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galaxy-dist commit 77575a5f348d: lims:
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280930211 14400 # Node ID 77575a5f348d7d10c1df423c5faa71abaefd5f8a # Parent 6e19bc97f2b8ba816ab20fc53a88f3504c992e00 lims: - bug fix: now a admin cannot delete a transfer dataset when the transfer has started. - added user warning when a dataset is deleted. --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -593,16 +593,25 @@ class RequestsAdmin( BaseController ): elif operation == "delete": id_list = util.listify( kwd['id'] ) + not_deleted = [] for id in id_list: sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) ) sample_id = sample_dataset.sample_id - trans.sa_session.delete( sample_dataset ) - trans.sa_session.flush() + if sample_dataset.status == sample_dataset.sample.transfer_status.NOT_STARTED: + trans.sa_session.delete( sample_dataset ) + trans.sa_session.flush() + else: + not_deleted.append(sample_dataset.name) + message = '%i dataset(s) have been successfully deleted. ' % (len(id_list) - len(not_deleted)) + status = 'done' + if not_deleted: + status = 'warning' + message = message + '%s could not be deleted. Only datasets with transfer status "Not Started" can be deleted. ' % str(not_deleted) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=sample_id, - status='done', - message="%i dataset(s) have been removed." % len(id_list)) ) + status=status, + message=message) ) elif operation == "rename": id_list = util.listify( kwd['id'] )

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galaxy-dist commit 6e19bc97f2b8: - Fix dbkey migrate script for downgrade and rare case when config is empty
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1280868063 14400 # Node ID 6e19bc97f2b8ba816ab20fc53a88f3504c992e00 # Parent 0366c4a4765631188f1515fbd77fddbbf1532d4f - Fix dbkey migrate script for downgrade and rare case when config is empty - Fix grid sorting in "Visualize in Trackster" modal box - Refactor out sort_order in grids, fixing a bug with sort arrow not showing --- a/templates/tracks/add_to_viz.mako +++ b/templates/tracks/add_to_viz.mako @@ -6,8 +6,3 @@ ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} -## Initialize the grid. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script> --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -136,7 +136,6 @@ class Grid( object ): extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. sort_key = None - sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: @@ -144,11 +143,9 @@ class Grid( object ): encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): - sort_order = 'desc' # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - sort_order = 'asc' # See reason for not using lower() to do case-insensitive search. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key @@ -226,7 +223,6 @@ class Grid( object ): cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, - sort_order=sort_order, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -739,8 +739,8 @@ href = "" extra = "" if column.sortable: - if sort_key == column.key: - if sort_order == "asc": + if sort_key.endswith(column.key): + if not sort_key.startswith("-"): href = url( sort=( "-" + column.key ) ) extra = "↓" else: --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -205,7 +205,7 @@ class UsesVisualization( SharableItemSec # Set dbkey. try: - dbkey = latest_revision.config['dbkey'] + dbkey = latest_revision.dbkey except KeyError: dbkey = None --- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py +++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py @@ -14,13 +14,13 @@ log = logging.getLogger( __name__ ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) -Visualization_table = Table( "visualization", metadata, autoload=True ) -Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) - def upgrade(): print __doc__ metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) # Create dbkey columns. x = Column( "dbkey", TEXT, index=True ) @@ -47,12 +47,16 @@ def upgrade(): for viz in all_viz: viz_id = viz['viz_id'] viz_rev_id = viz['viz_rev_id'] - dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") - db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) - db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) + if viz[Visualization_revision_table.c.config]: + dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") + db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) + db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) def downgrade(): metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) Visualization_table.c.dbkey.drop() Visualization_revision_table.c.dbkey.drop()

