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Merge pull request #1697 from martenson/merge-1601-dev

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merge 16.01 into dev
This commit is contained in:
Martin Cech
2016-02-08 14:23:14 -05:00
parent ae372ae33b 8acc7ebc04
commit d331b54b99
15 changed files with 210 additions and 210 deletions
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client/galaxy/scripts/mvc/library/library-folder-view.js
+2 -2
View File
@@ -98,7 +98,7 @@ var FolderView = Backbone.View.extend({
_serializeRoles : function(role_list){
var selected_roles = [];
for (var i = 0; i < role_list.length; i++) {
selected_roles.push(role_list[i] + ':' + role_list[i]);
selected_roles.push(role_list[i][1] + ':' + role_list[i][0]);
}
return selected_roles;
},
@@ -156,7 +156,7 @@ var FolderView = Backbone.View.extend({
$(element.val().split(",")).each(function() {
var item = this.split(':');
data.push({
id: item[1],
id: item[0],
name: item[1]
});
});
client/galaxy/style/less/base.less
+5 -5
View File
@@ -747,7 +747,7 @@ input[type="submit"], button {
// Messages
.errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge, .toolHelpBody .error, .toolHelpBody .warning, .toolHelpBody .note {
.errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge, .ui-form-help .error, .ui-form-help .warning, .ui-form-help .note {
.alert();
min-height: 36px;
padding-left: 52px;
@@ -785,7 +785,7 @@ input[type="submit"], button {
background-image: none;
}
.errormessage, .warningmessage, .donemessage, .infomessage, .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall, toolHelpBody .error, .toolHelpBody .warning, .toolHelpBody .note {
.errormessage, .warningmessage, .donemessage, .infomessage, .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall, .ui-form-help .error, .ui-form-help .warning, .ui-form-help .note {
.alert();
padding: 5px;
padding-left: 25px;
@@ -797,11 +797,11 @@ input[type="submit"], button {
background-position: 5px 5px;
}
.errormessage, .errormessagesmall, .toolHelpBody .error {
.errormessage, .errormessagesmall, .ui-form-help .error {
.alert-danger();
}
.warningmessage, .warningmessagesmall, .toolHelpBody .warning {
.warningmessage, .warningmessagesmall, .ui-form-help .warning {
.alert-warning();
background-image: url(warn_small.png);
}
@@ -811,7 +811,7 @@ input[type="submit"], button {
background-image: url(ok_small.png);
}
.infomessage, .infomessagesmall, .toolHelpBody .note {
.infomessage, .infomessagesmall, .ui-form-help .note {
.alert-info();
background-image: url(info_small.png);
}
doc/source/admin/framework_dependencies.rst
+42 -13
View File
@@ -29,10 +29,13 @@ Upon startup (with ``run.sh``), the startup scripts will:
3. Replace that virtualenv's pip with `Galaxy pip`_.
4. Download and install wheels from the Galaxy project wheel server,
4. If applicable, create a ``binary-compatibility.cfg`` (see the `Galaxy pip
and wheel`_ section for an explanation of this file).
5. Download and install wheels from the Galaxy project wheel server,
`wheels.galaxyproject.org`_, using pip.
5. Start Galaxy using ``.venv/bin/python``.
6. Start Galaxy using ``.venv/bin/python``.
.. _virtualenv: https://virtualenv.readthedocs.org/
.. _wheels.galaxyproject.org: https://wheels.galaxyproject.org/
@@ -194,13 +197,14 @@ dependencies. Because of this, it's necessary to make sure the metadata
detection step runs in Galaxy's virtualenv. If you run a relatively simple
Galaxy setup (e.g. single process, or multiple Python Paste processes started
using ``run.sh``) then this is assured for you automatically. In more
complicated setups (using a cluster, supervisor, and/or the "headless" Galaxy
handler) it may be necessary to make sure the handlers know where the
virtualenv (or a virtualenv containing Galaxy's dependencies) can be found.
complicated setups (supervisor, the "headless" Galaxy handler, and/or the
virtualenv used to start Galaxy is not a shared filesystem) it may be necessary
to make sure the handlers know where the virtualenv (or a virtualenv containing
Galaxy's dependencies) can be found.
