# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster greg@bx.psu.edu # Date 1276010264 14400 # Node ID cd7705e2e0c4264f4c9c1962cfb7eff6e1634c75 # Parent ffd110701ba557277eb0f6476145f3850a1544d1 Fixes for the reports webapp; grid pages now function as desired, and advanced search features are now functionally correct.

--- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -13,7 +13,7 @@ <h4 align="center">Click Total Jobs to see the user's jobs for that month</h4><table align="center" width="60%" class="colored"> %if len( jobs ) == 0: - <tr><td colspan="2">There are no jobs for user "${email}"</td></tr> + <tr><td colspan="2">There are no jobs for user "${util.restore_text( email )}"</td></tr> %else: <tr class="header"><td>Month</td> @@ -27,7 +27,7 @@ <tr class="tr"> %endif <td>${job[2]}&nbsp;${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='user_for_month', email=email, specified_date=job[0]+'-01' )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_date_handler', operation='user_for_month', email=email, specified_date=job[0] )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor

--- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -18,13 +18,19 @@ class SpecifiedDateListGrid( grids.Grid class StateColumn( grids.TextColumn ): def get_value( self, trans, grid, job ): return job.state + def filter( self, trans, user, query, column_filter ): + if column_filter == 'Unfinished': + return query.filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, + model.Job.table.c.state == model.Job.states.ERROR, + model.Job.table.c.state == model.Job.states.DELETED ) ) ) + return query class ToolColumn( grids.TextColumn ): def get_value( self, trans, grid, job ): return job.tool_id class CreateTimeColumn( grids.TextColumn ): def get_value( self, trans, grid, job ): return job.create_time - class UserColumn( grids.TextColumn ): + class UserColumn( grids.GridColumn ): def get_value( self, trans, grid, job ): if job.history: if job.history.user: @@ -32,10 +38,38 @@ class SpecifiedDateListGrid( grids.Grid return 'anonymous' # TODO: handle libraries... return 'no history' + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): + if column_filter == 'All': + return query + return query.filter( and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, + model.GalaxySession.table.c.user_id == model.User.table.c.id, + model.User.table.c.email == column_filter ) ) + class SpecifiedDateColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): + if column_filter == 'All': + return query + # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM, + # so we need to figure out which type of date we have + if column_filter.count( '-' ) == 2: + # We are filtering on a date like YYYY-MM-DD + year, month, day = map( int, column_filter.split( "-" ) ) + start_date = date( year, month, day ) + end_date = start_date + timedelta( days=1 ) + return query.filter( and_( self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) + if column_filter.count( '-' ) == 1: + # We are filtering on a month like YYYY-MM + year, month = map( int, column_filter.split( "-" ) ) + start_date = date( year, month, 1 ) + end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) + return query.filter( and_( self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) + # Grid definition use_async = False model_class = model.Job - title = "Jobs By Date" + title = "Jobs" template='/webapps/reports/grid.mako' default_sort_key = "id" columns = [ @@ -54,16 +88,29 @@ class SpecifiedDateListGrid( grids.Grid model_class=model.Job, link=( lambda item: dict( operation="tool_per_month", id=item.id, webapp="reports" ) ), attach_popup=False ), - CreateTimeColumn( "create_time", + CreateTimeColumn( "Creation Time", key="create_time", model_class=model.Job, attach_popup=False ), - UserColumn( "user", + UserColumn( "User", # Can't sort on this column since it is not a column in self.model_class model_class=model.User, link=( lambda item: dict( operation="user_per_month", id=item.id, webapp="reports" ) ), attach_popup=False ), - grids.StateColumn( "state", key="state", model_class=model.Job, visible=False, filterable="advanced" ) + # Columns that are valid for filtering but are not visible. + SpecifiedDateColumn( "Specified Date", + key="specified_date", + model_class=model.Job, + visible=False ), + EmailColumn( "Email", + key="email", + model_class=model.User, + visible=False ), + grids.StateColumn( "State", + key="state", + model_class=model.Job, + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[1], columns[2] ], @@ -76,113 +123,47 @@ class SpecifiedDateListGrid( grids.Grid preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - specified_date = kwd.get( 'specified_date', 'All' ) - if specified_date == 'All': - return trans.sa_session.query( self.model_class ) \ - .enable_eagerloads( False ) - year, month, day = map( int, specified_date.split( "-" ) ) - start_date = date( year, month, day ) - end_date = start_date + timedelta( days=1 ) return trans.sa_session.query( self.model_class ) \ - .filter( and_( self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) \ - .enable_eagerloads( False ) - -class SpecifiedDateInErrorListGrid( SpecifiedDateListGrid ): - def build_initial_query( self, trans, **kwd ): - specified_date = kwd.get( 'specified_date', 'All' ) - if specified_date == 'All': - return trans.sa_session.query( self.model_class ) \ - .filter( self.model_class.table.c.state == model.Job.states.ERROR ) \ - .enable_eagerloads( False ) - year, month, day = map( int, specified_date.split( "-" ) ) - start_date = date( year, month, day ) - end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ) \ - .filter( and_( self.model_class.table.c.state == model.Job.states.ERROR, - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) \ - .enable_eagerloads( False ) - -class AllUnfinishedListGrid( SpecifiedDateListGrid ): - def build_initial_query( self, trans, **kwd ): - specified_date = kwd.get( 'specified_date', 'All' ) - if specified_date == 'All': - return trans.sa_session.query( self.model_class ) \ - .filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ) ) \ - .enable_eagerloads( False ) - year, month, day = map( int, specified_date.split( "-" ) ) - start_date = date( year, month, day ) - end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ) \ - .filter( and_( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ), - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) \ - .enable_eagerloads( False ) - -class UserForMonthListGrid( SpecifiedDateListGrid ): - def build_initial_query( self, trans, **kwd ): - email = util.restore_text( kwd.get( 'email', '' ) ) - # If specified_date is not received, we'll default to the current month - specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) - specified_month = specified_date[ :7 ] - year, month = map( int, specified_month.split( "-" ) ) - start_date = date( year, month, 1 ) - end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) - return trans.sa_session.query( model.Job ) \ .join( model.GalaxySession ) \ .join( model.User ) \ - .filter( and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, - model.GalaxySession.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == email, - model.Job.table.c.create_time >= start_date, - model.Job.table.c.create_time < end_date ) ) \ - .enable_eagerloads( False ) - -class ToolForMonthListGrid( SpecifiedDateListGrid ): - def build_initial_query( self, trans, **kwd ): - # If specified_date is not received, we'll default to the current month - specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) - specified_month = specified_date[ :7 ] - tool_id = util.restore_text( kwd.get( 'tool_id', '' ) ) - year, month = map( int, specified_month.split( "-" ) ) - start_date = date( year, month, 1 ) - end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) - return trans.sa_session.query( self.model_class ) \ - .filter( and_( self.model_class.table.c.tool_id == tool_id, - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) \ .enable_eagerloads( False )

