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(merge dev)

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This commit is contained in:
carlfeberhard
2015-11-16 10:09:58 -05:00
parent 2956b12e9b cfe45d8e0c
commit b8870bfedc
27 changed files with 122 additions and 59 deletions
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client/galaxy/scripts/mvc/tool/tools.js
+1 -3
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@@ -531,9 +531,7 @@ var ToolLinkView = BaseView.extend({
Galaxy.upload.show();
});
}
// regular tools
if ( this.model.id !== 'upload1' && this.model.get( 'model_class' ) === 'Tool' ) {
else if ( this.model.get( 'model_class' ) === 'Tool' ) { // regular tools
var self = this;
$link.find('a').on('click', function(e) {
e.preventDefault();
client/galaxy/scripts/viz/trackster/tracks.js
+1 -1
View File
@@ -3259,7 +3259,7 @@ extend(LabelTrack.prototype, Track.prototype, {
new_div = $("<div/>").addClass('label-container');
while ( position < view.high ) {
var screenPosition = Math.floor( ( position - view.low ) / range * width );
new_div.append( $("<div/>").addClass('label').text(util.commatize( position )).css( {
new_div.append( $("<div/>").addClass('pos-label').text(commatize( position )).css( {
left: screenPosition
}));
position += tickDistance;
client/galaxy/style/less/trackster.less
+10 -10
View File
@@ -18,7 +18,7 @@
/* Used to push nav into title bar: */
height: 0;
}
text-align: center;
}
@@ -202,7 +202,7 @@
padding: 0px 2px;
text-align: left;
margin: 2px;
/* Make header opaque when focused on. */
&:hover {
background-color: #DDDDDD;
@@ -232,7 +232,7 @@
overflow: hidden;
}
.overlay {
.overlay {
position: absolute;
left: 0;
top: 0;
@@ -241,7 +241,7 @@
.track-tile {
position: absolute;
background: white;
canvas {
position: relative;
z-index: @base-index;
@@ -292,7 +292,7 @@
}
.label-track {
font-size: 10px;
font-size: 10px;
border: none;
padding: 0;
margin: 0;
@@ -300,11 +300,11 @@
overflow: hidden;
.label-container {
position: relative;
position: relative;
height: 1.3em;
}
.label {
.pos-label {
position: absolute;
border-left: solid #999 1px;
padding: 1px;
@@ -344,7 +344,7 @@
.nav-labeltrack {
border-top: solid #999 1px;
border-bottom: solid #333 1px;
}
}
// Styles for tools and filters.
input {
@@ -544,7 +544,7 @@ input {
top: 0px;
background-color: #ccf;
opacity: 0.5;
z-index: @overlay-index;
z-index: @overlay-index;
}
.mouse-pos {
@@ -565,7 +565,7 @@ input {
height: 12px;
}
// Highlight for element(s) being dragged. This definition must be after definition of draggable
// Highlight for element(s) being dragged. This definition must be after definition of draggable
// elements (e.g. track, group) in order to take precedence.