If your jobs are failing due to Python ``ImportError`` exceptions, this is most
likely the problem. If your jobs run on a cluster, you can use the ``<env>``
tag in ``job_conf.xml`` to source the virtualenv. For example:
likely the problem. If so, you can use the ``<env>`` tag in ``job_conf.xml`` to
source the virtualenv. For example:
.. code-block:: xml
@@ -523,7 +527,6 @@ explanation of the problem.
.. _PEP 513: https://www.python.org/dev/peps/pep-0513/
.. _pip pull request #3075: https://github.com/pypa/pip/pull/3075
.. _binary-compatibility.cfg: https://mail.python.org/pipermail/distutils-sig/2015-July/026617.html
Galaxy pip and wheel
--------------------
@@ -551,11 +554,6 @@ Two different types of wheels can be created:
wheels carry a ``linux_{arch}_{distro}_{version}`` platform tag (e.g.
``linux_x86_ubuntu_14_04``) and can be created using `Galaxy wheel`_.
Galaxy pip and Galaxy wheel also include support for the proposed
`binary-compatibility.cfg`_ file. This file allows distributions that are
binary compatibile (e.g. Red Hat Enterprise Linux 6 and CentOS 6) to use the
same wheels.
The `manylinux`_ project implements the "Simple" wheels in a more clearly
defined way and allows for the inclusion of "non-standard" external
dependencies directly into the wheel. Galaxy will officially support any
@@ -566,6 +564,37 @@ complete.
.. _manylinux: https://github.com/manylinux/manylinux/
.. _psycopg2: http://initd.org/psycopg/
Wheel platform compatibility
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Galaxy pip and Galaxy wheel also include support for the proposed
`binary-compatibility.cfg`_ file. This file allows distributions that are
binary compatibile (e.g. Red Hat Enterprise Linux 6 and CentOS 6) to use the
same wheels.
This is a JSON format file which can be installed in ``/etc/python`` or the
root of a virtualenv (`common_startup.sh`_ creates it here) and provides a
mapping between `PEP 425`_ platform tags. For example, the following
``binary-compatibility.cfg`` indicates that wheels built on the platform
``linux_x86_centos_6_7`` will have their platform tag overridden to
``linux_x86_rhel_6``. In addition, wheels tagged with ``linux_x86_64_rhel_6_7``
and ``linux_x86_64_rhel_6`` will be installable on a ``linux_x86_centos_6_7``
system:
.. code-block:: json
{
"linux_x86_64_centos_6_7": {
"build": "linux_x86_64_rhel_6",
"install": ["linux_x86_64_rhel_6_7", "linux_x86_64_rhel_6"]
}
}
Currently, Scientific Linux, CentOS, and Red Hat Enterprise Linux will be set
as binary compatible by `common_startup.sh`_.