class Jobs( BaseController ):

specified_date_list_grid = SpecifiedDateListGrid() - specified_date_in_error_list_grid = SpecifiedDateInErrorListGrid() - all_unfinished_list_grid = AllUnfinishedListGrid() - user_for_month_list_grid = UserForMonthListGrid() - tool_for_month_list_grid = ToolForMonthListGrid()

@web.expose - def specified_date( self, trans, **kwd ): + def specified_date_handler( self, trans, **kwd ): + # We add params to the keyword dict in this method in order to rename the param + # with an "f-" prefix, simulating filtering by clicking a search link. We have + # to take this approach because the "-" character is illegal in HTTP requests. + if 'f-specified_date' in kwd and 'specified_date' not in kwd: + # The user clicked a State link in the Advanced Search box, so 'specified_date' + # will have been eliminated. + pass + elif 'specified_date' not in kwd: + kwd[ 'f-specified_date' ] = 'All' + else: + kwd[ 'f-specified_date' ] = kwd[ 'specified_date' ] if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "job_info": return trans.response.send_redirect( web.url_for( controller='jobs', action='job_info', **kwd ) ) - if operation == "tool_per_month": - # The received id is the job id, so we need to get the jobs tool_id. + elif operation == "tool_for_month": + kwd[ 'f-tool_id' ] = kwd[ 'tool_id' ] + elif operation == "tool_per_month": + # The received id is the job id, so we need to get the job's tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id return trans.response.send_redirect( web.url_for( controller='jobs', action='tool_per_month', **kwd ) ) - if operation == "user_per_month": + elif operation == "user_for_month": + kwd[ 'f-email' ] = util.restore_text( kwd[ 'email' ] ) + elif operation == "user_per_month": # The received id is the job id, so we need to get the id of the user # that submitted the job. job_id = kwd.get( 'id', None ) @@ -196,43 +177,12 @@ class Jobs( BaseController ): return trans.response.send_redirect( web.url_for( controller='jobs', action='user_per_month', **kwd ) ) + elif operation == "specified_date_in_error": + kwd[ 'f-state' ] = 'error' + elif operation == "unfinished": + kwd[ 'f-state' ] = 'Unfinished' return self.specified_date_list_grid( trans, **kwd ) @web.expose - def today_all( self, trans, **kwd ): - kwd[ 'specified_date' ] = datetime.utcnow().strftime( "%Y-%m-%d" ) - return self.specified_date( trans, **kwd ) - @web.expose - def specified_date_in_error( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "job_info": - return trans.response.send_redirect( web.url_for( controller='jobs', - action='job_info', - **kwd ) ) - if operation == "tool_per_month": - # The received id is the job id, so we need to get the jobs tool_id. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'tool_id' ] = job.tool_id - return trans.response.send_redirect( web.url_for( controller='jobs', - action='tool_per_month', - **kwd ) ) - if operation == "user_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'email' ] = None # For anonymous users - if job.history: - if job.history.user: - email = job.history.user.email - kwd[ 'email' ] = email - # TODO: handle libraries - return trans.response.send_redirect( web.url_for( controller='jobs', - action='user_per_month', - **kwd ) ) - return self.specified_date_in_error_list_grid( trans, **kwd ) - @web.expose def specified_month_all( self, trans, **kwd ): params = util.Params( kwd ) message = '' @@ -302,37 +252,6 @@ class Jobs( BaseController ): jobs=jobs, message=message ) @web.expose - def all_unfinished( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "job_info": - return trans.response.send_redirect( web.url_for( controller='jobs', - action='job_info', - **kwd ) ) - if operation == "tool_per_month": - # The received id is the job id, so we need to get the jobs tool_id. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'tool_id' ] = job.tool_id - return trans.response.send_redirect( web.url_for( controller='jobs', - action='tool_per_month', - **kwd ) ) - if operation == "user_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'email' ] = None # For anonymous users - if job.history: - if job.history.user: - email = job.history.user.email - kwd[ 'email' ] = email - # TODO: handle libraries - return trans.response.send_redirect( web.url_for( controller='jobs', - action='user_per_month', - **kwd ) ) - return self.all_unfinished_list_grid( trans, **kwd ) - @web.expose def per_month_all( self, trans, **kwd ): params = util.Params( kwd ) message = '' @@ -414,37 +333,6 @@ class Jobs( BaseController ): email=util.sanitize_text( email ), jobs=jobs, message=message ) @web.expose - def user_for_month( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "job_info": - return trans.response.send_redirect( web.url_for( controller='jobs', - action='job_info', - **kwd ) ) - if operation == "tool_per_month": - # The received id is the job id, so we need to get the jobs tool_id. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'tool_id' ] = job.tool_id - return trans.response.send_redirect( web.url_for( controller='jobs', - action='tool_per_month', - **kwd ) ) - if operation == "user_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'email' ] = None # For anonymous users - if job.history: - if job.history.user: - email = job.history.user.email - kwd[ 'email' ] = email - # TODO: handle libraries - return trans.response.send_redirect( web.url_for( controller='jobs', - action='user_per_month', - **kwd ) ) - return self.user_for_month_list_grid( trans, **kwd ) - @web.expose def per_tool( self, trans, **kwd ): params = util.Params( kwd ) message = '' @@ -484,37 +372,6 @@ class Jobs( BaseController ): jobs=jobs, message=message ) @web.expose - def tool_for_month( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "job_info": - return trans.response.send_redirect( web.url_for( controller='jobs', - action='job_info', - **kwd ) ) - if operation == "tool_per_month": - # The received id is the job id, so we need to get the jobs tool_id. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'tool_id' ] = job.tool_id - return trans.response.send_redirect( web.url_for( controller='jobs', - action='tool_per_month', - **kwd ) ) - if operation == "user_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. - job_id = kwd.get( 'id', None ) - job = get_job( trans, job_id ) - kwd[ 'email' ] = None # For anonymous users - if job.history: - if job.history.user: - email = job.history.user.email - kwd[ 'email' ] = email - # TODO: handle libraries - return trans.response.send_redirect( web.url_for( controller='jobs', - action='user_per_month', - **kwd ) ) - return self.tool_for_month_list_grid( trans, **kwd ) - @web.expose def job_info( self, trans, **kwd ): params = util.Params( kwd ) message = '' @@ -523,9 +380,8 @@ class Jobs( BaseController ): .filter( and_( model.Job.table.c.id == job_id, model.Job.table.c.session_id == model.GalaxySession.table.c.id, model.GalaxySession.table.c.user_id == model.User.table.c.id ) ) \ + .enable_eagerloads( False ) \ .one() - # TODO: for some reason the job_info.id is not the same as job_id in the template, so we need to pass job_id - # This needs to be fixed ASAP! return trans.fill_template( '/webapps/reports/job_info.mako', job_id=job_id, job_info=job_info,

