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commit/galaxy-central: dannon: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/03d2ce228f7e/ changeset: 03d2ce228f7e user: dannon date: 2013-01-18 20:38:51 summary: Cloud Launch: Adjust event triggers to prevent redundant (though harmless) get_account_info invocations. Change get_account_info to POST vs GET. Adjust Cluster List creation to *always* insert the "New Cluster" option. Prevent nonexisting existing instance value from crashing zone detection during submission. affected #: 1 file diff -r 98f724202d9d3cea035d7de04d89465bcf3092b1 -r 03d2ce228f7e939871ff5d1d0564eebdda2cbb36 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -76,22 +76,24 @@ } }); //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("change paste keyup input propertychange", function(){ + $("#id_secret, #id_key_id").bind("paste input propertychange", function(){ secret_el = $("#id_secret"); key_el = $("#id_key_id"); if (secret_el.val().length === 40 && key_el.val().length === 20){ //Submit these to get_account_info, unhide fields, and update as appropriate - $.getJSON(ACCOUNT_URL, - {key_id: key_el.val(),secret:secret_el.val()}, - function(result){ + $.ajax({type: "POST", + url: ACCOUNT_URL, + dataType: 'json', + data: {key_id: key_el.val(),secret:secret_el.val()}, + success: function(result){ cloudlaunch_clusters = result.clusters; var kplist = $("#id_keypair"); var clusterlist = $("#id_existing_instance"); kplist.find('option').remove(); clusterlist.find('option').remove(); //Update fields with appropriate elements + clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); if (_.size(result.clusters) > 0){ - clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); _.each(result.clusters, function(cluster, index){ clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); }); @@ -104,7 +106,8 @@ kplist.append($('<option/>').val(keypair).text(keypair)); }); $('#hidden_options').show('fast'); - }); + } + }); } }); $('#loading_indicator').ajaxStart(function(){ @@ -130,7 +133,7 @@ //Dig up zone info for selected cluster, set hidden input. //This is not necessary to present to the user though the interface may prove useful. var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); - if( ei_val.value !== "New Cluster"){ + if( ei_val && (ei_val.value !== "New Cluster")){ var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); zdata.value = cluster.zone; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 18 Jan '13

18 Jan '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6aef91d12890/ changeset: 6aef91d12890 user: kellrott date: 2012-12-27 20:40:20 summary: The start of the API based annotation system affected #: 3 files diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -137,6 +137,12 @@ # Set annotation. annotation_assoc.annotation = annotation return annotation_assoc + + def delete_item_annotation( self, db_session, user, item): + annotation_assoc = self.get_item_annotation_obj( db_session, user, item ) + if annotation_assoc: + db_session.delete(annotation_assoc) + db_session.flush() def copy_item_annotation( self, db_session, source_user, source_item, target_user, target_item ): """ Copy an annotation from a user/item source to a user/item target. """ diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/webapps/galaxy/api/annotations.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -0,0 +1,76 @@ +""" +API operations on annotations. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.model.item_attrs import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * +import galaxy.datatypes +from galaxy.util.bunch import Bunch + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): + + @web.expose_api + def index( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.get_item_annotation_str( trans.sa_session, trans.get_user(), item ) + + + @web.expose_api + def create( self, trans, payload, **kwd ): + if "text" not in payload: + return "" + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + new_annotation = payload.get("text") + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) + + self.add_item_annotation( trans.sa_session, trans.get_user(), item, new_annotation ) + trans.sa_session.flush() + return new_annotation + return "" + + @web.expose_api + def delete( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.delete_item_annotation( trans.sa_session, trans.get_user(), item ) + + @web.expose_api + def undelete( self, trans, **kwd ): + raise HTTPNotImplemented() + +class HistoryAnnotationsController(BaseAnnotationsController): + controller_name = "history_annotations" + tagged_item_id = "history_id" + def _get_item_from_id(self, trans, idstr): + hist = self.get_history( trans, idstr ) + return hist + +class HistoryContentAnnotationsController(BaseAnnotationsController): + controller_name = "history_content_annotations" + tagged_item_id = "history_content_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_dataset(trans, idstr) + return hda + +class