[2] | 1 | from galaxy.web.base.controller import * |
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| 2 | from galaxy.web.framework.helpers import time_ago, iff, grids |
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| 3 | from galaxy.model.orm import * |
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| 4 | from galaxy import model, util |
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| 5 | from galaxy.web.form_builder import * |
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| 6 | import logging, os, csv |
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| 7 | |
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| 8 | log = logging.getLogger( __name__ ) |
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| 9 | |
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| 10 | class RequestsGrid( grids.Grid ): |
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| 11 | # Custom column types |
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| 12 | class NameColumn( grids.TextColumn ): |
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| 13 | def get_value( self, trans, grid, request ): |
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| 14 | return request.name |
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| 15 | class DescriptionColumn( grids.TextColumn ): |
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| 16 | def get_value(self, trans, grid, request): |
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| 17 | return request.desc |
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| 18 | class SamplesColumn( grids.GridColumn ): |
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| 19 | def get_value(self, trans, grid, request): |
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| 20 | return str( len( request.samples ) ) |
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| 21 | class TypeColumn( grids.TextColumn ): |
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| 22 | def get_value( self, trans, grid, request ): |
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| 23 | return request.type.name |
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| 24 | class StateColumn( grids.StateColumn ): |
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| 25 | def get_value(self, trans, grid, request ): |
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| 26 | state = request.state |
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| 27 | if state == request.states.REJECTED: |
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| 28 | state_color = 'error' |
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| 29 | elif state == request.states.NEW: |
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| 30 | state_color = 'new' |
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| 31 | elif state == request.states.SUBMITTED: |
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| 32 | state_color = 'running' |
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| 33 | elif state == request.states.COMPLETE: |
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| 34 | state_color = 'ok' |
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| 35 | else: |
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| 36 | state_color = state |
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| 37 | return '<div class="count-box state-color-%s">%s</div>' % ( state_color, state ) |
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| 38 | def filter( self, trans, user, query, column_filter ): |
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| 39 | """ Modify query to filter request by state. """ |
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| 40 | if column_filter == "All": |
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| 41 | return query |
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| 42 | if column_filter: |
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| 43 | return query.join( model.RequestEvent.table ) \ |
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| 44 | .filter( self.model_class.table.c.id == model.RequestEvent.table.c.request_id ) \ |
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| 45 | .filter( model.RequestEvent.table.c.state == column_filter ) \ |
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| 46 | .filter( model.RequestEvent.table.c.id.in_( select( columns=[ func.max( model.RequestEvent.table.c.id ) ], |
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| 47 | from_obj=model.RequestEvent.table, |
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| 48 | group_by=model.RequestEvent.table.c.request_id ) ) ) |
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| 49 | def get_accepted_filters( self ): |
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| 50 | """ Returns a list of accepted filters for this column. """ |
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| 51 | # TODO: is this method necessary? |
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| 52 | accepted_filter_labels_and_vals = [ model.Request.states.get( state ) for state in model.Request.states ] |
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| 53 | accepted_filter_labels_and_vals.append( "All" ) |
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| 54 | accepted_filters = [] |
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| 55 | for val in accepted_filter_labels_and_vals: |
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| 56 | label = val.lower() |
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| 57 | args = { self.key: val } |
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| 58 | accepted_filters.append( grids.GridColumnFilter( label, args ) ) |
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| 59 | return accepted_filters |
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| 60 | |
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| 61 | # Grid definition |
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| 62 | title = "Sequencing Requests" |
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| 63 | template = "requests/grid.mako" |
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| 64 | model_class = model.Request |
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| 65 | default_sort_key = "-update_time" |
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| 66 | num_rows_per_page = 50 |
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| 67 | preserve_state = True |
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| 68 | use_paging = True |
