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Fix shed-tools test -t workflow_tools.yml #155

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Merged
mvdbeek merged 1 commit into from
Feb 28, 2020
Merged

Fix shed-tools test -t workflow_tools.yml #155

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10 changes: 8 additions & 2 deletions src/ephemeris/generate_tool_list_from_ga_workflow_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@

import yaml

from .shed_tools_methods import format_tool_shed_url

INSTALL_TOOL_DEPENDENCIES = 'install_tool_dependencies: True'
INSTALL_REPOSITORY_DEPENDENCIES = 'install_repository_dependencies: True'
INSTALL_RESOLVER_DEPENDENCIES = 'install_resolver_dependencies: True'
Expand Down Expand Up @@ -57,8 +59,12 @@ def translate_workflow_dictionary_to_tool_list(tool_dictionary, panel_label):
starting_tool_list.append(tsr)
tool_list = []
for tool in starting_tool_list:
sub_dic = {'name': tool['name'], 'owner': tool['owner'], 'revisions': [tool['changeset_revision']],
'tool_panel_section_label': panel_label, 'tool_shed_url': 'https://' + tool['tool_shed']}
sub_dic = {
'name': tool['name'],
'owner': tool['owner'],
'revisions': [tool['changeset_revision']],
'tool_panel_section_label': panel_label,
'tool_shed_url': format_tool_shed_url(tool['tool_shed'])}
tool_list.append(sub_dic)
return tool_list

Expand Down
3 changes: 2 additions & 1 deletion src/ephemeris/get_tool_list_from_galaxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@

from . import get_galaxy_connection
from .common_parser import get_common_args
from .shed_tools_methods import format_tool_shed_url


def get_tool_panel(gi):
Expand All @@ -33,7 +34,7 @@ def handle_tool(tool_elem):
if tsr['name'] != name or tsr['owner'] != owner:
return

if tool_shed_url and tsr['tool_shed'] != tool_shed_url:
if tool_shed_url and format_tool_shed_url(tsr['tool_shed']) != format_tool_shed_url(tool_shed_url):
return

if changeset_revision and changeset_revision != tsr["changeset_revision"]:
Expand Down
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