.dragging {
border: 1px solid blue;
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+1 -1
View File
@@ -104,7 +104,7 @@ def main():
f.write('<div>%s\n<ol>' % (s))
for i, data in enumerate( flist ):
f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1], os.path.split(data)[-1]))
f.write("</div></body></html>")
f.write("</ol></div></div></body></html>")
f.close()
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
+1 -1
View File
@@ -72,7 +72,7 @@ def main():
f.write('<div>%s\n<ol>' % (s))
for i, data in enumerate( flist ):
f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1], os.path.split(data)[-1]))
f.write("</div></body></html>")
f.write("</ol></div></div></body></html>")
f.close()
lib/galaxy/model/orm/scripts.py
+5 -1
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@@ -19,6 +19,7 @@ DATABASE = {
'repo': 'lib/galaxy/model/migrate',
'old_config_file': 'universe_wsgi.ini',
'default_sqlite_file': './database/universe.sqlite',
'config_override': 'GALAXY_CONFIG_',
},
"tool_shed":
{
@@ -26,6 +27,7 @@ DATABASE = {
'config_file': 'config/tool_shed.ini',
'old_config_file': 'tool_shed_wsgi.ini',
'default_sqlite_file': './database/community.sqlite',
'config_override': 'TOOL_SHED_CONFIG_',
},
"install":
{
@@ -33,6 +35,7 @@ DATABASE = {
'old_config_file': 'universe_wsgi.ini',
'config_prefix': 'install_',
'default_sqlite_file': './database/install.sqlite',
'config_override': 'GALAXY_INSTALL_CONFIG_',
},
}
@@ -92,11 +95,12 @@ def get_config( argv, cwd=None ):
config_file = read_config_file_arg( argv, default, old_default )
repo = database_defaults[ 'repo' ]
config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX )
config_override = database_defaults.get( 'config_override', 'GALAXY_CONFIG_' )
default_sqlite_file = database_defaults[ 'default_sqlite_file' ]
if cwd:
config_file = os.path.join( cwd, config_file )
properties = load_app_properties( ini_file=config_file )
properties = load_app_properties( ini_file=config_file, config_prefix=config_override )
if ("%sdatabase_connection" % config_prefix) in properties:
db_url = properties[ "%sdatabase_connection" % config_prefix ]
lib/galaxy/tools/toolbox/base.py
+6 -6
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@@ -918,9 +918,9 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
# _tools_by_id and _tool_versions_by_id
self.register_tool( new_tool )
message = "Reloaded the tool:<br/>"
message += "<b>name:</b> %s<br/>" % old_tool.name
message += "<b>id:</b> %s<br/>" % old_tool.id
message += "<b>version:</b> %s" % old_tool.version
message += "<b>name:</b> %s<br/>" % escape( old_tool.name )
message += "<b>id:</b> %s<br/>" % escape( old_tool.id )
message += "<b>version:</b> %s" % escape( old_tool.version )
status = 'done'
return message, status
@@ -952,9 +952,9 @@ class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
del self.data_manager_tools[ tool_id ]
# TODO: do we need to manually remove from the integrated panel here?
message = "Removed the tool:<br/>"
message += "<b>name:</b> %s<br/>" % tool.name
message += "<b>id:</b> %s<br/>" % tool.id
message += "<b>version:</b> %s" % tool.version
message += "<b>name:</b> %s<br/>" % escape( tool.name )
message += "<b>id:</b> %s<br/>" % escape( tool.id )
message += "<b>version:</b> %s" % escape( tool.version )
status = 'done'
return message, status
lib/galaxy/web/base/controllers/admin.py
+1 -1
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@@ -98,7 +98,7 @@ class Admin( object ):
toolbox = self.app.toolbox
tool_id = None
if params.get( 'reload_tool_button', False ):
tool_id = params.get('tool_id', None)
tool_id = kwd.get( 'tool_id', None )
galaxy.queue_worker.send_control_task(trans.app, 'reload_tool', noop_self=True, kwargs={'tool_id': tool_id} )
message, status = trans.app.toolbox.reload_tool_by_id( tool_id)
return trans.fill_template( '/admin/reload_tool.mako',
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+4 -2
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@@ -250,8 +250,10 @@ class ToolShedRepositoriesController( BaseAPIController ):
action='show',
id=trans.security.encode_id( tool_shed_repository.id ) )
return tool_shed_repository_dict
return map( to_dict, installed_tool_shed_repositories )
if installed_tool_shed_repositories:
return map( to_dict, installed_tool_shed_repositories )
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict( status="ok", message=message )
@expose_api
def install_repository_revisions( self, trans, payload, **kwd ):
lib/galaxy/webapps/tool_shed/api/repositories.py
+2 -1
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@@ -216,7 +216,8 @@ class RepositoriesController( BaseAPIController ):
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id )
repository_metadata_dict[ 'valid_tools' ] = repository_metadata.metadata[ 'tools' ]
if 'tools' in repository_metadata.metadata:
repository_metadata_dict[ 'valid_tools' ] = repository_metadata.metadata[ 'tools' ]