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| 69 | default_filter = dict( state="All", deleted="False" ) |
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| 70 | columns = [ |
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| 71 | NameColumn( "Name", |
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| 72 | key="name", |
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| 73 | link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ), |
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| 74 | attach_popup=True, |
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| 75 | filterable="advanced" ), |
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| 76 | DescriptionColumn( "Description", |
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| 77 | key='desc', |
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| 78 | filterable="advanced" ), |
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| 79 | SamplesColumn( "Samples", |
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| 80 | link=( lambda item: iff( item.deleted, None, dict( operation="manage_request", id=item.id ) ) ) ), |
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| 81 | TypeColumn( "Sequencer", |
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| 82 | link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ) ), |
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| 83 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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| 84 | grids.DeletedColumn( "Deleted", |
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| 85 | key="deleted", |
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| 86 | visible=False, |
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| 87 | filterable="advanced" ), |
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| 88 | StateColumn( "State", |
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| 89 | key='state', |
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| 90 | filterable="advanced", |
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| 91 | link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) |
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| 92 | ) |
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| 93 | ] |
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| 94 | columns.append( grids.MulticolFilterColumn( "Search", |
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| 95 | cols_to_filter=[ columns[0], columns[1] ], |
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| 96 | key="free-text-search", |
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| 97 | visible=False, |
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| 98 | filterable="standard" ) ) |
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| 99 | operations = [ |
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| 100 | grids.GridOperation( "Submit", |
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| 101 | allow_multiple=False, |
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| 102 | condition=( lambda item: not item.deleted and item.is_unsubmitted and item.samples ), |
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| 103 | confirm="Samples cannot be added to this request after it is submitted. Click OK to submit." ) |
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| 104 | ] |
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| 105 | |
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| 106 | class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): |
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| 107 | @web.json |
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| 108 | def sample_state_updates( self, trans, ids=None, states=None ): |
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| 109 | # Avoid caching |
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| 110 | trans.response.headers['Pragma'] = 'no-cache' |
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| 111 | trans.response.headers['Expires'] = '0' |
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| 112 | # Create new HTML for any that have changed |
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| 113 | rval = {} |
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| 114 | if ids is not None and states is not None: |
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| 115 | ids = map( int, ids.split( "," ) ) |
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| 116 | states = states.split( "," ) |
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| 117 | for id, state in zip( ids, states ): |
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| 118 | sample = trans.sa_session.query( self.app.model.Sample ).get( id ) |
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| 119 | if sample.state.name != state: |
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| 120 | rval[ id ] = { "state": sample.state.name, |
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| 121 | "datasets": len( sample.datasets ), |
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| 122 | "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", |
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| 123 | sample=sample), |
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| 124 | 'utf-8' ), |
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| 125 | "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", |
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| 126 | sample=sample ), |
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| 127 | 'utf-8' ) } |
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| 128 | return rval |
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| 129 | @web.expose |
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| 130 | @web.require_login( "create sequencing requests" ) |
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| 131 | def create_request( self, trans, cntrller, **kwd ): |
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| 132 | params = util.Params( kwd ) |
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| 133 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
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| 134 | message = util.restore_text( params.get( 'message', '' ) ) |
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| 135 | status = params.get( 'status', 'done' ) |
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| 136 | request_type_id = params.get( 'request_type_id', 'none' ) |
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| 137 | if request_type_id != 'none': |
