diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index 5d7a3b86730..6a294d9fc97 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -90,9 +90,6 @@ export default {
case "custom_builds":
activeLinks[key]["onclick"] = this.openManageCustomBuilds;
break;
- case "genomespace":
- activeLinks[key]["onclick"] = this.requestGenomeSpace;
- break;
case "logout":
activeLinks[key]["onclick"] = this.signOut;
break;
@@ -138,9 +135,6 @@ export default {
});
}
},
- requestGenomeSpace() {
- window.location.href = `${getAppRoot()}openid/openid_auth?openid_provider=genomespace`;
- },
signOut() {
const Galaxy = getGalaxyInstance();
Galaxy.modal.show({
diff --git a/client/galaxy/scripts/components/User/UserPreferencesModel.js b/client/galaxy/scripts/components/User/UserPreferencesModel.js
index 3a8ac11ac3e..5078266abf4 100644
--- a/client/galaxy/scripts/components/User/UserPreferencesModel.js
+++ b/client/galaxy/scripts/components/User/UserPreferencesModel.js
@@ -73,11 +73,6 @@ export const getUserPreferencesModel = () => {
description: _l("Add or remove custom builds using history datasets."),
icon: "fa-cubes"
},
- genomespace: {
- title: _l("Request GenomeSpace token"),
- description: _l("Requests token through OpenID."),
- icon: "fa-openid"
- },
logout: {
title: _l("Sign out"),
description: _l("Click here to sign out of all sessions."),
diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js
index 35e48d6063b..076c42bf8bf 100644
--- a/client/galaxy/scripts/mvc/form/form-parameters.js
+++ b/client/galaxy/scripts/mvc/form/form-parameters.js
@@ -9,7 +9,6 @@ import Ui from "mvc/ui/ui-misc";
import SelectContent from "mvc/ui/ui-select-content";
import SelectLibrary from "mvc/ui/ui-select-library";
import SelectFtp from "mvc/ui/ui-select-ftp";
-import SelectGenomeSpace from "mvc/ui/ui-select-genomespace";
import RulesEdit from "mvc/ui/ui-rules-edit";
import ColorPicker from "mvc/ui/ui-color-picker";
import DataPicker from "mvc/ui/ui-data-picker";
@@ -38,7 +37,6 @@ export default Backbone.Model.extend({
ftpfile: "_fieldFtp",
upload: "_fieldUpload",
rules: "_fieldRulesEdit",
- genomespacefile: "_fieldGenomeSpace",
data_dialog: "_fieldDialog"
},
@@ -237,15 +235,6 @@ export default Backbone.Model.extend({
});
},
- /** GenomeSpace file select field
- */
- _fieldGenomeSpace: function(input_def) {
- return new SelectGenomeSpace.View({
- id: `field-${input_def.id}`,
- onchange: input_def.onchange
- });
- },
-
_fieldRulesEdit: function(input_def) {
return new RulesEdit.View({
id: `field-${input_def.id}`,
diff --git a/client/galaxy/scripts/mvc/tool/tool-genomespace.js b/client/galaxy/scripts/mvc/tool/tool-genomespace.js
deleted file mode 100644
index a4523fac27a..00000000000
--- a/client/galaxy/scripts/mvc/tool/tool-genomespace.js
+++ /dev/null
@@ -1,27 +0,0 @@
-// Provides support for interacting with the GenomeSpace File Browser popup dialogue
-import { getGalaxyInstance } from "app";
-
-// tool form templates
-export default {
- openFileBrowser: function(options) {
- const Galaxy = getGalaxyInstance();
- var GS_UI_URL = Galaxy.config.genomespace_ui_url;
- var GS_UPLOAD_URL = `${GS_UI_URL}upload/loadUrlToGenomespace.html?getLocation=true`;
-
- var newWin = window.open(GS_UPLOAD_URL, "GenomeSpace File Browser", "height=360px,width=600px");
-
- window.addEventListener(
- "message",
- e => {
- if (options.successCallback && e.data.destination) {
- options.successCallback(e.data);
- }
- },
- false
- );
-
- newWin.focus();
-
- if (options["errorCallback"] != null) newWin.setCallbackOnGSUploadError = Galaxy.config["errorCallback"];
- }
-};
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js b/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