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galaxy-dist commit 07e7db914c6d: Modified Group tool by adding Mode function to the list of aggregate operations.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User gua110 # Date 1280420469 14400 # Node ID 07e7db914c6d2090ef7579a5e2c0583af50c39f3 # Parent 79baa9583d9390bb6341d3484aa9f55b8e3808f8 Modified Group tool by adding Mode function to the list of aggregate operations. --- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -23,6 +23,12 @@ def main(): cols.append(var.split()[1]) rounds.append(var.split()[2]) + if 'Mode' in ops: + try: + r.library('prettyR') + except: + stop_err('R package prettyR could not be loaded. Please make sure it is installed.') + """ At this point, ops, cols and rounds will look something like this: ops: ['mean', 'min', 'c'] @@ -46,9 +52,10 @@ def main(): except: stop_err( "Group column not specified." ) + str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs for k,col in enumerate(cols): col = int(col)-1 - if ops[k] not in ['c', 'length', 'unique', 'random', 'cuniq']: + if ops[k] not in str_ops: # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the # only aggregation functions that can be used on columns containing strings. try: @@ -109,7 +116,7 @@ def main(): valid = True # Before appending the current value, make sure it is numeric if the # operation for the column requires it. - if ops[i] not in ['c','length', 'unique','random','cuniq']: + if ops[i] not in str_ops: try: float( fields[col].strip()) except: @@ -128,13 +135,14 @@ def main(): due to the sort on group_col we've applied to the data above. """ out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate( ops ): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -148,7 +156,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -165,8 +176,13 @@ def main(): out_str += "\t" + str(rout) else: out_str += "\t" + str(rout) - - print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str prev_item = item prev_vals = [] @@ -195,14 +211,15 @@ def main(): # Handle the last grouped value out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate(ops): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op try: - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -216,7 +233,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -238,7 +258,13 @@ def main(): if not first_invalid_line: first_invalid_line = ii+1 - print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) --- a/tools/stats/grouping.xml +++ b/tools/stats/grouping.xml @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.0"> +<tool id="Grouping1" name="Group" version="1.9.1"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py @@ -22,6 +22,7 @@ <param name="optype" type="select" label="Type"><option value="mean">Mean</option><option value="median">Median</option> + <option value="Mode">Mode</option><option value="max">Maximum</option><option value="min">Minimum</option><option value="sum">Sum</option> @@ -77,10 +78,12 @@ **Syntax** -This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Sum, Max, Min and Concatenate on other columns. +This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Median, Mode, Sum, Max, Min, Count, Random draw and Concatenate on other columns. - All invalid, blank and comment lines are skipped when performing the aggregate functions. The number of skipped lines is displayed in the resulting history item. +- If multiple modes are present, all are reported. + ----- **Example**

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galaxy-dist commit 66e03194e2da: lims:
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280424157 14400 # Node ID 66e03194e2dae00723d446509e077a869f274922 # Parent 07e7db914c6d2090ef7579a5e2c0583af50c39f3 lims: - sample dataset size now appear correctly in the grid. The path of the datasets no longer appears with it. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1624,7 +1624,7 @@ class Sample( object ): output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n', pexpect.TIMEOUT:print_ticks}, timeout=10) - return output.split('\t')[0] + return output.replace(filepath, '').strip() class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None):

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galaxy-dist commit a8ef6a46d622: Added AttributeValueSplitterFilter to tool select parameter filters so that GFF attributes can be read and used as tool inputs. Updated gff_filtering tool to use this filter.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1280439706 14400 # Node ID a8ef6a46d6221d8eb3a7bc919fc3e2b13c1bc2aa # Parent 66e03194e2dae00723d446509e077a869f274922 Added AttributeValueSplitterFilter to tool select parameter filters so that GFF attributes can be read and used as tool inputs. Updated gff_filtering tool to use this filter. --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -206,6 +206,40 @@ class MultipleSplitterFilter( Filter ): for field in fields[column].split( self.separator ): rval.append( fields[0:column] + [field] + fields[column:] ) return rval + +class AttributeValueSplitterFilter( Filter ): + """ + Filters a list of attribute-value pairs to be unique attribute names. + + Type: attribute_value_splitter + + Required Attributes: + column: column in options to compare with + Optional Attributes: + pair_separator: Split column by this (,) + name_val_separator: Split name-value pair by this ( whitespace ) + """ + def __init__( self, d_option, elem ): + Filter.__init__( self, d_option, elem ) + self.pair_separator = elem.get( "pair_separator", "," ) + self.name_val_separator = elem.get( "name_val_separator", None ) + self.columns = elem.get( "column", None ) + assert self.columns is not None, "Required 'columns' attribute missing from filter" + self.columns = [ int ( column ) for column in self.columns.split( "," ) ] + def filter_options( self, options, trans, other_values ): + attr_names = [] + rval = [] + for fields in options: + for column in self.columns: + for pair in fields[column].split( self.pair_separator ): + ary = pair.split( self.name_val_separator ) + if len( ary ) == 2: + name, value = ary + if name not in attr_names: + rval.append( fields[0:column] + [name] + fields[column:] ) + attr_names.append( name ) + return rval + class AdditionalValueFilter( Filter ): """ @@ -322,6 +356,7 @@ filter_types = dict( data_meta = DataMet static_value = StaticValueFilter, unique_value = UniqueValueFilter, multiple_splitter = MultipleSplitterFilter, + attribute_value_splitter = AttributeValueSplitterFilter, add_value = AdditionalValueFilter, remove_value = RemoveValueFilter, sort_by = SortByColumnFilter ) --- a/tools/ngs_rna/gff_filtering.xml +++ b/tools/ngs_rna/gff_filtering.xml @@ -5,8 +5,12 @@ </command><inputs><param format="gff" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> - <param name="attribute_name" size="40" type="text" label="Attribute name" help=""> - <validator type="empty_field" message="Enter a valid attribute name."/> + <param name="attribute_name" type="select" label="Attribute name" help=""> + <options from_dataset="input"> + <column name="name" index="8"/> + <column name="value" index="8"/> + <filter type="attribute_value_splitter" pair_separator=";" column="8"/> + </options></param><param name="attribute_type" type="select" label="Attribute type"><option value="float">Float</option>