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| 138 | request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) |
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| 139 | else: |
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| 140 | request_type = None |
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| 141 | # user_id will not be 'none' if an admin user is submitting this request on behalf of another user |
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| 142 | # and they selected that user's id from the user_id SelectField. |
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| 143 | user_id_encoded = True |
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| 144 | user_id = params.get( 'user_id', 'none' ) |
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| 145 | if user_id != 'none': |
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| 146 | try: |
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| 147 | user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) |
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| 148 | except TypeError, e: |
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| 149 | # We must have an email address rather than an encoded user id |
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| 150 | # This is because the galaxy.base.js creates a search+select box |
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| 151 | # when there are more than 20 items in a selectfield |
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| 152 | user = trans.sa_session.query( trans.model.User ) \ |
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| 153 | .filter( trans.model.User.table.c.email==util.restore_text( user_id ) ) \ |
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| 154 | .first() |
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| 155 | user_id_encoded = False |
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| 156 | |
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| 157 | elif not is_admin: |
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| 158 | user = trans.user |
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| 159 | else: |
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| 160 | user = None |
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| 161 | if params.get( 'create_request_button', False ) or params.get( 'add_sample_button', False ): |
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| 162 | name = util.restore_text( params.get( 'name', '' ) ) |
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| 163 | if is_admin and user_id == 'none': |
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| 164 | message = 'Select the user on behalf of whom you are submitting this request.' |
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| 165 | status = 'error' |
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| 166 | elif user is None: |
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| 167 | message = 'Invalid user ID (%s)' % str(user_id) |
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| 168 | status = 'error' |
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| 169 | elif not name: |
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| 170 | message = 'Enter the name of the request.' |
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| 171 | status = 'error' |
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| 172 | else: |
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| 173 | request = self.__save_request( trans, cntrller, **kwd ) |
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| 174 | message = 'The request has been created.' |
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| 175 | if params.get( 'create_request_button', False ): |
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| 176 | return trans.response.send_redirect( web.url_for( controller=cntrller, |
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| 177 | action='browse_requests', |
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| 178 | message=message , |
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| 179 | status='done' ) ) |
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| 180 | elif params.get( 'add_sample_button', False ): |
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| 181 | return self.__add_sample( trans, cntrller, request, **kwd ) |
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| 182 | request_type_select_field = self.__build_request_type_id_select_field( trans, selected_value=request_type_id ) |
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| 183 | # Widgets to be rendered on the request form |
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| 184 | widgets = [] |
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| 185 | if request_type is not None or status == 'error': |
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| 186 | # Either the user selected a request_type or an error exists on the form. |
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| 187 | widgets.append( dict( label='Name of the Experiment', |
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| 188 | widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ), |
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| 189 | helptext='(Required)') ) |
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| 190 | widgets.append( dict( label='Description', |
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| 191 | widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) )), |
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| 192 | helptext='(Optional)') ) |
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| 193 | if request_type is not None: |
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| 194 | widgets += request_type.request_form.get_widgets( user, **kwd ) |
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| 195 | # In case there is an error on the form, make sure to populate widget fields with anything the user |
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| 196 | # may have already entered. |
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| 197 | self.populate_widgets_from_kwd( trans, widgets, **kwd ) |
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| 198 | if request_type is not None or status == 'error': |
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| 199 | # Either the user selected a request_type or an error exists on the form. |
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| 200 | if is_admin: |
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| 201 | if not user_id_encoded: |