.. _binary-compatibility.cfg: https://mail.python.org/pipermail/distutils-sig/2015-July/026617.html
Adding additional wheels as Galaxy dependencies
-----------------------------------------------
lib/galaxy/datatypes/text.py
+2 -2
View File
@@ -91,9 +91,9 @@ class Ipynb( Json ):
config = trans.app.config
trust = getattr( config, 'trust_ipython_notebook_conversion', False )
if trust:
return self._display_data_trusted(trans, dataset, preview=preview, fileame=filename, to_ext=to_ext, chunk=chunk, **kwd)
return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd)
else:
return super(Ipynb, self).display_data( trans, dataset, preview=preview, fileame=filename, to_ext=to_ext, chunk=chunk, **kwd )
return super(Ipynb, self).display_data( trans, dataset, preview=preview, filename=filename, to_ext=to_ext, chunk=chunk, **kwd )
def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
preview = string_as_bool( preview )
lib/galaxy/webapps/galaxy/api/folder_contents.py
+9 -11
View File
@@ -240,23 +240,21 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
@expose_api
def create( self, trans, encoded_folder_id, payload, **kwd ):
"""
create( self, trans, library_id, payload, **kwd )
* POST /api/folders/{encoded_id}/contents
create a new library file from an HDA
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
:type encoded_folder_id: an encoded id string
:param payload: dictionary structure containing:
:param from_hda_id: (optional) the id of an accessible HDA to copy into the library
:type from_hda_id: encoded id
:param ldda_message: (optional) the new message attribute of the LDDA created
:type ldda_message: str
:param extended_metadata: (optional) dub-dictionary containing any extended metadata to associate with the item
:type extended_metadata: dict
:type payload: dict
* folder_id: the parent folder of the new item
* from_hda_id: (optional) the id of an accessible HDA to copy
into the library
* ldda_message: (optional) the new message attribute of the LDDA
created
* extended_metadata: (optional) dub-dictionary containing any
extended metadata to associate with the item
:returns: a dictionary containing the id, name,
and 'show' url of the new item
:returns: a dictionary containing the id, name, and 'show' url of the new item
:rtype: dict
:raises: ObjectAttributeInvalidException,
lib/galaxy/webapps/galaxy/api/folders.py
+53 -77
View File
@@ -3,11 +3,9 @@ API operations on library folders.
"""
from galaxy import util
from galaxy import exceptions
from galaxy.managers import folders
from galaxy.managers import folders, roles
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems
from sqlalchemy.orm.exc import MultipleResultsFound
from sqlalchemy.orm.exc import NoResultFound
import logging
log = logging.getLogger( __name__ )
@@ -18,6 +16,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
def __init__( self, app ):
super( FoldersController, self ).__init__( app )
self.folder_manager = folders.FolderManager()
self.role_manager = roles.RoleManager( app )
@expose_api
def index( self, trans, **kwd ):
@@ -48,35 +47,29 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
return return_dict
@expose_api
def create( self, trans, encoded_parent_folder_id, **kwd ):
def create( self, trans, encoded_parent_folder_id, payload=None, **kwd ):
"""
create( self, trans, encoded_parent_folder_id, **kwd )
*POST /api/folders/{encoded_parent_folder_id}
Create a new folder object underneath the one specified in the parameters.
Create a new folder object underneath the one specified in the parameters.
:param encoded_parent_folder_id: the parent folder's id (required)
:param encoded_parent_folder_id: (required) the parent folder's id
:type encoded_parent_folder_id: an encoded id string (should be prefixed by 'F')
:param name: the name of the new folder (required)
:type name: str
:param description: the description of the new folder
:type description: str
:param payload: dictionary structure containing:
:param name: (required) the name of the new folder
:type name: str
:param description: the description of the new folder
:type description: str
:type dictionary
:returns: information about newly created folder, notably including ID
:rtype: dictionary
:raises: RequestParameterMissingException
"""
payload = kwd.get( 'payload', None )
if payload is None:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
name = payload.get( 'name', None )
if payload:
kwd.update(payload)
name = kwd.get( 'name', None )
if name is None:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
description = payload.get( 'description', '' )
description = kwd.get( 'description', '' )
decoded_parent_folder_id = self.folder_manager.cut_and_decode( trans, encoded_parent_folder_id )
parent_folder = self.folder_manager.get( trans, decoded_parent_folder_id )
new_folder = self.folder_manager.create( trans, parent_folder.id, name, description )
@@ -98,7 +91,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
:returns: dictionary with all applicable permissions' values
:rtype: dictionary
:raises: ObjectNotFound, InsufficientPermissionsException
:raises: InsufficientPermissionsException
"""
current_user_roles = trans.get_current_user_roles()
is_admin = trans.user_is_admin()
@@ -134,35 +127,32 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" )
@expose_api
def set_permissions( self, trans, encoded_folder_id, **kwd ):
def set_permissions( self, trans, encoded_folder_id, payload=None, **kwd ):
"""
def set_permissions( self, trans, encoded_folder_id, **kwd ):
*POST /api/folders/{encoded_folder_id}/permissions
*POST /api/folders/{encoded_folder_id}/permissions
Set permissions of the given folder to the given role ids.