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galaxy-dist commit 8d255150cb3e: Use env for the API example scripts instead of directly referring to /usr/bin/python
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1280416695 14400 # Node ID 8d255150cb3e868974777eee030843d2c3e7ad16 # Parent c653ccfa1a1ef7c2a384ee4b3ab72da0b391ae14 Use env for the API example scripts instead of directly referring to /usr/bin/python --- a/scripts/api/library_upload_from_import_dir.py +++ b/scripts/api/library_upload_from_import_dir.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/library_create_library.py +++ b/scripts/api/library_create_library.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/library_create_folder.py +++ b/scripts/api/library_create_folder.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/display.py +++ b/scripts/api/display.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) )

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galaxy-dist commit c653ccfa1a1e: Allow access to /api without HTTP_REMOTE_USER set if use_remote_user = True, since the API controllers handle authentication internally.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1280416580 14400 # Node ID c653ccfa1a1ef7c2a384ee4b3ab72da0b391ae14 # Parent ab48c0e20a948f310ad3b072c23560faa8433aa3 Allow access to /api without HTTP_REMOTE_USER set if use_remote_user = True, since the API controllers handle authentication internally. --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -75,8 +75,8 @@ class RemoteUser( object ): # Apache sets REMOTE_USER to the string '(null)' when using the # Rewrite* method for passing REMOTE_USER and a user is # un-authenticated. Any other possible values need to go here as well. + path_info = environ.get('PATH_INFO', '') if environ.has_key( 'HTTP_REMOTE_USER' ) and environ[ 'HTTP_REMOTE_USER' ] != '(null)': - path_info = environ.get('PATH_INFO', '') if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): if self.maildomain is not None: environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain @@ -96,7 +96,7 @@ class RemoteUser( object ): if path_info.startswith( '/user/create' ) and environ[ 'HTTP_REMOTE_USER' ] in self.admin_users: pass # admins can create users elif path_info.startswith( '/user/api_keys' ): - pass + pass # api keys can be managed when remote_user is in use elif path_info.startswith( '/user' ): title = "Access to Galaxy user controls is disabled" message = """ @@ -105,6 +105,9 @@ class RemoteUser( object ): """ return self.error( start_response, title, message ) return self.app( environ, start_response ) + elif path_info.startswith( '/api/' ): + # The API handles its own authentication via keys + return self.app( environ, start_response ) else: title = "Access to Galaxy is denied" message = """

