pull Request
+        uses: peter-evans/[email protected]
+
+
+

requests/newtools.yml

@@ -0,0 +1,55 @@
+tools:
+  - name: bionano_scaffold
+    owner: bgruening
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 96cacb31d571
+  - name: merqury
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 9d79beb19ac3
+  - name: meryl
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 51c2360aa807
+  - name: purge_dups
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 76d4cbefff85
+  - name: bellerophon
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - eca6296a091a
+  - name: salsa
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - ba7b0f11e470
+  - name: pretext_map
+    owner: iuc
+    tool_panel_section_label: Assembly
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 02831bf9e95f
+  - name: pretext_snapshot
+    owner: iuc
+    tool_panel_section_label: Graph/Display Data
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - 7c9417381ad5
+  - name: blast2go
+    owner: peterjc
+    tool_panel_section_label: Annotation
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - e23b621eb7bb

requests/tool_request_blast2go.yml

@@ -0,0 +1,7 @@
+tools:
+  - name: blast2go
+    owner: peterjc
+    tool_panel_section_label: Annotation
+    tool_shed_url: toolshed.g2.bx.psu.edu
+    revisions:
+    - e23b621eb7bb"