WorkflowAnnotationsController(BaseAnnotationsController): + controller_name = "workflow_annotations" + tagged_item_id = "workflow_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_stored_workflow(trans, idstr) + return hda diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 6aef91d128904c405356e9fa2f3afa43368c8e8a lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -105,6 +105,17 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + + _add_item_annotation_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + _add_item_annotation_controller( webapp, + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) + _add_item_annotation_controller( webapp, + name_prefix="workflow_", + path_prefix='/api/workflows/:workflow_id' ) + webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -185,6 +196,12 @@ conditions=dict(method=["GET"])) + +def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sannotations" % name_prefix + name = "%sannotation" % name_prefix + webapp.api_mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful https://bitbucket.org/galaxy/galaxy-central/commits/f8fac0ad9808/ changeset: f8fac0ad9808 user: kellrott date: 2013-01-18 17:52:33 summary: Removing '*' imports from annotations API module affected #: 1 file diff -r 6aef91d128904c405356e9fa2f3afa43368c8e8a -r f8fac0ad9808825e4ac7228a9da5e0f8d8a3ca48 lib/galaxy/webapps/galaxy/api/annotations.py --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -4,10 +4,9 @@ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.model.item_attrs import * +from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin +from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * import galaxy.datatypes from galaxy.util.bunch import Bunch https://bitbucket.org/galaxy/galaxy-central/commits/98f724202d9d/ changeset: 98f724202d9d user: jgoecks date: 2013-01-18 18:02:51 summary: Merged in kellrott/galaxy-central (pull request #101) The start of the API based annotation system affected #: 3 files diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -137,6 +137,12 @@ # Set annotation. annotation_assoc.annotation = annotation return annotation_assoc + + def delete_item_annotation( self, db_session, user, item): + annotation_assoc = self.get_item_annotation_obj( db_session, user, item ) + if annotation_assoc: + db_session.delete(annotation_assoc) + db_session.flush() def copy_item_annotation( self, db_session, source_user, source_item, target_user, target_item ): """ Copy an annotation from a user/item source to a user/item target. """ diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/webapps/galaxy/api/annotations.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -0,0 +1,75 @@ +""" +API operations on annotations. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin +from galaxy.model.item_attrs import UsesAnnotations +from galaxy.util.sanitize_html import sanitize_html +import galaxy.datatypes +from galaxy.util.bunch import Bunch + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): + + @web.expose_api + def index( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.get_item_annotation_str( trans.sa_session, trans.get_user(), item ) + + + @web.expose_api + def create( self, trans, payload, **kwd ): + if "text" not in payload: + return "" + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + new_annotation = payload.get("text") + # Sanitize annotation before adding it. + new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) + + self.add_item_annotation( trans.sa_session, trans.get_user(), item, new_annotation ) + trans.sa_session.flush() + return new_annotation + return "" + + @web.expose_api + def delete( self, trans, **kwd ): + idnum = kwd[self.tagged_item_id] + item = self._get_item_from_id(trans, idnum) + if item is not None: + return self.delete_item_annotation( trans.sa_session, trans.get_user(), item ) + + @web.expose_api + def undelete( self, trans, **kwd ): + raise HTTPNotImplemented() + +class HistoryAnnotationsController(BaseAnnotationsController): + controller_name = "history_annotations" + tagged_item_id = "history_id" + def _get_item_from_id(self, trans, idstr): + hist = self.get_history( trans, idstr ) + return hist + +class HistoryContentAnnotationsController(BaseAnnotationsController): + controller_name = "history_content_annotations" + tagged_item_id = "history_content_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_dataset(trans, idstr) + return hda + +class WorkflowAnnotationsController(BaseAnnotationsController): + controller_name = "workflow_annotations" + tagged_item_id = "workflow_id" + def _get_item_from_id(self, trans, idstr): + hda = self.get_stored_workflow(trans, idstr) + return hda diff -r 666d744054ded20d79e3d2c6eb65012455de96b5 -r 98f724202d9d3cea035d7de04d89465bcf3092b1 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -107,6 +107,17 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) + + _add_item_annotation_controller( webapp, + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + _add_item_annotation_controller( webapp, + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) + _add_item_annotation_controller( webapp, + name_prefix="workflow_", + path_prefix='/api/workflows/:workflow_id' ) + webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -193,6 +204,12 @@ conditions=dict(method=["GET"])) + +def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): + controller = "%sannotations" % name_prefix + name = "%sannotation" % name_prefix + webapp.api_mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + def wrap_in_middleware( app, global_conf, **local_conf ): """ Based on the configuration wrap `app` in a set of common and useful Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Readd add/remove buttons' HTML element class names that was omitted due to a poor merge of pull request #24.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/666d744054de/ changeset: 666d744054de user: jgoecks date: 2013-01-18 17:59:11 summary: Readd add/remove buttons' HTML element class names that was omitted due to a poor merge of pull request #24. affected #: 1 file diff -r a0db2696ba21ff636d3fd75699fe995c0e8c2262 -r 666d744054ded20d79e3d2c6eb65012455de96b5 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -151,7 +151,7 @@ <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} %if input.min < num_repeats: - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif </div> %if rep_errors.has_key( '__index__' ): @@ -159,7 +159,7 @@ %endif %endfor %if input.max > num_repeats: - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif </div> %elif input.type == "conditional": Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Removed hg merge conflict markers.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0db2696ba21/ changeset: a0db2696ba21 user: inithello date: 2013-01-18 17:42:35 summary: Removed hg merge conflict markers. affected #: 1 file diff -r 864e960c52474fe6cb19129196b0ccccf48856bd -r a0db2696ba21ff636d3fd75699fe995c0e8c2262 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -150,25 +150,17 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} -<<<<<<< local - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> -======= %if input.min < num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif ->>>>>>> other </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor -<<<<<<< local - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> -======= %if input.max > num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif ->>>>>>> other </div> %elif input.type == "conditional": <% Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Tool shed import fixes.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/864e960c5247/ changeset: 864e960c5247 user: greg date: 2013-01-18 17:40:29 summary: Tool shed import fixes. affected #: 7 files diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -1,9 +1,9 @@ -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController +from galaxy import web, util from galaxy.web.base.controllers.admin import Admin from galaxy.webapps.community import model from galaxy.model.orm import and_ -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.web.form_builder import SelectField +from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import galaxy.util.shed_util_common as suc from repository import RepositoryGrid, CategoryGrid diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,10 +1,6 @@ import logging from galaxy.model.item_attrs import UsesItemRatings -from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands - log = logging.getLogger( __name__ ) class ItemRatings( UsesItemRatings ): diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,5 +1,6 @@ import os, logging -from galaxy.web.base.controller import * +from galaxy import web +from galaxy.web.base.controller import BaseUIController from galaxy.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata from galaxy import eggs diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -1,9 +1,9 @@ import os, logging -from galaxy import util -from galaxy.web.base.controller import * +from galaxy import web, util +from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField from galaxy.webapps.community import model -from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func import common diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,5 +1,6 @@ import sys, os, shutil, logging, tarfile, tempfile, urllib -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController +from galaxy import web, util from galaxy.datatypes import checkers import galaxy.util.shed_util_common as suc diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/framework/middleware/hg.py --- a/lib/galaxy/webapps/community/framework/middleware/hg.py +++ b/lib/galaxy/webapps/community/framework/middleware/hg.py @@ -2,7 +2,7 @@ Middleware for handling hg authentication for users pushing change sets to local repositories. """ import os, logging -from sqlalchemy import * +import sqlalchemy from paste.auth.basic import AuthBasicAuthenticator from paste.httpheaders import REMOTE_USER, AUTH_TYPE @@ -43,7 +43,7 @@ username = path_info_components[1] name = path_info_components[2] # Instantiate a database connection - engine = create_engine( self.db_url ) + engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() result_set = connection.execute( "select id from galaxy_user where username = '%s'" % username.lower() ) for row in result_set: @@ -101,7 +101,7 @@ return self.