# Get the repo_info_dict for installing the repository.
repo_info_dict, \
includes_tools, \
lib/galaxy/webapps/tool_shed/buildapp.py
+5
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@@ -16,6 +16,7 @@ from galaxy.webapps.util import build_template_error_formatters
from galaxy.webapps.tool_shed.framework.middleware import hg
from galaxy import util
from galaxy.config import process_is_uwsgi
from galaxy.util.properties import load_app_properties
log = logging.getLogger( __name__ )
@@ -49,6 +50,10 @@ def add_ui_controllers( webapp, app ):
def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
kwargs = load_app_properties(
kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_'
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
+3 -2
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@@ -5,6 +5,7 @@ import os
import sqlalchemy
import sys
import tempfile
import urlparse
from paste.auth.basic import AuthBasicAuthenticator
from paste.httpheaders import AUTH_TYPE
from paste.httpheaders import REMOTE_USER
@@ -49,11 +50,11 @@ class Hg( object ):
# a clone or a pull. However, we do not want to increment the times_downloaded count if we're only setting repository
# metadata.
if cmd == 'getbundle' and not self.setting_repository_metadata:
common, _ = environ[ 'HTTP_X_HGARG_1' ].split( '&' )
hg_args = urlparse.parse_qs( environ[ 'HTTP_X_HGARG_1' ] )
# The 'common' parameter indicates the full sha-1 hash of the changeset the client currently has checked out. If
# this is 0000000000000000000000000000000000000000, then the client is performing a fresh checkout. If it has any
# other value, the client is getting updates to an existing checkout.
if common == 'common=0000000000000000000000000000000000000000':
if 'common' in hg_args and hg_args[ 'common' ][-1] == '0000000000000000000000000000000000000000':
# Increment the value of the times_downloaded column in the repository table for the cloned repository.
if 'PATH_INFO' in environ:
# Instantiate a database connection
static/maps/mvc/tool/tools.js.map
+1 -1
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static/maps/mvc/tools.js.map
+1
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static/maps/viz/trackster/tracks.js.map
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/mvc/tool/tools.js
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/mvc/tools.js
+2
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File diff suppressed because one or more lines are too long
static/scripts/viz/trackster/tracks.js
+1 -1
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File diff suppressed because one or more lines are too long
static/style/blue/trackster.css
+1 -1
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File diff suppressed because one or more lines are too long
templates/admin/reload_tool.mako
+2 -2
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@@ -31,7 +31,7 @@ $().ready(function() {
<select name="tool_id">
%for val in toolbox.tool_panel_contents( trans ):
%if isinstance( val, Tool ):
<option value="${val.id}">${val.name|h}</option>
<option value="${val.id|h}">${val.name|h}</option>
%elif isinstance( val, ToolSection ):
<optgroup label="${val.name|h}">
<% section = val %>
@@ -41,7 +41,7 @@ $().ready(function() {
%if section_val.id == tool_id:
<% selected_str = " selected=\"selected\"" %>
%endif
<option value="${section_val.id}"${selected_str}>${section_val.name|h}</option>
<option value="${section_val.id|h}"${selected_str}>${section_val.name|h}</option>