deleted file mode 100644
index 64b0a232f0f..00000000000
--- a/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
+++ /dev/null
@@ -1,79 +0,0 @@
-import Backbone from "backbone";
-import _l from "utils/localization";
-import Ui from "mvc/ui/ui-misc";
-import GenomespaceBrowser from "mvc/tool/tool-genomespace";
-/**
- * GenomeSpace file selector
- */
-var View = Backbone.View.extend({
- // initialize
- initialize: function(options) {
- // link this
- var self = this;
- this.options = options;
-
- // create insert new list element button
- this.browse_button = new Ui.Button({
- title: _l("Browse"),
- icon: "fa fa-sign-in",
- cls: "btn btn-secondary float-left",
- tooltip: _l("Browse GenomeSpace"),
- onclick: function() {
- self.browseGenomeSpace(options);
- }
- });
-
- // create genomespace filepath textbox
- this.filename_textbox = new Ui.Input();
-
- // create elements
- this.setElement(this._template(options));
- this.$(".ui-browse-button").append(this.browse_button.$el);
- this.$(".ui-filename-textbox").append(this.filename_textbox.$el);
- },
-
- /** Browse GenomeSpace */
- browseGenomeSpace: function(options) {
- var self = this;
- GenomespaceBrowser.openFileBrowser({
- successCallback: function(data) {
- self.value(data.destination);
- }
- });
- },
-
- /** Main Template */
- _template: function(options) {
- return ``;
- },
-
- /** Return/Set currently selected genomespace filename */
- value: function(new_value) {
- // check if new_value is defined
- if (new_value !== undefined) {
- this._setValue(new_value);
- } else {
- return this._getValue();
- }
- },
-
- // get value
- _getValue: function() {
- return this.filename_textbox.value();
- },
-
- // set value
- _setValue: function(new_value) {
- if (new_value) {
- this.filename_textbox.value(new_value);
- }
- this.options.onchange && this.options.onchange(new_value);
- }
-});
-
-export default {
- View: View
-};
diff --git a/client/galaxy/scripts/nls/fr/locale.js b/client/galaxy/scripts/nls/fr/locale.js
index 3e0f8c1ad91..df0eb2a39fb 100644
--- a/client/galaxy/scripts/nls/fr/locale.js
+++ b/client/galaxy/scripts/nls/fr/locale.js
@@ -339,9 +339,6 @@ define({
"Delete this repeat block": false,
placeholder: false,
Repeat: false,
- // ---------------------------------------------------------------------------- ui-select-genomespace
- "Browse GenomeSpace": false,
- Browse: false,
// ---------------------------------------------------------------------------- ui-frames
Error: false,
Close: false,
diff --git a/client/galaxy/scripts/nls/locale.js b/client/galaxy/scripts/nls/locale.js
index bd635ce8e4b..afb604e5a03 100644
--- a/client/galaxy/scripts/nls/locale.js
+++ b/client/galaxy/scripts/nls/locale.js
@@ -339,9 +339,6 @@ define({
"Delete this repeat block": false,
placeholder: false,
Repeat: false,
- // ---------------------------------------------------------------------------- ui-select-genomespace
- "Browse GenomeSpace": false,
- Browse: false,
// ---------------------------------------------------------------------------- ui-frames
Error: false,
Close: false,
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 40d9919ae41..8fa39190080 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1584,17 +1584,6 @@
:Type: str
-~~~~~~~~~~~~~~~~~~~~~~
-``genomespace_ui_url``
-~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
- Points to the GenomeSpace UI service which will be used by the
- GenomeSpace importer and exporter tools
-:Default: ``https://gsui.genomespace.org/jsui/``
-:Type: str
-
-
~~~~~~~~~~~~~
``terms_url``
~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 977f49bbb13..620e61b3ad3 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -837,10 +837,6 @@ galaxy:
# The URL linked by the "Videos" link in the "Help" menu.
#screencasts_url: https://vimeo.com/galaxyproject
- # Points to the GenomeSpace UI service which will be used by the
- # GenomeSpace importer and exporter tools
- #genomespace_ui_url: https://gsui.genomespace.org/jsui/
-
# The URL linked by the "Terms and Conditions" link in the "Help"
# menu, as well as on the user registration and login forms and in the
# activation emails.
diff --git a/lib/galaxy/config/sample/tool_conf.xml.main b/lib/galaxy/config/sample/tool_conf.xml.main
index 99aa2052798..7569b7ad0d7 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.main
+++ b/lib/galaxy/config/sample/tool_conf.xml.main
@@ -16,12 +16,9 @@
-
-
diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index a1f35da1733..fd6f80066f5 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -20,12 +20,9 @@
-
-
diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 48114734ccc..3c3ce61385a 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -78,7 +78,7 @@ svgwrite = "*"
pyparsing = "*"
"Fabric3" = "*"
paramiko = "*"
-python-genomespaceclient = "<2.0"
+cloudbridge = "*"
social_auth_core = {version = "==3.1.0+gx0", extras = ['openidconnect']}
cloudauthz = "==0.6.0"
gxformat2 = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 536f8e30e89..7388ad1a691 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -44,21 +44,20 @@ pytest-postgresql==1.4.1
pytest-pythonpath==0.7.3
pytest==4.6.6
pytz==2019.3
-pyyaml==5.2
recommonmark==0.6.0
requests==2.22.0
scandir==1.10.0 ; python_version < '3.5'
selenium==3.141.0
six==1.11.0
snowballstemmer==2.0.0
-sphinx-markdown-tables==0.0.10
+sphinx-markdown-tables==0.0.12
sphinx-rtd-theme==0.4.3
sphinx==1.8.5
sphinxcontrib-websupport==1.1.2
testfixtures==6.10.3
twill==0.9.1 ; python_version < '3'
typing==3.7.4.1 ; python_version < '3.5'
-urllib3==1.25.7 ; python_version == '2.7'
+urllib3==1.25.7
watchdog==0.9.0
-wcwidth==0.1.7 ; sys_platform != 'win32'
+wcwidth==0.1.7
zipp==0.6.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 2104230a1a2..1807fb9ba43 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -60,7 +60,7 @@ funcsigs==1.0.2 ; python_version < '3.3'
functools32==3.2.3.post2 ; python_version < '3.2'
future==0.18.2
futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
-galaxy-sequence-utils==1.1.3
+galaxy-sequence-utils==1.1.4
google-api-python-client==1.7.8
google-auth-httplib2==0.0.3
google-auth==1.7.1
@@ -127,7 +127,7 @@ pulsar-galaxy-lib==0.14.0.dev1
pyasn1-modules==0.2.7
pyasn1==0.4.8
pycparser==2.19
-pycryptodome==3.9.4
+pycryptodome==3.9.6
pyeventsystem==0.1.0
pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
pyjwt==1.7.1
@@ -141,7 +141,6 @@ pysam==0.15.2
pysftp==0.2.9
python-cinderclient==4.0.0
python-dateutil==2.8.1
-python-genomespaceclient==1.2.0
python-glanceclient==2.12.0
python-jose==3.0.1
python-keystoneclient==3.17.0
@@ -187,7 +186,7 @@ typing==3.7.4.1 ; python_version < '3.5'
tzlocal==2.0.0
unicodecsv==0.14.1 ; python_version < '3.0'
uritemplate==3.0.0
-urllib3==1.25.7 ; python_version == '2.7'
+urllib3==1.25.7
vine==1.3.0
warlock==1.3.3
wcwidth==0.1.7 ; sys_platform != 'win32'
diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh
index 93b7dac5b4c..ea2cf862b38 100755
--- a/lib/galaxy/dependencies/pipfiles/update.sh
+++ b/lib/galaxy/dependencies/pipfiles/update.sh
@@ -73,6 +73,7 @@ for env in $ENVS; do
-e "s/^\(python-dateutil==[^ ;]\{1,\}\).*$/\1/" \
-e "s/^\(subprocess32==[^ ;]\{1,\}\).*$/\1 ; python_version < '3.0'/" \
-e "s/^\(typing==[^ ;]\{1,\}\).*$/\1 ; python_version < '3.5'/" \
+ -e "s/^\(urllib3==[^ ;]\{1,\}\).*$/\1/" \
pinned-requirements.txt pinned-dev-requirements.txt
if ! grep '==' pinned-dev-requirements.txt ; then
rm -f pinned-dev-requirements.txt
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index b5ddd1e1ec1..4e5d1ec363a 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -51,7 +51,6 @@ class ConfigSerializer(base.ModelSerializer):
'search_url' : _required_attribute,
'mailing_lists' : _defaults_to(self.app.config.mailing_lists_url),
'screencasts_url' : _required_attribute,
- 'genomespace_ui_url' : _required_attribute,
'citation_url' : _required_attribute,
'support_url' : _required_attribute,
'helpsite_url' : _required_attribute,
diff --git a/lib/galaxy/openid/genomespace.xml b/lib/galaxy/openid/genomespace.xml
deleted file mode 100644
index 65bf95ecbc5..00000000000
--- a/lib/galaxy/openid/genomespace.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-
-
- https://identity.genomespace.org/identityServer/xrd.jsp
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/lib/galaxy/openid/openid_conf.xml b/lib/galaxy/openid/openid_conf.xml
index 7a1e3dd9909..5730ae4dd86 100644
--- a/lib/galaxy/openid/openid_conf.xml
+++ b/lib/galaxy/openid/openid_conf.xml
@@ -1,4 +1,3 @@
-
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 4dabd33e329..686e4ce796b 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -177,8 +177,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
"gd_phylogenetic_tree",
"gd_population_structure",
"gd_prepare_population_structure",
- # Datasources
- "genomespace_importer"
]