__authenticate( username, password ) def __authenticate( self, username, password ): # Instantiate a database connection - engine = create_engine( self.db_url ) + engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() ) for row in result_set: diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1,15 +1,24 @@ -import urllib2, tempfile -from admin import * +import logging, os, shutil, tempfile, urllib2 +from admin import AdminGalaxy +from galaxy import model, web, util +from galaxy.web.form_builder import SelectField, CheckboxField +from galaxy.web.framework.helpers import iff, grids from galaxy.util import json +from galaxy.model.orm import or_ import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util from galaxy.webapps.community.util import container_util, workflow_util from galaxy import eggs, tools +import pkg_resources eggs.require( 'mercurial' ) from mercurial import hg, ui, commands +pkg_resources.require( 'elementtree' ) +from elementtree import ElementTree +from elementtree.ElementTree import Element + log = logging.getLogger( __name__ ) class InstalledRepositoryGrid( grids.Grid ): @@ -447,7 +456,7 @@ @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @@ -469,7 +478,7 @@ tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) + ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -557,14 +566,14 @@ @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = url_for( '/', qualified=True ) + galaxy_url = web.url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @@ -993,7 +1002,7 @@ # Send a request to the tool shed to install the repository. url = suc.url_join( tool_shed_url, 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ - ( repository.name, repository.owner, repository.installed_changeset_revision, ( url_for( '/', qualified=True ) ) ) ) + ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) ) return trans.response.send_redirect( url ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 18 Jan '13

18 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9a440d0b2a1c/ changeset: 9a440d0b2a1c user: james_taylor date: 2013-01-18 16:44:18 summary: modals: make wider by default and scroll like trello affected #: 3 files diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -311,9 +311,10 @@ } #overlay { - position: fixed; + position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; + overflow-y: auto; } #overlay.is_modal #overlay-background, .overlay-background { diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -537,6 +537,9 @@ .btn.active,.btn:active{color:inherit;} .dropdown-menu{max-width:auto;} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} +.modal{position:absolute;top:50px;width:660px;margin-left:-330px;} +.modal:after{content:"";height:0px;position:relative;top:50px;display:block;border:solid transparent 1px;} +.modal-body{height:auto;max-height:none;} .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} @@ -865,7 +868,7 @@ .panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay{position:absolute;top:0;left:0;width:100%;height:100%;z-index:20000;overflow-y:auto;} #overlay.is_modal #overlay-background,.overlay-background{background:rgba(0, 0, 0, 0.5);} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} diff -r a4113cc1cb5eaa68091c9a73375f00555b66dd11 -r 9a440d0b2a1ca00e71564f9258211a9eb9830fee static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -98,6 +98,31 @@ margin-right: 0.5ex; } +// Modal -- wider by default, scroll like Trello + +.modal { + position: absolute; + top: 50px; + width: 660px; + margin-left: -330px; +} + + +.modal:after { + content: ""; + height: 0px; + position: relative; + top: 50px; + display: block; + border: solid transparent 1px; +}; + + +.modal-body { + height: auto; + max-height: none; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { https://bitbucket.org/galaxy/galaxy-central/commits/add133ca7596/ changeset: add133ca7596 user: james_taylor date: 2013-01-18 17:31:21 summary: merge affected #: 3 files diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -311,9 +311,10 @@ } #overlay { - position: fixed; + position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; + overflow-y: auto; } #overlay.is_modal #overlay-background, .overlay-background { diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -537,6 +537,9 @@ .btn.active,.btn:active{color:inherit;} .dropdown-menu{max-width:auto;} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} +.modal{position:absolute;top:50px;width:660px;margin-left:-330px;} +.modal:after{content:"";height:0px;position:relative;top:50px;display:block;border:solid transparent 1px;} +.modal-body{height:auto;max-height:none;} .