%endif
%endfor
%endif
templates/show_params.mako
+5 -2
View File
@@ -132,8 +132,11 @@
%if job:
<tr><td>Tool Exit Code:</td><td>${ job.exit_code | h }</td></tr>
%endif
<tr><td>API ID:</td><td>${encoded_hda_id}</td></tr>
<tr><td>History ID:</td><td>${encoded_history_id}</td></tr>
<tr><td>History Content API ID:</td><td>${encoded_hda_id}</td></tr>
%if job:
<tr><td>Job API ID:</td><td>${trans.security.encode_id( job.id )}</td></tr>
%endif
<tr><td>History API ID:</td><td>${encoded_history_id}</td></tr>
%if hda.dataset.uuid:
<tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr>
%endif
test/docker/base/Dockerfile
+29 -11
View File
@@ -18,9 +18,15 @@ RUN apt-get update -y && apt-get install -y software-properties-common curl && \
} | debconf-set-selections && \
apt-get update -y && \
apt-get install -y libpq-dev postgresql postgresql-client postgresql-plpython-9.3 \
ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_MAJOR}"* \
slurm-llnl libmunge-dev slurm-drmaa-dev \
nodejs && \
ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_MAJOR}"* \
slurm-llnl libmunge-dev slurm-drmaa-dev ant atop axel bioperl cmake curl \
g++ gcc gfortran git-core htop iftop iotop ipython libffi-dev liblapack-dev \
libncurses5-dev libopenblas-dev libpam0g-dev libpq-dev libsparsehash-dev make \
mercurial nginx-extras nmon patch postgresql postgresql \
postgresql-client postgresql-plpython-9.3 python-boto python-dev \
python-prettytable python-psycopg2 python-virtualenv python-pip \
postgresql-server-dev-9.3 rsync slurm-drmaa-dev supervisor swig sysstat unzip \
wget zlib1g-dev nodejs && \
npm install -g grunt-contrib-qunit grunt grunt-cli casperjs phantomjs && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -35,20 +41,21 @@ ADD provision.yml /tmp/ansible/provision.yml
ENV GALAXY_ROOT=/galaxy
RUN mkdir /etc/galaxy && \
cd /tmp/ansible && \
mkdir roles && \
RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
mkdir roles/galaxyprojectdotorg.galaxy-os && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
mkdir roles/galaxyprojectdotorg.cloudman-database && \
wget -qO- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
wget --quiet -O- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
mkdir roles/galaxyprojectdotorg.galaxy && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
mkdir roles/galaxyprojectdotorg.galaxy-extras && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
mkdir roles/galaxyprojectdotorg.galaxy-toolshed && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-toolshed/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-toolshed && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=toolshed -c local -e "@ansible_vars.yml" && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN cd $GALAXY_ROOT && \
@@ -59,7 +66,16 @@ RUN cd $GALAXY_ROOT && \
echo "Prepopuating sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" sh create_db.sh && \
sh /opt/galaxy/start_mysql.sh && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh
echo "Prepopuating mysql database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh && \
echo "Prepopulating toolshed postgres database" && \
su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" sh create_db.sh tool_shed && \
echo "Prepopuating toolshed sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" sh create_db.sh tool_shed && \
sh /opt/galaxy/start_mysql.sh && \
echo "Prepopuating toolshed mysql database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh tool_shed