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| 202 | selected_user_id = trans.security.encode_id( user.id ) |
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| 203 | else: |
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| 204 | selected_user_id = user_id |
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| 205 | user_widget = dict( label='Select user', |
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| 206 | widget=self.__build_user_id_select_field( trans, selected_value=selected_user_id ), |
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| 207 | helptext='Submit the request on behalf of the selected user (Required)') |
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| 208 | widgets = [ user_widget ] + widgets |
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| 209 | return trans.fill_template( '/requests/common/create_request.mako', |
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| 210 | cntrller=cntrller, |
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| 211 | request_type_select_field=request_type_select_field, |
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| 212 | request_type_select_field_selected=request_type_id, |
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| 213 | widgets=widgets, |
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| 214 | message=message, |
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| 215 | status=status ) |
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| 216 | @web.expose |
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| 217 | @web.require_login( "edit sequencing requests" ) |
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| 218 | def edit_basic_request_info( self, trans, cntrller, **kwd ): |
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| 219 | params = util.Params( kwd ) |
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| 220 | message = util.restore_text( params.get( 'message', '' ) ) |
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| 221 | status = params.get( 'status', 'done' ) |
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| 222 | request_id = params.get( 'id', None ) |
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| 223 | try: |
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| 224 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
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| 225 | except: |
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| 226 | return invalid_id_redirect( trans, cntrller, request_id ) |
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| 227 | name = util.restore_text( params.get( 'name', '' ) ) |
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| 228 | desc = util.restore_text( params.get( 'desc', '' ) ) |
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| 229 | if params.get( 'edit_basic_request_info_button', False ) or params.get( 'edit_samples_button', False ): |
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| 230 | if not name: |
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| 231 | status = 'error' |
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| 232 | message = 'Enter the name of the request' |
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| 233 | else: |
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| 234 | request = self.__save_request( trans, cntrller, request=request, **kwd ) |
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| 235 | message = 'The changes made to request (%s) have been saved.' % request.name |
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| 236 | # Widgets to be rendered on the request form |
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| 237 | widgets = [] |
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| 238 | widgets.append( dict( label='Name', |
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| 239 | widget=TextField( 'name', 40, request.name ), |
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| 240 | helptext='(Required)' ) ) |
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| 241 | widgets.append( dict( label='Description', |
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| 242 | widget=TextField( 'desc', 40, request.desc ), |
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| 243 | helptext='(Optional)' ) ) |
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| 244 | widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd ) |
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| 245 | # In case there is an error on the form, make sure to populate widget fields with anything the user |
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| 246 | # may have already entered. |
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| 247 | self.populate_widgets_from_kwd( trans, widgets, **kwd ) |
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| 248 | return trans.fill_template( 'requests/common/edit_basic_request_info.mako', |
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| 249 | cntrller=cntrller, |
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| 250 | request_type=request.type, |
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| 251 | request=request, |
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| 252 | widgets=widgets, |
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| 253 | message=message, |
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| 254 | status=status ) |
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| 255 | def __save_request( self, trans, cntrller, request=None, **kwd ): |
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| 256 | """ |
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| 257 | Saves changes to an existing request, or creates a new |
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| 258 | request if received request is None. |
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| 259 | """ |
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| 260 | params = util.Params( kwd ) |
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| 261 | request_type_id = params.get( 'request_type_id', None ) |
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| 262 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
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| 263 | if request is None: |
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| 264 | # We're creating a new request, so we need the associated request_type |
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| 265 | request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) |
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| 266 | if is_admin: |