:param encoded_folder_id: the encoded id of the folder to set the permissions of
:type encoded_folder_id: an encoded id string
:param action: (required) describes what action should be performed
available actions: set_permissions
:type action: string
:param add_ids[]: list of Role.id defining roles that should have add item permission on the folder
:type add_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder
:type modify_ids[]: string or list
:rtype: dictionary
:param payload: dictionary structure containing:
:param action: (required) describes what action should be performed
:type action: string
:param add_ids[]: list of Role.id defining roles that should have add item permission on the folder
:type add_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder
:type modify_ids[]: string or list
:type dictionary
:returns: dict of current roles for all available permission types.
:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
RequestParameterMissingException
:rtype: dictionary
:raises: RequestParameterInvalidException, InsufficientPermissionsException, RequestParameterMissingException
"""
if payload:
kwd.update(payload)
is_admin = trans.user_is_admin()
current_user_roles = trans.get_current_user_roles()
decoded_folder_id = self.folder_manager.decode_folder_id( trans, self.folder_manager.cut_the_prefix( encoded_folder_id ) )
decoded_folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )
folder = self.folder_manager.get( trans, decoded_folder_id )
if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) ):
raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to modify permissions of this folder.' )
@@ -180,7 +170,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
valid_add_roles = []
invalid_add_roles_names = []
for role_id in new_add_roles_ids:
role = self._load_role( trans, role_id )
role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) )
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder )
if role in valid_roles:
@@ -194,7 +184,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
valid_manage_roles = []
invalid_manage_roles_names = []
for role_id in new_manage_roles_ids:
role = self._load_role( trans, role_id )
role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) )
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder )
if role in valid_roles:
@@ -208,7 +198,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
valid_modify_roles = []
invalid_modify_roles_names = []
for role_id in new_modify_roles_ids:
role = self._load_role( trans, role_id )
role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) )
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder )
if role in valid_roles:
@@ -254,59 +244,45 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
return folder_dict
@expose_api
def update( self, trans, encoded_folder_id, **kwd ):
def update( self, trans, encoded_folder_id, payload=None, **kwd ):
"""
* PATCH /api/folders/{encoded_folder_id}
Updates the folder defined by an ``encoded_folder_id`` with the data in the payload.
Update the folder defined by an ``encoded_folder_id`` with the data in the payload.
.. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
:param id: the encoded id of the folder
:type id: an encoded id string
:param payload: (required) dictionary structure containing::
'name': new folder's name, cannot be empty
'description': new folder's description
:type payload: dict
:returns: detailed folder information
:rtype: dict
:raises: RequestParameterMissingException
"""
decoded_folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )
folder = self.folder_manager.get( trans, decoded_folder_id )
payload = kwd.get( 'payload', None )
if payload:
name = payload.get( 'name', None )
if not name:
raise exceptions.RequestParameterMissingException( "Parameter 'name' of library folder is required. You cannot remove it." )
description = payload.get( 'description', None )
else:
raise exceptions.RequestParameterMissingException( "You did not specify any payload." )
kwd.update(payload)
name = kwd.get( 'name', None )
if not name:
raise exceptions.RequestParameterMissingException( "Parameter 'name' of library folder is required. You cannot remove it." )
description = kwd.get( 'description', None )
updated_folder = self.folder_manager.update( trans, folder, name, description )
folder_dict = self.folder_manager.get_folder_dict( trans, updated_folder )
return folder_dict
# TODO move to Role manager
def _load_role( self, trans, role_name ):
def __decode_id( self, trans, encoded_id, object_name=None ):
"""
Method loads the role from the DB based on the given role name.
