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abims
e-infra
gga_load_data
Commits
dbd5d298
Commit
dbd5d298
authored
3 years ago
by
Arthur Le Bars
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removed obsolete code
parent
696dea98
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2 merge requests
!9
Release 2.0 (merge dev to master)
,
!5
Workflow v2
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gga_load_data.py
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dbd5d298
...
@@ -87,37 +87,6 @@ class LoadData(speciesData.SpeciesData):
...
@@ -87,37 +87,6 @@ class LoadData(speciesData.SpeciesData):
get_organism_tool_version
=
get_organism_tool
[
"
version
"
]
get_organism_tool_version
=
get_organism_tool
[
"
version
"
]
delete_organism_tool_version
=
delete_organism_tool
[
"
version
"
]
delete_organism_tool_version
=
delete_organism_tool
[
"
version
"
]
# if delete_organism_tool["version"] != "2.3.4+galaxy0":
# toolshed_dict = delete_organism_tool["tool_shed_repository"]
# logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
# changeset_revision = "b1aa4f9d82fe"
# name = toolshed_dict["name"]
# owner = toolshed_dict["owner"]
# toolshed = "https://" + toolshed_dict["tool_shed"]
# logging.warning("Installing changeset for %s" % toolshed_dict["name"])
# self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
# changeset_revision=changeset_revision,
# install_tool_dependencies=True,
# install_repository_dependencies=False,
# install_resolver_dependencies=True)
# if get_organism_tool["version"] != "2.3.4+galaxy0":
# toolshed_dict = get_organism_tool["tool_shed_repository"]
# logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
# changeset_revision = "831229e6cda2"
# name = toolshed_dict["name"]
# owner = toolshed_dict["owner"]
# toolshed = "https://" + toolshed_dict["tool_shed"]
# logging.warning("Installing changeset for %s" % toolshed_dict["name"])
# self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
# changeset_revision=changeset_revision,
# install_tool_dependencies=True,
# install_repository_dependencies=False,
# install_resolver_dependencies=True)
logging
.
debug
(
"
Getting
'
Homo sapiens
'
ID in instance
'
s chado database
"
)
logging
.
debug
(
"
Getting
'
Homo sapiens
'
ID in instance
'
s chado database
"
)
get_sapiens_id_job
=
self
.
instance
.
tools
.
run_tool
(
get_sapiens_id_job
=
self
.
instance
.
tools
.
run_tool
(
tool_id
=
"
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s
"
%
get_organism_tool_version
,
tool_id
=
"
toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s
"
%
get_organism_tool_version
,
...
...
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