# Tools that needed galaxy on the PATH in the past but no longer do along
# with the version at which they were fixed.
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 43d65298a36..5dc7379af03 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -648,19 +648,6 @@ class FTPFileToolParameter(ToolParameter):
return d
-class GenomespaceFileToolParameter(ToolParameter):
- """
- Parameter that takes one of two values.
- """
-
- def __init__(self, tool, input_source):
- super(GenomespaceFileToolParameter, self).__init__(tool, input_source)
- self.value = input_source.get('value')
-
- def get_initial_value(self, trans, other_values):
- return self.value
-
-
class HiddenToolParameter(ToolParameter):
"""
Parameter that takes one of two values.
@@ -2351,7 +2338,6 @@ parameter_types = dict(
baseurl=BaseURLToolParameter,
file=FileToolParameter,
ftpfile=FTPFileToolParameter,
- genomespacefile=GenomespaceFileToolParameter,
data=DataToolParameter,
data_collection=DataCollectionToolParameter,
library_data=LibraryDatasetToolParameter,
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 772fce1a3b9..db3be55aa3e 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1179,14 +1179,6 @@ mapping:
desc: |
The URL linked by the "Videos" link in the "Help" menu.
- genomespace_ui_url:
- type: str
- default: https://gsui.genomespace.org/jsui/
- required: false
- desc: |
- Points to the GenomeSpace UI service which will be used by
- the GenomeSpace importer and exporter tools
-
terms_url:
type: str
required: false
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index 87e0b46d777..ca928d2814e 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -1,13 +1,3 @@
-import os
-from collections import namedtuple
-from datetime import timedelta
-
-import pytest
-
-from galaxy.util import listify
-from galaxy_test.driver.driver_util import GalaxyTestDriver
-
-
"""
This tests: (1) automatic creation of configuration properties; and
(2) assignment of default values that are specified in the schema and, in
@@ -35,9 +25,16 @@ Configuration options NOT tested:
- job_config (no obvious testable defaults)
"""
+import os
+from collections import namedtuple
+from datetime import timedelta
-OptionData = namedtuple('OptionData', 'key, expected, loaded')
+import pytest
+from galaxy.util import listify
+from galaxy_test.driver.driver_util import GalaxyTestDriver
+
+OptionData = namedtuple('OptionData', ('key', 'expected', 'loaded'))
# Configuration properties that are paths should be absolute paths, by default resolved w.r.t root.
PATH_CONFIG_PROPERTIES = [
@@ -155,6 +152,7 @@ DO_NOT_TEST = [
'allow_user_deletion', # broken: default overridden
'amqp_internal_connection', # may or may not be testable; refactor config/
'api_allow_run_as', # may or may not be testable: test value assigned
+ 'build_sites_config_file', # broken: remove 'config/' prefix from schema
'chunk_upload_size', # broken: default overridden
'cleanup_job', # broken: default overridden
'conda_auto_init', # broken: default overridden
@@ -203,7 +201,7 @@ DO_NOT_TEST = [
'user_tool_label_filters', # broken: default overridden
'user_tool_section_filters', # broken: default overridden
'webhooks_dir', # broken; also remove 'config/' prefix from schema
- 'workflow_resource_params_mapper', # broken
+ 'workflow_resource_params_mapper', # broken: remove 'config/' prefix from schema
]
diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py
deleted file mode 100644
index bca99e5e009..00000000000
--- a/tools/genomespace/genomespace_exporter.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import argparse
-import binascii
-import os
-import sys
-
-from genomespaceclient import GenomeSpaceClient
-
-
-def upload_to_genomespace(token, input_file, target_url):
- token = token or os.environ.get('GS_TOKEN')
- gs_client = GenomeSpaceClient(token=token)
- gs_client.copy(input_file, target_url)
- print("File successfully copied.")