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| 267 | # The admin user is creating a request on behalf of another user |
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| 268 | user_id = params.get( 'user_id', '' ) |
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| 269 | user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) |
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| 270 | else: |
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| 271 | user = trans.user |
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| 272 | else: |
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| 273 | # We're saving changes to an existing request |
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| 274 | user = request.user |
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| 275 | request_type = request.type |
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| 276 | name = util.restore_text( params.get( 'name', '' ) ) |
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| 277 | desc = util.restore_text( params.get( 'desc', '' ) ) |
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| 278 | notification = dict( email=[ user.email ], sample_states=[ request_type.state.id ], body='', subject='' ) |
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| 279 | values = [] |
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| 280 | for index, field in enumerate( request_type.request_form.fields ): |
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| 281 | field_type = field[ 'type' ] |
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| 282 | field_value = params.get( 'field_%i' % index, '' ) |
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| 283 | if field[ 'type' ] == 'AddressField': |
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| 284 | value = util.restore_text( field_value ) |
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| 285 | if value == 'new': |
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| 286 | # Save this new address in the list of this user's addresses |
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| 287 | user_address = trans.model.UserAddress( user=user ) |
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| 288 | self.save_widget_field( trans, user_address, index, **kwd ) |
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| 289 | trans.sa_session.refresh( user ) |
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| 290 | values.append( int( user_address.id ) ) |
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| 291 | elif value in [ '', 'none', 'None', None ]: |
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| 292 | values.append( '' ) |
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| 293 | else: |
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| 294 | values.append( int( value ) ) |
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| 295 | elif field[ 'type' ] == 'CheckboxField': |
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| 296 | values.append( CheckboxField.is_checked( field_value )) |
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| 297 | else: |
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| 298 | values.append( util.restore_text( field_value ) ) |
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| 299 | form_values = trans.model.FormValues( request_type.request_form, values ) |
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| 300 | trans.sa_session.add( form_values ) |
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| 301 | trans.sa_session.flush() |
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| 302 | if request is None: |
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| 303 | # We're creating a new request |
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| 304 | request = trans.model.Request( name, desc, request_type, user, form_values, notification ) |
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| 305 | trans.sa_session.add( request ) |
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| 306 | trans.sa_session.flush() |
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| 307 | trans.sa_session.refresh( request ) |
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| 308 | # Create an event with state 'New' for this new request |
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| 309 | if request.user != trans.user: |
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| 310 | sample_event_comment = "Request created by user %s for user %s." % ( trans.user.email, request.user.email ) |
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| 311 | else: |
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| 312 | sample_event_comment = "Request created." |
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| 313 | event = trans.model.RequestEvent( request, request.states.NEW, sample_event_comment ) |
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| 314 | trans.sa_session.add( event ) |
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| 315 | trans.sa_session.flush() |
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| 316 | else: |
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| 317 | # We're saving changes to an existing request |
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| 318 | request.name = name |
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| 319 | request.desc = desc |
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| 320 | request.type = request_type |
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| 321 | request.user = user |
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| 322 | request.notification = notification |
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| 323 | request.values = form_values |
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| 324 | trans.sa_session.add( request ) |
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| 325 | trans.sa_session.flush() |
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| 326 | return request |
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| 327 | @web.expose |
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| 328 | @web.require_login( "submit sequencing requests" ) |
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| 329 | def submit_request( self, trans, cntrller, **kwd ): |
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| 330 | params = util.Params( kwd ) |
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| 331 | request_id = params.get( 'id', None ) |