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} @@ -865,7 +868,7 @@ .panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay{position:absolute;top:0;left:0;width:100%;height:100%;z-index:20000;overflow-y:auto;} #overlay.is_modal #overlay-background,.overlay-background{background:rgba(0, 0, 0, 0.5);} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r add133ca7596281900e31933e6b0748812323517 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -98,6 +98,31 @@ margin-right: 0.5ex; } +// Modal -- wider by default, scroll like Trello + +.modal { + position: absolute; + top: 50px; + width: 660px; + margin-left: -330px; +} + + +.modal:after { + content: ""; + height: 0px; + position: relative; + top: 50px; + display: block; + border: solid transparent 1px; +}; + + +.modal-body { + height: auto; + max-height: none; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: Show/enable display icon-button for non-ready-state hdas
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9d44cf4b68e/ changeset: b9d44cf4b68e user: carlfeberhard date: 2013-01-18 16:45:20 summary: history panel: Show/enable display icon-button for non-ready-state hdas affected #: 1 file diff -r c8cb184472b913c635fb34f31e4122c3c1f77e87 -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -198,15 +198,14 @@ * @returns {jQuery} rendered DOM */ _render_displayButton : function(){ - // don't show display if not in ready state or not accessible - // DO show if in error (ala previous history panel) - if( ( !this.model.inReadyState() ) - //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + // don't show display if not viewable or not accessible + // (do show if in error, running) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.displayButton = null; return null; } + //NOTE: line 88 in history_common.mako should be handled by the url template generation var displayBtnData = { icon_class : 'display', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8cb184472b9/ changeset: c8cb184472b9 user: dannon date: 2013-01-18 16:26:57 summary: Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary. affected #: 1 file diff -r d36e35dd83bf18a47f26dc6eb779549c15782fbd -r c8cb184472b913c635fb34f31e4122c3c1f77e87 doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -23,10 +23,6 @@ Quickstart ========== -Set the following option in universe_wsgi.ini and start the server:: - - enable_api = True - Log in as your user, navigate to the API Keys page in the User menu, and generate a new API key. Make a note of the API key, and then pull up a terminal. Now we'll use the display.py script in your galaxy/scripts/api Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix circular repository dependency issue that so far uccurs only on the test tool shed.
by Bitbucket 18 Jan '13

18 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d36e35dd83bf/ changeset: d36e35dd83bf user: greg date: 2013-01-18 16:16:20 summary: Fix circular repository dependency issue that so far uccurs only on the test tool shed. affected #: 1 file diff -r c86a704ba3f60bc51c9f998e0061d9b9f9507242 -r d36e35dd83bf18a47f26dc6eb779549c15782fbd lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -2779,6 +2779,7 @@ def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): current_repository_key_rd_dicts = [] + filtered_current_repository_key_rd_dicts = [] for rd in repository_dependencies_dict[ 'repository_dependencies' ]: new_key_rd_dict = {} new_key_rd_dict[ current_repository_key ] = rd @@ -2790,6 +2791,7 @@ for key_rd_dict in current_repository_key_rd_dicts: is_circular = False if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + filtered_current_repository_key_rd_dicts.append( key_rd_dict ) repository_dependency = key_rd_dict[ current_repository_key ] if current_repository_key in all_repository_dependencies: # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. @@ -2813,7 +2815,7 @@ new_key_rd_dict = {} new_key_rd_dict[ current_repository_key ] = repository_dependency key_rd_dicts_to_be_processed.append( new_key_rd_dict ) - return current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies + return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add missing imports to shed_util_common.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c86a704ba3f6/ changeset: c86a704ba3f6 user: greg date: 2013-01-17 22:42:11 summary: Add missing imports to shed_util_common. affected #: 1 file diff -r dd395d9b8a01255412b3e56219d11639ccce2e50 -r c86a704ba3f60bc51c9f998e0061d9b9f9507242 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1,4 +1,6 @@ import os, shutil, tempfile, logging, string, threading, urllib2, filecmp +from datetime import datetime +from time import gmtime, strftime from galaxy import web, util from galaxy.tools import parameters from galaxy.util import inflector, json Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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