Try to decode the id.
:param role_name: name of the role to load from the DB
:type role_name: string
:rtype: Role
:returns: the loaded Role object
:raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
:param object_name: Name of the object the id belongs to. (optional)
:type object_name: str
"""
try:
role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase( 'Multiple roles found with the same name. Name: ' + str( role_name ) )
except NoResultFound:
raise exceptions.RequestParameterInvalidException( 'No role found with the name provided. Name: ' + str( role_name ) )
except Exception, e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
return role
return trans.security.decode_id( encoded_id )
except TypeError:
raise exceptions.MalformedId( 'Malformed %s id specified, unable to decode.' % object_name if object_name is not None else '' )
except ValueError:
raise exceptions.MalformedId( 'Wrong %s id specified, unable to decode.' % object_name if object_name is not None else '' )
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+21 -18
View File
@@ -400,9 +400,8 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
return rval
@expose_api
def load( self, trans, **kwd ):
def load( self, trans, payload=None, **kwd ):
"""
load( self, trans, **kwd ):
* POST /api/libraries/datasets
Load dataset from the given source into the library.
Source can be:
@@ -413,25 +412,29 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}
(admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
:type encoded_folder_id: an encoded id string
:param source: source the datasets should be loaded from
:type source: str
:param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy
while linking is set to True all symlinks will be resolved _once_
:type link_data: bool
:param preserve_dirs: flag whether to preserve the directory structure when importing dir
if False only datasets will be imported
:type preserve_dirs: bool
:param file_type: file type of the loaded datasets, defaults to 'auto' (autodetect)
:type file_type: str
:param dbkey: dbkey of the loaded genome, defaults to '?' (unknown)
:type dbkey: str
:param payload: dictionary structure containing:
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
:type encoded_folder_id: an encoded id string
:param source: source the datasets should be loaded from
:type source: str
:param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy
while linking is set to True all symlinks will be resolved _once_
:type link_data: bool
:param preserve_dirs: flag whether to preserve the directory structure when importing dir
if False only datasets will be imported
:type preserve_dirs: bool
:param file_type: file type of the loaded datasets, defaults to 'auto' (autodetect)
:type file_type: str
:param dbkey: dbkey of the loaded genome, defaults to '?' (unknown)
:type dbkey: str
:type dictionary
:returns: dict containing information about the created upload job
:rtype: dictionary
:raises: RequestParameterMissingException, AdminRequiredException, ConfigDoesNotAllowException, RequestParameterInvalidException
InsufficientPermissionsException, ObjectNotFound
"""
if payload:
kwd.update(payload)
kwd[ 'space_to_tab' ] = 'False'
kwd[ 'to_posix_lines' ] = 'True'
kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
lib/galaxy/webapps/galaxy/api/libraries.py
+59 -62
View File
@@ -54,6 +54,8 @@ class LibrariesController( BaseAPIController ):
return trans.security.decode_id( encoded_id )
except TypeError:
raise exceptions.MalformedId( 'Malformed %s id specified, unable to decode.' % object_name if object_name is not None else '' )
except ValueError:
raise exceptions.MalformedId( 'Wrong %s id specified, unable to decode.' % object_name if object_name is not None else '' )
@expose_api_anonymous
def show( self, trans, id, deleted='False', **kwd ):
@@ -81,31 +83,32 @@ class LibrariesController( BaseAPIController ):
return library_dict
@expose_api
def create( self, trans, payload, **kwd ):
def create( self, trans, payload=None, **kwd ):
"""
create( self, trans, payload, **kwd )
* POST /api/libraries:
Creates a new library. Only ``name`` parameter is required.
Creates a new library.
.. note:: Currently, only admin users can create libraries.