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| 332 | message = util.restore_text( params.get( 'message', '' ) ) |
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| 333 | status = util.restore_text( params.get( 'status', 'done' ) ) |
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| 334 | try: |
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| 335 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
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| 336 | except: |
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| 337 | return invalid_id_redirect( trans, cntrller, request_id ) |
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| 338 | ok = True |
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| 339 | if not request.samples: |
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| 340 | message = 'Add at least 1 sample to this request before submitting.' |
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| 341 | ok = False |
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| 342 | if ok: |
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| 343 | message = self.__validate_request( trans, cntrller, request ) |
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| 344 | if message or not ok: |
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| 345 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
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| 346 | action='edit_basic_request_info', |
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| 347 | cntrller=cntrller, |
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| 348 | id = request_id, |
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| 349 | status='error', |
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| 350 | message=message ) ) |
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| 351 | # Change the request state to 'Submitted' |
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| 352 | if request.user.email is not trans.user: |
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| 353 | sample_event_comment = "Request submitted by %s on behalf of %s." % ( trans.user.email, request.user.email ) |
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| 354 | else: |
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| 355 | sample_event_comment = "" |
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| 356 | event = trans.model.RequestEvent( request, request.states.SUBMITTED, sample_event_comment ) |
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| 357 | trans.sa_session.add( event ) |
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| 358 | # change the state of each of the samples of thus request |
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| 359 | new_state = request.type.states[0] |
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| 360 | for sample in request.samples: |
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| 361 | event = trans.model.SampleEvent( sample, new_state, 'Samples created.' ) |
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| 362 | trans.sa_session.add( event ) |
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| 363 | trans.sa_session.add( request ) |
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| 364 | trans.sa_session.flush() |
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| 365 | request.send_email_notification( trans, new_state ) |
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| 366 | message = 'The request has been submitted.' |
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| 367 | return trans.response.send_redirect( web.url_for( controller=cntrller, |
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| 368 | action='browse_requests', |
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| 369 | cntrller=cntrller, |
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| 370 | id=request_id, |
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| 371 | status=status, |
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| 372 | message=message ) ) |
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| 373 | @web.expose |
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| 374 | @web.require_login( "sequencing request page" ) |
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| 375 | def manage_request( self, trans, cntrller, **kwd ): |
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| 376 | params = util.Params( kwd ) |
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| 377 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
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| 378 | message = util.restore_text( params.get( 'message', '' ) ) |
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| 379 | status = params.get( 'status', 'done' ) |
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| 380 | request_id = params.get( 'id', None ) |
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| 381 | try: |
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| 382 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
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| 383 | except: |
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| 384 | return invalid_id_redirect( trans, cntrller, request_id ) |
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| 385 | sample_state_id = params.get( 'sample_state_id', None ) |
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| 386 | # Get the user entered sample information |
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| 387 | current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) |
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| 388 | selected_samples = self.__get_selected_samples( trans, request, **kwd ) |
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| 389 | selected_value = params.get( 'sample_operation', 'none' ) |
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| 390 | if selected_value != 'none' and not selected_samples: |
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| 391 | message = 'Select at least one sample before selecting an operation.' |
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| 392 | status = 'error' |
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| 393 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
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| 394 | action='manage_request', |
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| 395 | cntrller=cntrller, |
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| 396 | id=request_id, |
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| 397 | status=status, |