-
-
-def process_args(args):
- parser = argparse.ArgumentParser()
- parser.add_argument('-i', '--input_file', type=str,
- help="File to export", required=True)
- parser.add_argument('-o', '--target_url', type=str,
- help="GenomeSpace output target folder location", required=True)
- parser.add_argument('-t', '--token', type=str,
- help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
- " If none, the environment variable GS_TOKEN will be respected.", required=False)
-
- args = parser.parse_args(args[1:])
- return args
-
-
-def main():
- args = process_args(sys.argv)
- upload_to_genomespace(args.token,
- binascii.unhexlify(args.input_file).decode('utf-8'),
- binascii.unhexlify(args.target_url).decode('utf-8'))
-
-
-if __name__ == "__main__":
- sys.exit(main())
diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml
deleted file mode 100644
index 392d3eef55c..00000000000
--- a/tools/genomespace/genomespace_exporter.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-
-
- - send data to GenomeSpace
-
-
- #set $token = $__user__.preferences.get('genomespace_token', None)
- #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.')
- $token
-
-
- python $__tool_directory__/genomespace_exporter.py
- #set $target_folder = $genomespace_browser.split('^')[0]
- #assert $target_folder, Exception('You must select a valid target folder.')
-
- #import binascii
- --input_file '${ binascii.hexlify(str($input1).encode("utf8")) }'
- #if $filename:
- --target_url '${ binascii.hexlify(str($target_folder + "/" + str($filename)).encode("utf8") ) }'
- #else:
- --target_url '${ binascii.hexlify(($target_folder + "/" + "Galaxy History Item %s (%s) - %s: %s.%s" % ($__app__.security.encode_id($input1.id), $__app__.security.encode_id($output_log.id), $input1.hid, $input1.element_identifier.replace("/", "_"), $input1.ext)).encode("utf8")) }'
- #end if
-
-
-
-
-
-
-
-
-
-
-
-This Tool allows you to export data to GenomeSpace. Click the Browse button to select a file to export.
-
-To use this tool, you must have logged in using your GenomeSpace OpenID.
-You can associate your OpenID credentials under the User Preferences panel.
-Click here_ to refresh your GenomeSpace token.
-
-.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
-
-
diff --git a/tools/genomespace/genomespace_file_browser.py b/tools/genomespace/genomespace_file_browser.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/tools/genomespace/genomespace_importer.py b/tools/genomespace/genomespace_importer.py
deleted file mode 100644
index 8ecf787dbc6..00000000000
--- a/tools/genomespace/genomespace_importer.py
+++ /dev/null
@@ -1,260 +0,0 @@
-import argparse
-import json
-import os
-import sys
-import uuid
-
-from genomespaceclient import GenomeSpaceClient
-
-import galaxy
-from galaxy.datatypes import sniff
-from galaxy.datatypes.registry import Registry
-
-
-# Mappings for known genomespace formats to galaxy formats
-GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
- 'lifes': 'lifes',
- 'cn': 'cn',
- 'gtf': 'gtf',
- 'res': 'res',
- 'xcn': 'xcn',
- 'lowercasetxt': 'lowercasetxt',
- 'bed': 'bed',
- 'cbs': 'cbs',
- 'genomicatab': 'genomicatab',
- 'gxp': 'gxp',
- 'reversedtxt': 'reversedtxt',
- 'nowhitespace': 'nowhitespace',
- 'unknown': 'unknown',
- 'txt': 'txt',
- 'uppercasetxt': 'uppercasetxt',
- 'gistic': 'gistic',
- 'gff': 'gff',
- 'gmt': 'gmt',
- 'gct': 'gct'}
-
-
-def _prepare_json_list(param_list):
- """
- JSON serialization Support functions for exec_before_job hook
- """
- rval = []
- for value in param_list:
- if isinstance(value, dict):
- rval.append(_prepare_json_param_dict(value))
- elif isinstance(value, list):
- rval.append(_prepare_json_list(value))
- else:
- rval.append(str(value))
- return rval
-
-
-def _prepare_json_param_dict(param_dict):
- """
- JSON serialization Support functions for exec_before_job hook
- """
- rval = {}
- for key, value in param_dict.items():
- if isinstance(value, dict):
- rval[key] = _prepare_json_param_dict(value)
- elif isinstance(value, list):
- rval[key] = _prepare_json_list(value)
- else:
- rval[key] = str(value)
- return rval
-
-
-def exec_before_job(app, inp_data, out_data, param_dict=None, tool=None):
- """
- Galaxy override hook
- See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccode.3E_tag_set
- Since only tools with tool_type="data_source" provides functionality for having a JSON param file such as this:
- https://wiki.galaxyproject.org/Admin/Tools/DataManagers/DataManagerJSONSyntax#Example_JSON_input_to_tool,
- this hook is used to manually create a similar JSON file.