# bcftools for Galaxy.
RUN mkdir -p /tmp/install && \
@@ -72,6 +88,8 @@ RUN mkdir -p /tmp/install && \
cd && rm -rf /tmp/install
ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
EXPOSE :9009
EXPOSE :8080
EXPOSE :80
ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"]
test/docker/base/ansible_vars.yml
+10 -1
View File
@@ -21,7 +21,6 @@ galaxy_manage_database: no
galaxy_user_name: "root"
galaxy_extras_install_packages: true
galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
galxy_config_file: "/galaxy/config/galaxy.ini.sample"
galaxy_web_processes: 1
galaxy_handler_processes: 2
@@ -37,3 +36,13 @@ galaxy_extras_config_supervisor: true
galaxy_extras_config_galaxy_root: false
galaxy_extras_config_galaxy_job_metrics: false
galaxy_extras_config_uwsgi: true
manage_shed_db: yes
galaxy_toolshed_manage_static_setup: yes
galaxy_toolshed_manage_database: no
galaxy_toolshed_server_dir: "/galaxy"
galaxy_toolshed_venv_dir: "{{ galaxy_venv_dir }}"
galaxy_toolshed_config_file: "{{ galaxy_toolshed_server_dir }}/config/tool_shed.ini"
galaxy_toolshed_config_templates:
- {dest: '{{ galaxy_toolshed_config_file }}', src: tool_shed.ini.j2}
test/docker/base/provision.yml
+3 -2
View File
@@ -11,5 +11,6 @@
- role: galaxyprojectdotorg.galaxy
sudo: yes
tags: galaxy
- role: galaxyprojectdotorg.galaxy-toolshed
sudo: yes
tags: toolshed
test/docker/base/run_test_wrapper.sh
+10
View File
@@ -6,19 +6,27 @@ if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
then
su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
sleep 3
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed"
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
then
sh /opt/galaxy/start_mysql.sh
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock"
TOOL_SHED_TEST_DBURI="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock"
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ];
then
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite"
TOOL_SHED_TEST_DBURI="sqlite:////opt/galaxy/toolshed.sqlite"
else
echo "Unknown database type"
exit 1
fi
export GALAXY_TEST_DBURI
export TOOL_SHED_TEST_DBURI
export GALAXY_TEST_INSTALL_DB_MERGED
cd /galaxy
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI";
@@ -37,6 +45,7 @@ then
else
GALAXY_CONFIG_MASTER_API_KEY=${GALAXY_CONFIG_MASTER_API_KEY:-"testmasterapikey"}
GALAXY_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}
TOOL_SHED_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/tool_shed.ini.sample}
GALAXY_CONFIG_CHECK_MIGRATE_TOOLS=false
if [ -z "$GALAXY_MULTI_PROCESS" ];
then
@@ -49,6 +58,7 @@ else
export GALAXY_CONFIG_MASTER_API_KEY
export GALAXY_CONFIG_FILE
export TOOL_SHED_CONFIG_FILE
export GALAXY_CONFIG_CHECK_MIGRATE_TOOLS
export GALAXY_CONFIG_JOB_CONFIG_FILE
export GALAXY_CONFIG_FILE_PATH
test/docker/base/start_mysql.sh
+13 -5
View File
@@ -4,6 +4,7 @@ set -e
MYSQL_USER=galaxy
MYSQL_PASSWORD=galaxy
MYSQL_DATABASE=galaxy
SHED_MYSQL_DATABASE=toolshed
mkdir -p /var/lib/mysql
chown -R mysql:mysql /var/lib/mysql
@@ -22,15 +23,22 @@ cat > "$tempSqlFile" <<-EOSQL
EOSQL
if [ "$MYSQL_DATABASE" ]; then
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile"
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile"
fi
if [ "$SHED_MYSQL_DATABASE" ]; then
echo "CREATE DATABASE IF NOT EXISTS \`$SHED_MYSQL_DATABASE\` ;" >> "$tempSqlFile"
fi
if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then
echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile"
echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile"
if [ "$MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
if [ "$MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
if [ "$SHED_MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$SHED_MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
fi
echo 'FLUSH PRIVILEGES ;' >> "$tempSqlFile"
tools/data_source/upload.py
+2 -2
View File
@@ -348,7 +348,7 @@ def add_file( dataset, registry, json_file, output_path ):
datatype.groom_dataset_content( output_path )
def add_composite_file( dataset, registry, json_file, output_path, files_path ):
def add_composite_file( dataset, json_file, output_path, files_path ):
if dataset.composite_files:
os.mkdir( files_path )
for name, value in dataset.composite_files.iteritems():
@@ -414,7 +414,7 @@ def __main__():
sys.exit( 1 )
if dataset.type == 'composite':
files_path = output_paths[int( dataset.dataset_id )][1]
add_composite_file( dataset, registry, json_file, output_path, files_path )
add_composite_file( dataset, json_file, output_path, files_path )
else:
add_file( dataset, registry, json_file, output_path )