diff env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_list.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_list.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+
+import argparse
+import logging
+from glob import glob
+from html.parser import HTMLParser
+
+import requests
+
+QUAY_API_ENDPOINT = 'https://quay.io/api/v1/repository'
+
+
+def get_quay_containers(repository='biocontainers'):
+    """
+    Get all quay containers in the biocontainers repo
+    """
+    containers = []
+
+    repos_parameters = {'public': 'true', 'namespace': repository}
+    repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'}
+    repos_response = requests.get(
+        QUAY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=12)
+
+    repos = repos_response.json()['repositories']
+
+    for repo in repos:
+        logging.info(repo)
+        tags_response = requests.get(
+            "{}/{}/{}".format(QUAY_API_ENDPOINT, repository, repo['name']))
+        tags = tags_response.json()['tags']
+        for tag in tags:
+            containers.append('{}:{}'.format(repo['name'], tag))
+
+    return containers
+
+
+def get_singularity_containers():
+    """
+    Get all existing singularity containers from "https://depot.galaxyproject.org/singularity/"
+    """
+    class GetContainerNames(HTMLParser):  # small parser which gets list of containers
+        def __init__(self):
+            HTMLParser.__init__(self)
+            self.containers = []
+
+        def handle_starttag(self, tag, attrs):
+            try:
+                for attr in attrs:
+                    if attr[0] == 'href' and attr[1] != '../':
+                        self.containers.append(attr[1].replace('%3A', ':'))
+            except IndexError:
+                pass
+
+    parser = GetContainerNames()
+    index = requests.get("https://depot.galaxyproject.org/singularity/")
+    parser.feed(index.text)
+    return parser.containers
+
+
+def get_conda_envs(filepath):
+    """
+    Get list of already existing envs
+    """
+    return [n.split('__')[-1].replace('@', ':') for n in glob('%s/*' % filepath)]
+
+
+def get_missing_containers(quay_list, singularity_list, blocklist_file=None):
+    r"""
+    Return list of quay containers that do not exist as singularity containers. Files stored in a blocklist will be ignored
+    """
+    blocklist = []
+    if blocklist_file:
+        with open(blocklist_file) as fh:
+            blocklist = fh.read().split('\n')
+    return [n for n in quay_list if n not in singularity_list and n not in blocklist]
+
+
+def get_missing_envs(quay_list, conda_list, blocklist_file=None):
+    r"""
+    Compares list of conda envs and docker containers and returns missing conda envs
+    """
+    blocklist = []
+    if blocklist_file:
+        with open(blocklist_file) as fh:
+            blocklist = fh.read().split('\n')
+
+    return [n for n in quay_list if n.split('--')[0] not in conda_list and n.split('--')[0] not in blocklist]
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Returns list of Docker containers in the quay.io biocontainers repository.')
+    parser.add_argument('--source', '-s',
+                        help="Docker, Singularity or Conda.")
+    parser.add_argument('--not-singularity', dest='not_singularity', action="store_true",
+                        help="Exclude Docker containers from which Singularity containers have already been built.")
+    parser.add_argument('--not-conda', dest='not_conda', action="store_true",
+                        help="Exclude Docker containers from which Conda environments have already been extracted.")
+    parser.add_argument('--conda-filepath', dest='conda_filepath', default=None,
+                        help="If searching for conda environments or employing the --not-conda option, a filepath where the environments are located.")
+    parser.add_argument('-b', '--blocklist', '--blacklist', dest='blocklist', default=None,
+                        help="Provide a 'blocklist file' containing containers which should be excluded from the list.")
+    parser.add_argument('-f', '--file', dest='output', default=None,
+                        help="File to write list to. If not given output will be returned on the command line.")
+
+    args = parser.parse_args()
+
+    if args.source == 'docker':
+        containers = get_quay_containers()
+        if args.not_singularity:
+            containers = get_missing_containers(
+                containers, get_singularity_containers(), args.blocklist)
+        if args.not_conda:
+            containers = get_missing_envs(containers, get_conda_envs(
+                args.conda_filepath), args.blocklist)
+    elif args.source == 'singularity':
+        containers = get_singularity_containers()
+    elif args.source == 'conda':
+        containers = get_conda_envs(args.conda_filepath)
+    else:
+        print("The 'source' argument was not understood.")
+        return
+
+    if args.output:
+        with open(args.output, 'a') as f:
+            for container in containers:
+                f.write('%s\n' % container)
+    else:
+        print(containers)
+
+
+if __name__ == '__main__':
+    main()