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galaxy-dist commit 0736d9af9e6e: Allow access to API Key creation when use_remote_user is true.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1280416177 14400 # Node ID 0736d9af9e6e7facef8fad93baa3a303e0cf9526 # Parent d27912281a74ba74a8df6f5d72db7c553ca846c5 Allow access to API Key creation when use_remote_user is true. --- /dev/null +++ b/templates/webapps/galaxy/user/api_keys.mako @@ -0,0 +1,35 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <form name="user_api_keys" id="user_api_keys" action="${h.url_for( controller='user', action='api_keys' )}" method="post" > + <div class="toolFormTitle">Web API Key</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Current API key:</label> + %if user.api_keys: + ${user.api_keys[0].key} + %else: + none set + %endif + </div> + <div class="form-row"> + <input type="submit" name="new_api_key_button" value="Generate a new key now"/> + %if user.api_keys: + (invalidates old key) + %endif + <div class="toolParamHelp" style="clear: both;"> + An API key will allow you to access Galaxy via its web + API (documentation forthcoming). Please note that + <strong>this key acts as an alternate means to access + your account, and should be treated with the same care + as your login password</strong>. + </div> + </div> + </div> + </form> +</div> --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -95,6 +95,8 @@ class RemoteUser( object ): return self.error( start_response, title, message ) if path_info.startswith( '/user/create' ) and environ[ 'HTTP_REMOTE_USER' ] in self.admin_users: pass # admins can create users + elif path_info.startswith( '/user/api_keys' ): + pass elif path_info.startswith( '/user' ): title = "Access to Galaxy user controls is disabled" message = """ --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -1003,24 +1003,20 @@ class User( BaseController ): @web.expose - def new_api_key( self, trans, **kwd ): + def api_keys( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) error = '' - user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) if params.get( 'new_api_key_button', None ) == 'Generate a new key now': new_key = trans.app.model.APIKeys() - new_key.user_id = user.id + new_key.user_id = trans.user.id new_key.key = trans.app.security.get_new_guid() trans.sa_session.add( new_key ) trans.sa_session.flush() message = "Generated a new web API key" status = "done" - return trans.response.send_redirect( web.url_for( controller='user', - action='show_info', - admin_view=admin_view, - user_id=user.id, - message=message, - status=status ) ) + return trans.fill_template( 'webapps/galaxy/user/api_keys.mako', + user=trans.user, + message=message, + status=status ) --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -130,6 +130,9 @@ %if app.config.get_bool( 'enable_pages', False ): <li><a href="${h.url_for( controller='/page', action='list' )}">Pages</a></li> %endif + %if app.config.enable_api: + <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='api_keys' )}">API Keys</a></li> + %endif </ul></div></td> --- a/templates/webapps/galaxy/user/info.mako +++ b/templates/webapps/galaxy/user/info.mako @@ -120,36 +120,3 @@ </div></form></div> - -<p/> - -%if trans.app.config.enable_api: - <div class="toolForm"> - <form name="user_api_keys" id="user_api_keys" action="${h.url_for( controller='user', action='new_api_key', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">Web API Key</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Current API key:</label> - %if user.api_keys: - ${user.api_keys[0].key} - %else: - none set - %endif - </div> - <div class="form-row"> - <input type="submit" name="new_api_key_button" value="Generate a new key now"/> - %if user.api_keys: - (invalidates old key) - %endif - <div class="toolParamHelp" style="clear: both;"> - An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - <strong>this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password</strong>. - </div> - </div> - </div> - </form> - </div> -%endif --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -12,6 +12,9 @@ %if webapp == 'galaxy': <li><a href="${h.url_for( controller='user', action='show_info' )}">${_('Manage your information')}</a></li><li><a href="${h.url_for( controller='user', action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> + %if trans.app.config.enable_api: + <li><a href="${h.url_for( controller='user', action='api_keys' )}">${_('Manage your API Keys')}</a> for new histories</li> + %endif %else: <li><a href="${h.url_for( controller='user', action='show_info', webapp='community' )}">${_('Manage your information')}</a></li> %endif

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galaxy-dist commit ab48c0e20a94: Merge with 0736d9af9e6e7facef8fad93baa3a303e0cf9526
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280416325 14400 # Node ID ab48c0e20a948f310ad3b072c23560faa8433aa3 # Parent b0cf8217826e7a289eec88fd31894683818d2bee # Parent 0736d9af9e6e7facef8fad93baa3a303e0cf9526 Merge with 0736d9af9e6e7facef8fad93baa3a303e0cf9526

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galaxy-dist commit 79baa9583d93: lims:
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280417621 14400 # Node ID 79baa9583d9390bb6341d3484aa9f55b8e3808f8 # Parent 8d255150cb3e868974777eee030843d2c3e7ad16 lims: - fixed a migration script bug when moving the sample datasets info from the 'sample' to 'sample_dataset' table --- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py +++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py @@ -61,19 +61,20 @@ def upgrade(): result = db_session.execute( cmd ) for r in result: sample_id = r[0] - dataset_files = from_json_string(r[1]) - for df in dataset_files: - cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" - cmd = cmd % ( nextval('sample_dataset'), - localtimestamp(), - localtimestamp(), - str(sample_id), - df['name'], - df['filepath'], - df['status'], - df['error_msg'].replace('"', '').replace("'", ""), - df['size'] ) - db_session.execute( cmd ) + if r[1]: + dataset_files = from_json_string(r[1]) + for df in dataset_files: + cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" + cmd = cmd % ( nextval('sample_dataset'), + localtimestamp(), + localtimestamp(), + str(sample_id), + df['name'], + df['filepath'], + df['status'].replace('"', '').replace("'", ""), + "", + df['size'].replace('"', '').replace("'", "") ) + db_session.execute( cmd ) # Delete the dataset_files column in the Sample table try:

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