- However, this hook does not provide access to GALAXY_DATATYPES_CONF_FILE and GALAXY_ROOT_DIR
- properties, so these must be passed in as commandline params.
- """
- if param_dict is None:
- param_dict = {}
- json_params = {}
- json_params['param_dict'] = _prepare_json_param_dict(param_dict)
- json_params['output_data'] = []
- json_params['job_config'] = dict(GALAXY_DATATYPES_CONF_FILE=param_dict.get('GALAXY_DATATYPES_CONF_FILE'),
- GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'),
- TOOL_PROVIDED_JOB_METADATA_FILE=galaxy.jobs.TOOL_PROVIDED_JOB_METADATA_FILE)
- json_filename = None
- for i, (out_name, data) in enumerate(out_data.items()):
- file_name = data.get_file_name()
- data_dict = dict(out_data_name=out_name,
- ext=data.ext,
- dataset_id=data.dataset.id,
- hda_id=data.id,
- file_name=file_name)
- json_params['output_data'].append(data_dict)
- if json_filename is None:
- json_filename = file_name
- with open(json_filename, 'w') as out:
- out.write(json.dumps(json_params))
-
-
-def get_galaxy_ext_from_genomespace_format(format):
- return GENOMESPACE_EXT_TO_GALAXY_EXT.get(format, None)
-
-
-def get_galaxy_ext_from_file_ext(filename):
- if not filename:
- return None
- filename = filename.lower()
- ext = filename.rsplit('.', 1)[-1]
- return get_galaxy_ext_from_genomespace_format(ext)
-
-
-def sniff_and_handle_data_type(json_params, output_file):
- """
- The sniff.handle_uploaded_dataset_file() method in Galaxy performs dual
- functions: it sniffs the filetype and if it's a compressed archive for
- a non compressed datatype such as fasta, it will be unpacked.
- """
- try:
- datatypes_registry = Registry()
- datatypes_registry.load_datatypes(
- root_dir=json_params['job_config']['GALAXY_ROOT_DIR'],
- config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
- file_type = sniff.handle_uploaded_dataset_file(
- output_file,
- datatypes_registry)
- return file_type
- except Exception:
- return None
-
-
-def determine_output_filename(input_url, metadata, json_params, primary_dataset):
- """
- Determines the output file name. If only a single output file, the dataset name
- is used. If multiple files are being downloaded, each file is given a unique dataset
- name
- """
- output_filename = json_params['output_data'][0]['file_name']
-
- if not primary_dataset or not output_filename:
- hda_id = json_params['output_data'][0]['hda_id']
- output_filename = 'primary_%i_%s_visible_%s' % (hda_id, metadata.name, uuid.uuid4())
-
- return os.path.join(os.getcwd(), output_filename)
-
-
-def determine_file_type(input_url, output_filename, metadata, json_params, sniffed_type):
- """
- Determine the Galaxy data format for this file.
