diff env/lib/python3.7/site-packages/ephemeris/shed_tools_methods.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

--- a/env/lib/python3.7/site-packages/ephemeris/shed_tools_methods.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-from bioblend.toolshed import ToolShedInstance
-
-
-VALID_KEYS = [
-    "name",
-    "owner",
-    "changeset_revision",
-    "tool_panel_section_id",
-    "tool_panel_section_label",
-    "tool_shed_url",
-    "install_repository_dependencies",
-    "install_resolver_dependencies",
-    "install_tool_dependencies"
-]
-
-
-def complete_repo_information(tool,
-                              default_toolshed_url,
-                              require_tool_panel_info,
-                              default_install_tool_dependencies,
-                              default_install_repository_dependencies,
-                              default_install_resolver_dependencies,
-                              force_latest_revision):
-    repo = dict()
-    # We need those values. Throw a KeyError when not present
-    repo['name'] = tool['name']
-    repo['owner'] = tool['owner']
-    repo['tool_panel_section_id'] = tool.get('tool_panel_section_id')
-    repo['tool_panel_section_label'] = tool.get('tool_panel_section_label')
-    if require_tool_panel_info and repo['tool_panel_section_id'] is None and repo[
-            'tool_panel_section_label'] is None and 'data_manager' not in repo.get('name'):
-        raise KeyError("Either tool_panel_section_id or tool_panel_section_name must be defined for tool '{0}'.".format(
-            repo.get('name')))
-    repo['tool_shed_url'] = format_tool_shed_url(tool.get('tool_shed_url', default_toolshed_url))
-    repo['changeset_revision'] = tool.get('changeset_revision')
-    repo = get_changeset_revisions(repo, force_latest_revision)
-    repo['install_repository_dependencies'] = tool.get('install_repository_dependencies',
-                                                       default_install_repository_dependencies)
-    repo['install_resolver_dependencies'] = tool.get('install_resolver_dependencies',
-                                                     default_install_resolver_dependencies)
-    repo['install_tool_dependencies'] = tool.get('install_tool_dependencies', default_install_tool_dependencies)
-    return repo
-
-
-def format_tool_shed_url(tool_shed_url):
-    formatted_tool_shed_url = tool_shed_url
-    if not formatted_tool_shed_url.endswith('/'):
-        formatted_tool_shed_url += '/'
-    if not formatted_tool_shed_url.startswith('http'):
-        formatted_tool_shed_url = 'https://' + formatted_tool_shed_url
-    return formatted_tool_shed_url
-
-
-def get_changeset_revisions(repository, force_latest_revision=False):
-    """
-    Select the correct changeset revision for a repository,
-    and make sure the repository exists
-    (i.e a request to the tool shed with name and owner returns a list of revisions).
-    Return repository or None, if the repository could not be found on the specified tool shed.
-    """
-    # Do not connect to the internet when not necessary
-    if repository.get('changeset_revision') is None or force_latest_revision:
-        ts = ToolShedInstance(url=repository['tool_shed_url'])
-        # Get the set revision or set it to the latest installable revision
-        installable_revisions = ts.repositories.get_ordered_installable_revisions(repository['name'],
-                                                                                  repository['owner'])
-        if not installable_revisions:  #
-            raise LookupError("Repo does not exist in tool shed: {0}".format(repository))
-        repository['changeset_revision'] = installable_revisions[-1]
-
-    return repository
-
-
-def flatten_repo_info(repositories):
-    """
-    Flatten the dict containing info about what tools to install.
-    The tool definition YAML file allows multiple revisions to be listed for
-    the same tool. To enable simple, iterative processing of the info in this
-    script, flatten the `tools_info` list to include one entry per tool revision.
-
-    :type repositories: list of dicts
-    :param repositories: Each dict in this list should contain info about a tool.
-    :rtype: list of dicts
-    :return: Return a list of dicts that correspond to the input argument such
-             that if an input element contained `revisions` key with multiple
-             values, those will be returned as separate list items.
-    """
-
-    flattened_list = []
-    for repo_info in repositories:
-        new_repo_info = dict()
-        for key, value in repo_info.items():
-            if key in VALID_KEYS:
-                new_repo_info[key] = value
-        if 'revisions' in repo_info:
-            revisions = repo_info.get('revisions', [])
-            if not revisions:  # Revisions are empty list or None
-                flattened_list.append(new_repo_info)
-            else:
-                for revision in revisions:
-                    # A new dictionary must be created, otherwise there will
-                    # be aliasing of dictionaries. Which leads to multiple
-                    # repos with the same revision in the end result.
-                    new_revision_dict = dict(**new_repo_info)
-                    new_revision_dict['changeset_revision'] = revision
-                    flattened_list.append(new_revision_dict)
-        else:  # Revision was not defined at all
-            flattened_list.append(new_repo_info)
-    return flattened_list