:param payload: dictionary structure containing::
'name': the new library's name (required)
'description': the new library's description (optional)
'synopsis': the new library's synopsis (optional)
:param name: (required) the new library's name
:type name: str
:param description: the new library's description
:type description: str
:param synopsis: the new library's synopsis
:type synopsis: str
:type payload: dict
:returns: detailed library information
:rtype: dict
:raises: ItemAccessibilityException, RequestParameterMissingException
:raises: RequestParameterMissingException
"""
params = util.Params( payload )
name = util.restore_text( params.get( 'name', None ) )
if payload:
kwd.update(payload)
name = kwd.get('name', None)
if not name:
raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
description = util.restore_text( params.get( 'description', '' ) )
synopsis = util.restore_text( params.get( 'synopsis', '' ) )
description = kwd.get( 'description', '' )
synopsis = kwd.get( 'synopsis', '' )
if synopsis in [ 'None', None ]:
synopsis = ''
library = self.library_manager.create( trans, name, description, synopsis )
@@ -113,7 +116,7 @@ class LibrariesController( BaseAPIController ):
return library_dict
@expose_api
def update( self, trans, id, **kwd ):
def update( self, trans, id, payload=None, **kwd ):
"""
* PATCH /api/libraries/{encoded_id}
Updates the library defined by an ``encoded_id`` with the data in the payload.
@@ -122,38 +125,33 @@ class LibrariesController( BaseAPIController ):
:param id: the encoded id of the library
:type id: an encoded id string
:param payload: (required) dictionary structure containing::
'name': new library's name, cannot be empty
'description': new library's description
'synopsis': new library's synopsis
:param payload: dictionary structure containing::
:param name: new library's name, cannot be empty
:type name: str
:param description: new library's description
:type description: str
:param synopsis: new library's synopsis
:type synopsis: str
:type payload: dict
:returns: detailed library information
:rtype: dict
:raises: ItemAccessibilityException, MalformedId, ObjectNotFound, RequestParameterInvalidException, RequestParameterMissingException
:raises: RequestParameterMissingException
"""
library = self.library_manager.get( trans, self.__decode_id( trans, id, 'library' ) )
payload = kwd.get( 'payload', None )
if payload:
name = payload.get( 'name', None )
if name == '':
raise exceptions.RequestParameterMissingException( "Parameter 'name' of library is required. You cannot remove it." )
if payload.get( 'description', None ) or payload.get( 'description', None ) == '':
description = payload.get( 'description', None )
if payload.get( 'synopsis', None ) or payload.get( 'synopsis', None ) == '':
synopsis = payload.get( 'synopsis', None )
else:
raise exceptions.RequestParameterMissingException( "You did not specify any payload." )
kwd.update(payload)
name = kwd.get( 'name', None )
if name == '':
raise exceptions.RequestParameterMissingException( "Parameter 'name' of library is required. You cannot remove it." )
description = kwd.get( 'description', None )
synopsis = kwd.get( 'synopsis', None )
updated_library = self.library_manager.update( trans, library, name, description, synopsis )
library_dict = self.library_manager.get_library_dict( trans, updated_library )
return library_dict
@expose_api
def delete( self, trans, id, **kwd ):
def delete( self, trans, id, payload=None, **kwd ):
"""
delete( self, trans, id, **kwd )
* DELETE /api/libraries/{id}
marks the library with the given ``id`` as `deleted` (or removes the `deleted` mark if the `undelete` param is true)
@@ -162,16 +160,17 @@ class LibrariesController( BaseAPIController ):
:param id: the encoded id of the library to un/delete
:type id: an encoded id string
:param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
:type undelete: bool
:param payload: dictionary structure containing:
:param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
:type undelete: bool
:type: dictionary
:returns: detailed library information
:rtype: dictionary
.. seealso:: :attr:`galaxy.model.Library.dict_element_visible_keys`
:raises: ItemAccessibilityException, MalformedId, ObjectNotFound
"""
if payload:
kwd.update(payload)
library = self.library_manager.get( trans, self.__decode_id( trans, id, 'library' ))