- """
- # Use genomespace metadata to map type
- file_format = metadata.data_format.name if metadata.data_format else None
- file_type = get_galaxy_ext_from_genomespace_format(file_format)
-
- # If genomespace metadata has no identifiable format, attempt to sniff type
- if not file_type:
- file_type = sniffed_type
-
- # Still no type? Attempt to use filename extension to determine a type
- if not file_type:
- file_type = get_galaxy_ext_from_file_ext(metadata.name)
-
- # Nothing works, use default
- if not file_type:
- file_type = "data"
-
- return file_type
-
-
-def save_result_metadata(output_filename, file_type, metadata, json_params,
- primary_dataset=False):
- """
- Generates a new job metadata file (typically galaxy.json) with details of
- all downloaded files, which Galaxy can read and use to display history items
- and associated metadata
- """
- dataset_id = json_params['output_data'][0]['dataset_id']
- with open(json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'ab') as metadata_parameter_file:
- if primary_dataset:
- metadata_parameter_file.write("%s\n" % json.dumps(dict(type='dataset',
- dataset_id=dataset_id,
- ext=file_type,
- name="GenomeSpace importer on %s" % (metadata.name))))
- else:
- metadata_parameter_file.write("%s\n" % json.dumps(dict(type='new_primary_dataset',
- base_dataset_id=dataset_id,
- ext=file_type,
- filename=output_filename,
- name="GenomeSpace importer on %s" % (metadata.name))))
-
-
-def download_single_file(gs_client, input_url, json_params,
- primary_dataset=False):
- # 1. Get file metadata
- metadata = gs_client.get_metadata(input_url)
-
- # 2. Determine output file name
- output_filename = determine_output_filename(input_url, metadata, json_params, primary_dataset)
-
- # 3. Download file
- gs_client.copy(input_url, output_filename)
-
- # 4. Decompress file if compressed and sniff type
- sniffed_type = sniff_and_handle_data_type(json_params, output_filename)
-
- # 5. Determine file type from available metadata
- file_type = determine_file_type(input_url, output_filename, metadata, json_params, sniffed_type)
-
- # 6. Write job output metadata
- save_result_metadata(output_filename, file_type, metadata, json_params,
- primary_dataset=primary_dataset)
-
-
-def download_from_genomespace_importer(json_parameter_file, root, data_conf, custom_token):
- with open(json_parameter_file, 'r') as param_file:
- json_params = json.load(param_file)
-
- # Add in missing job config properties that could not be set in the exec_before_job hook
- json_params['job_config']['GALAXY_ROOT_DIR'] = root
- json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'] = data_conf
-
- # Extract input_urls and token (format is input_urls^token). If a custom_token is
- # provided, use that instead.
- url_with_token = json_params.get('param_dict', {}).get("URL", "")
- if custom_token:
- input_urls = url_with_token.split('^')[0]
- token = custom_token
- else:
- input_urls, token = url_with_token.split('^')
- input_url_list = input_urls.split(",")
-
- gs_client = GenomeSpaceClient(token=token)
-
- for idx, input_url in enumerate(input_url_list):
- download_single_file(gs_client, input_url, json_params,
- primary_dataset=(idx == 0))
-
-
-def process_args(args):
- parser = argparse.ArgumentParser()
- parser.add_argument('-p', '--json_parameter_file', type=str,
- help="JSON parameter file", required=True)
- parser.add_argument('-r', '--galaxy_root', type=str,
- help="Galaxy root dir", required=True)
- parser.add_argument('-c', '--data_conf', type=str,
- help="Galaxy data types conf file for mapping file types", required=True)
- parser.add_argument('-t', '--token', type=str,
- help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
- " If none, the environment variable GS_TOKEN will be respected.", required=False)
-
- args = parser.parse_args(args[1:])
- return args
-
-
-def main():
- args = process_args(sys.argv)
- download_from_genomespace_importer(args.json_parameter_file, args.galaxy_root, args.data_conf, args.token or os.environ.get("GS_TOKEN"))
-
-
-if __name__ == "__main__":
- sys.exit(main())
diff --git a/tools/genomespace/genomespace_importer.xml b/tools/genomespace/genomespace_importer.xml
deleted file mode 100644
index 543a540a3e2..00000000000
--- a/tools/genomespace/genomespace_importer.xml
+++ /dev/null
@@ -1,39 +0,0 @@
-
-
- - receive data from GenomeSpace
-
-
- #set $token = $__user__.preferences.get('genomespace_token', None)
- #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.')
- $token
-
-
-
-
-
-
-
-
-
-
-
-This tool allows you to import data from GenomeSpace. Click the Browse button to select a file to import.
-
-To use this tool, you must have logged in using your GenomeSpace OpenID.
-You can associate your OpenID credentials under the User Preferences panel.
-Click here_ to refresh your GenomeSpace token.
-
-.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
-
-