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| 398 | message=message ) ) |
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| 399 | sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) |
---|
| 400 | sample_operation_selected_value = sample_operation_select_field.get_selected( return_value=True ) |
---|
| 401 | if params.get( 'import_samples_button', False ): |
---|
| 402 | # Import sample field values from a csv file |
---|
| 403 | return self.__import_samples( trans, cntrller, request, current_samples, libraries, **kwd ) |
---|
| 404 | elif params.get( 'add_sample_button', False ): |
---|
| 405 | return self.__add_sample( trans, cntrller, request, **kwd ) |
---|
| 406 | elif params.get( 'save_samples_button', False ): |
---|
| 407 | return self.__save_sample( trans, cntrller, request, current_samples, **kwd ) |
---|
| 408 | elif params.get( 'edit_samples_button', False ): |
---|
| 409 | managing_samples = True |
---|
| 410 | elif params.get( 'cancel_changes_button', False ): |
---|
| 411 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 412 | action='manage_request', |
---|
| 413 | cntrller=cntrller, |
---|
| 414 | id=request_id ) ) |
---|
| 415 | pass |
---|
| 416 | elif params.get( 'change_state_button', False ): |
---|
| 417 | sample_event_comment = util.restore_text( params.get( 'sample_event_comment', '' ) ) |
---|
| 418 | new_state = trans.sa_session.query( trans.model.SampleState ).get( trans.security.decode_id( sample_state_id ) ) |
---|
| 419 | for sample_id in selected_samples: |
---|
| 420 | sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) |
---|
| 421 | event = trans.model.SampleEvent( sample, new_state, sample_event_comment ) |
---|
| 422 | trans.sa_session.add( event ) |
---|
| 423 | trans.sa_session.flush() |
---|
| 424 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 425 | cntrller=cntrller, |
---|
| 426 | action='update_request_state', |
---|
| 427 | request_id=request_id ) ) |
---|
| 428 | elif params.get( 'cancel_change_state_button', False ): |
---|
| 429 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 430 | action='manage_request', |
---|
| 431 | cntrller=cntrller, |
---|
| 432 | id=request_id ) ) |
---|
| 433 | elif params.get( 'change_lib_button', False ): |
---|
| 434 | library_id = params.get( 'sample_0_library_id', None ) |
---|
| 435 | try: |
---|
| 436 | library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) |
---|
| 437 | except: |
---|
| 438 | invalid_id_redirect( trans, cntrller, library_id ) |
---|
| 439 | folder_id = params.get( 'sample_0_folder_id', None ) |
---|
| 440 | try: |
---|
| 441 | folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) |
---|
| 442 | except: |
---|
| 443 | invalid_id_redirect( trans, cntrller, folder_id ) |
---|
| 444 | for sample_id in selected_samples: |
---|
| 445 | sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) |
---|
| 446 | sample.library = library |
---|
| 447 | sample.folder = folder |
---|
| 448 | trans.sa_session.add( sample ) |
---|
| 449 | trans.sa_session.flush() |
---|
| 450 | trans.sa_session.refresh( request ) |
---|
| 451 | message = 'Changes made to the selected samples have been saved. ' |
---|
| 452 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 453 | action='manage_request', |
---|
| 454 | cntrller=cntrller, |
---|
| 455 | id=request_id, |
---|
| 456 | status=status, |
---|
| 457 | message=message ) ) |
---|
| 458 | elif params.get( 'cancel_change_lib_button', False ): |
---|
| 459 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 460 | action='manage_request', |
---|
| 461 | cntrller=cntrller, |
---|
| 462 | id=trans.security.encode_id( request.id ) ) ) |
---|
| 463 | request_widgets = self.__get_request_widgets( trans, request.id ) |
---|
| 464 | sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) |
---|
| 465 | libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, |
---|
| 466 | request.user, |
---|
| 467 | 0, |
---|
| 468 | libraries, |
---|
| 469 | None, |
---|
| 470 | **kwd ) |
---|
| 471 | # Build the sample_state_id_select_field SelectField |
---|
| 472 | sample_state_id_select_field = self.__build_sample_state_id_select_field( trans, request, sample_state_id ) |
---|
| 473 | return trans.fill_template( '/requests/common/manage_request.mako', |
---|
| 474 | cntrller=cntrller, |
---|
| 475 | request=request, |
---|
| 476 | selected_samples=selected_samples, |
---|
| 477 | request_widgets=request_widgets, |
---|
| 478 | current_samples=current_samples, |
---|
| 479 | sample_copy=sample_copy, |
---|
| 480 | libraries=libraries, |
---|
| 481 | sample_operation_select_field=sample_operation_select_field, |
---|
| 482 | libraries_select_field=libraries_select_field, |
---|
| 483 | folders_select_field=folders_select_field, |
---|
| 484 | sample_state_id_select_field=sample_state_id_select_field, |
---|
| 485 | managing_samples=managing_samples, |
---|
| 486 | status=status, |
---|
| 487 | message=message ) |
---|
| 488 | @web.expose |
---|
| 489 | @web.require_login( "delete sequencing requests" ) |
---|
| 490 | def delete_request( self, trans, cntrller, **kwd ): |
---|
| 491 | params = util.Params( kwd ) |
---|
| 492 | id_list = util.listify( kwd.get( 'id', '' ) ) |
---|
| 493 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 494 | status = util.restore_text( params.get( 'status', 'done' ) ) |
---|
| 495 | num_deleted = 0 |
---|
| 496 | for id in id_list: |
---|
| 497 | ok_for_now = True |
---|
| 498 | try: |
---|
| 499 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) |
---|
| 500 | except: |
---|
| 501 | message += "Invalid request ID (%s). " % str( id ) |
---|
| 502 | status = 'error' |
---|
| 503 | ok_for_now = False |
---|
| 504 | if ok_for_now: |
---|
| 505 | request.deleted = True |
---|
| 506 | trans.sa_session.add( request ) |
---|
| 507 | # delete all the samples belonging to this request |
---|
| 508 | for s in request.samples: |
---|
| 509 | s.deleted = True |
---|
| 510 | trans.sa_session.add( s ) |
---|
| 511 | trans.sa_session.flush() |
---|
| 512 | num_deleted += 1 |
---|
| 513 | message += '%i requests have been deleted.' % num_deleted |
---|
| 514 | return trans.response.send_redirect( web.url_for( controller=cntrller, |
---|
| 515 | action='browse_requests', |
---|
| 516 | status=status, |
---|
| 517 | message=message ) ) |
---|
| 518 | @web.expose |
---|
| 519 | @web.require_login( "undelete sequencing requests" ) |
---|
| 520 | def undelete_request( self, trans, cntrller, **kwd ): |
---|
| 521 | params = util.Params( kwd ) |
---|
| 522 | id_list = util.listify( kwd.get( 'id', '' ) ) |
---|
| 523 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 524 | status = util.restore_text( params.get( 'status', 'done' ) ) |