--- a/templates/webapps/reports/job_info.mako +++ b/templates/webapps/reports/job_info.mako @@ -18,7 +18,6 @@ </tr><tr><td>${job_info.state}</td> - ## TODO for some reason, job_info.id is not the job.id <td>${job_id}</td><td>${job_info.create_time}</td><td>${job_info.update_time}</td>

--- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -27,7 +27,7 @@ %endif <td>${job[0]}</td><td>${month_label}&nbsp;${job[3]},&nbsp;${year_label}</td> - <td><a href="${h.url_for( controller='jobs', action='specified_date_in_error', specified_date=job[1] )}">${job[2]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_date_handler', operation='specified_date_in_error', specified_date=job[1] )}">${job[2]}</a></td></tr><% ctr += 1 %> %endfor

--- a/templates/grid_common.mako +++ b/templates/grid_common.mako @@ -67,36 +67,6 @@ <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span></form> - ###################### - ## TODO: eliminate this elif condition when the categorical-filter style in grid_common.mako is fixed to that it no - ## longer mangles the request by eliminating parameters from it before it reaches the server. Since the categorical-filter - ## style is not used here, paging will not work... - ###################### - %elif isinstance( column, StateColumn ): - kwargs: ${kwargs}<br/> - <span id="${column.key}-filtering-criteria"> - %for i, filter in enumerate( column.get_accepted_filters() ): - <% - # HACK: we know that each filter will have only a single argument, so get that single argument. - for key, arg in filter.args.items(): - filter_key = key - filter_arg = arg - %> - %if i > 0: - | - %endif - %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: - <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> - %else: - <% - my_dict = {} - my_dict.update( kwargs ) - my_dict.update( filter.get_url_args() ) - %> - <a href="${url( my_dict )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a> - %endif - %endfor - </span> %else: <span id="${column.key}-filtering-criteria"> %for i, filter in enumerate( column.get_accepted_filters() ):

--- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -161,16 +161,6 @@ });

// Initialize categorical filters. - // #################### - // TODO: This style is used in grid_common.mako to wrap the links created for certain GridColumn - // subclasses ( e.g., DeletedColumn, StateColumn, etc ) where the link labels are generated in the - // class's get_accepted_filters() method. The problem is that when the link is clicked, this style - // will eliminate all request parameters except for those that are included in the cur_filter_dict - // dictionary that is used to build the url_args variable in this template. This process needs to - // be corrected so that the only changes made to the request are updating the values of parameters - // in the request with the new values obtained from cur_filter_dict, leaving all remaining request - // parameters alone. There is another related TODO in the set_categorical_filter() function below. - // #################### $('.categorical-filter > a').each( function() { $(this).click( function() { var filter_key = $(this).attr('filter_key'); @@ -407,11 +397,6 @@ }

// Set new value for categorical filter. - // #################### - // TODO: this function mangles the initial request by eliminating many of the request parameters - // before calling update_grid(). This needs to be fixed - see the TODO in the categorical-filter - // style above. - // #################### function set_categorical_filter(name, new_value) { // Update filter hyperlinks to reflect new filter value. var category_filter = categorical_filters[name];

--- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -61,6 +61,10 @@ </%def><%def name="left_panel()"> + <% + from datetime import datetime + from time import mktime, strftime, localtime + %><div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>Reports</div></div> @@ -73,10 +77,10 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='today_all' )}">Today's jobs</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_date_handler', specified_date=datetime.utcnow().strftime( "%Y-%m-%d" ) )}">Today's jobs</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_all' )}">Jobs per day this month</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Jobs in error per day this month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='all_unfinished' )}">All unfinished jobs</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_date_handler', operation='unfinished' )}">All unfinished jobs</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_all' )}">Jobs per month</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Jobs in error per month</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user' )}">Jobs per user</a></div>

--- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -25,7 +25,7 @@ <tr class="tr"> %endif <td>${job[2]}&nbsp;${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='tool_for_month', tool_id=tool_id, specified_date=job[0]+'-01' )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_date_handler', operation='tool_for_month', tool_id=tool_id, specified_date=job[0] )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor

--- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -31,7 +31,7 @@ <td>${month_label}&nbsp;${job[5]},&nbsp;${year_label}</td><td>${job[2]}</td><td>${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='specified_date', specified_date=job[1], webapp='reports' )}">${job[4]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_date_handler', specified_date=job[1], webapp='reports' )}">${job[4]}</a></td></tr><% ctr += 1 %> %endfor