undelete = util.string_as_bool( kwd.get( 'undelete', False ) )
library = self.library_manager.delete( trans, library, undelete )
@@ -197,7 +196,7 @@ class LibrariesController( BaseAPIController ):
:returns: dictionary with all applicable permissions' values
:rtype: dictionary
:raises: ObjectNotFound, InsufficientPermissionsException
:raises: InsufficientPermissionsException
"""
current_user_roles = trans.get_current_user_roles()
is_admin = trans.user_is_admin()
@@ -239,33 +238,33 @@ class LibrariesController( BaseAPIController ):
raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" )
@expose_api
def set_permissions( self, trans, encoded_library_id, **kwd ):
def set_permissions( self, trans, encoded_library_id, payload=None, **kwd ):
"""
def set_permissions( self, trans, encoded_dataset_id, **kwd ):
*POST /api/libraries/{encoded_library_id}/permissions
*POST /api/libraries/{encoded_library_id}/permissions
Set permissions of the given library to the given role ids.
:param encoded_library_id: the encoded id of the library to set the permissions of
:type encoded_library_id: an encoded id string
:param action: (required) describes what action should be performed
available actions: remove_restrictions, set_permissions
:type action: string
:param access_ids[]: list of Role.id defining roles that should have access permission on the library
:type access_ids[]: string or list
:param add_ids[]: list of Role.id defining roles that should have add item permission on the library
:type add_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the library
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the library
:type modify_ids[]: string or list
:rtype: dictionary
:param payload: dictionary structure containing:
:param action: (required) describes what action should be performed
available actions: remove_restrictions, set_permissions
:type action: str
:param access_ids[]: list of Role.id defining roles that should have access permission on the library
:type access_ids[]: string or list
:param add_ids[]: list of Role.id defining roles that should have add item permission on the library
:type add_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the library
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the library
:type modify_ids[]: string or list
:type: dictionary
:returns: dict of current roles for all available permission types
:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
:rtype: dictionary
:raises: RequestParameterInvalidException, InsufficientPermissionsException, InternalServerError
RequestParameterMissingException
"""
if payload:
kwd.update(payload)
is_admin = trans.user_is_admin()
current_user_roles = trans.get_current_user_roles()
library = self.library_manager.get( trans, self.__decode_id( trans, encoded_library_id, 'library' ) )
@@ -280,8 +279,6 @@ class LibrariesController( BaseAPIController ):
action = kwd.get( 'action', None )
if action is None:
payload = kwd.get( 'payload', None )
del kwd[ 'payload' ]
if payload is not None:
return self.set_permissions_old( trans, library, payload, **kwd )
else:
scripts/binary_compatibility.py
+2 -1
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@@ -34,7 +34,8 @@ from pip.platform import get_specific_platform
compatible_platforms = {
'centos': 'rhel'
'centos': 'rhel',
'scientific': 'rhel',
}
scripts/common_startup.sh
+1 -5
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@@ -101,11 +101,7 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
python -c "import urllib; urllib.urlretrieve('$vurl', '$vsrc')"
fi
echo "Verifying $vsrc checksum is $vsha"
if command -v sha256sum >/dev/null; then
echo "$vsha $vsrc" | sha256sum -c --strict
else
python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
fi
python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
tar zxf $vsrc -C $vtmp
python $vtmp/virtualenv-$vvers/virtualenv.py "$GALAXY_VIRTUAL_ENV"
rm -rf $vtmp
static/maps/mvc/library/library-folder-view.js.map
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static/scripts/bundled/libs.bundled.js
+10 -10
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static/scripts/bundled/libs.bundled.js.map
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static/scripts/mvc/library/library-folder-view.js
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static/style/blue/base.css
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