---|
| 525 | num_undeleted = 0 |
---|
| 526 | for id in id_list: |
---|
| 527 | ok_for_now = True |
---|
| 528 | try: |
---|
| 529 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) |
---|
| 530 | except: |
---|
| 531 | message += "Invalid request ID (%s). " % str( id ) |
---|
| 532 | status = 'error' |
---|
| 533 | ok_for_now = False |
---|
| 534 | if ok_for_now: |
---|
| 535 | request.deleted = False |
---|
| 536 | trans.sa_session.add( request ) |
---|
| 537 | # undelete all the samples belonging to this request |
---|
| 538 | for s in request.samples: |
---|
| 539 | s.deleted = False |
---|
| 540 | trans.sa_session.add( s ) |
---|
| 541 | trans.sa_session.flush() |
---|
| 542 | num_undeleted += 1 |
---|
| 543 | message += '%i requests have been undeleted.' % num_undeleted |
---|
| 544 | return trans.response.send_redirect( web.url_for( controller=cntrller, |
---|
| 545 | action='browse_requests', |
---|
| 546 | status=status, |
---|
| 547 | message=message ) ) |
---|
| 548 | @web.expose |
---|
| 549 | @web.require_login( "sequencing request events" ) |
---|
| 550 | def request_events( self, trans, cntrller, **kwd ): |
---|
| 551 | params = util.Params( kwd ) |
---|
| 552 | request_id = params.get( 'id', None ) |
---|
| 553 | try: |
---|
| 554 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
---|
| 555 | except: |
---|
| 556 | return invalid_id_redirect( trans, cntrller, request_id ) |
---|
| 557 | events_list = [] |
---|
| 558 | for event in request.events: |
---|
| 559 | events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) |
---|
| 560 | return trans.fill_template( '/requests/common/events.mako', |
---|
| 561 | cntrller=cntrller, |
---|
| 562 | events_list=events_list, |
---|
| 563 | request=request ) |
---|
| 564 | @web.expose |
---|
| 565 | @web.require_login( "edit email notification settings" ) |
---|
| 566 | def edit_email_settings( self, trans, cntrller, **kwd ): |
---|
| 567 | """ |
---|
| 568 | Allow for changing the email notification settings where email is sent to a list of users |
---|
| 569 | whenever the request state changes to one selected for notification. |
---|
| 570 | """ |
---|
| 571 | params = util.Params( kwd ) |
---|
| 572 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 573 | status = params.get( 'status', 'done' ) |
---|
| 574 | request_id = params.get( 'id', None ) |
---|
| 575 | try: |
---|
| 576 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
---|
| 577 | except: |
---|
| 578 | return invalid_id_redirect( trans, cntrller, request_id ) |
---|
| 579 | email_address = CheckboxField.is_checked( params.get( 'email_address', '' ) ) |
---|
| 580 | additional_email_addresses = params.get( 'additional_email_addresses', '' ) |
---|
| 581 | # Get the list of checked sample state CheckBoxFields |
---|
| 582 | checked_sample_states = [] |
---|
| 583 | for index, sample_state in enumerate( request.type.states ): |
---|
| 584 | if CheckboxField.is_checked( params.get( 'sample_state_%i' % sample_state.id, '' ) ): |
---|
| 585 | checked_sample_states.append( sample_state.id ) |
---|
| 586 | if additional_email_addresses: |
---|
| 587 | additional_email_addresses = additional_email_addresses.split( '\r\n' ) |
---|
| 588 | if email_address or additional_email_addresses: |
---|
| 589 | # The user added 1 or more email addresses |
---|
| 590 | email_addresses = [] |
---|
| 591 | if email_address: |
---|
| 592 | email_addresses.append( request.user.email ) |
---|
| 593 | for email_address in additional_email_addresses: |
---|
| 594 | email_addresses.append( util.restore_text( email_address ) ) |
---|
| 595 | # Make sure email addresses are valid |
---|
| 596 | err_msg = '' |
---|
| 597 | for email_address in email_addresses: |
---|
| 598 | err_msg += self.__validate_email( email_address ) |
---|
| 599 | if err_msg: |
---|
| 600 | status = 'error' |
---|
| 601 | message += err_msg |
---|
| 602 | else: |
---|
| 603 | request.notification = dict( email=email_addresses, |
---|
| 604 | sample_states=checked_sample_states, |
---|
| 605 | body='', |
---|
| 606 | subject='' ) |
---|
| 607 | else: |
---|
| 608 | # The user may have eliminated email addresses that were previously set |
---|
| 609 | request.notification = None |
---|
| 610 | if checked_sample_states: |
---|
| 611 | message = 'All sample states have been unchecked since no email addresses have been selected or entered. ' |
---|
| 612 | trans.sa_session.add( request ) |
---|
| 613 | trans.sa_session.flush() |
---|
| 614 | trans.sa_session.refresh( request ) |
---|
| 615 | message += 'The changes made to the email notification settings have been saved.' |
---|
| 616 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 617 | action='edit_basic_request_info', |
---|
| 618 | cntrller=cntrller, |
---|
| 619 | id=request_id, |
---|
| 620 | message=message , |
---|
| 621 | status=status ) ) |
---|
| 622 | @web.expose |
---|
| 623 | @web.require_login( "update sequencing request state" ) |
---|
| 624 | def update_request_state( self, trans, cntrller, **kwd ): |
---|
| 625 | params = util.Params( kwd ) |
---|
| 626 | message = params.get( 'message', '' ) |
---|
| 627 | status = params.get( 'status', 'done' ) |
---|
| 628 | request_id = params.get( 'request_id', None ) |
---|
| 629 | try: |
---|
| 630 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
---|
| 631 | except: |
---|
| 632 | return invalid_id_redirect( trans, cntrller, request_id ) |
---|
| 633 | # Make sure all the samples of the current request have the same state |
---|
| 634 | common_state = request.samples_have_common_state |
---|
| 635 | if not common_state: |
---|
| 636 | # If the current request state is complete and one of its samples moved from |
---|
| 637 | # the final sample state, then move the request state to In-progress |
---|
| 638 | if request.is_complete: |
---|
| 639 | message = "At least 1 sample state moved from the final sample state, so now the request is in the '%s' state" % request.states.SUBMITTED |
---|
| 640 | event = trans.model.RequestEvent( request, request.states.SUBMITTED, message ) |
---|
| 641 | trans.sa_session.add( event ) |
---|
| 642 | trans.sa_session.flush() |
---|
| 643 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 644 | action='manage_request', |
---|
| 645 | cntrller=cntrller, |
---|
| 646 | id=request_id, |
---|
| 647 | status=status, |
---|
| 648 | message=message ) ) |
---|
| 649 | final_state = False |
---|
| 650 | request_type_state = request.type.state |
---|
| 651 | if common_state.id == request_type_state.id: |
---|
| 652 | # since all the samples are in the final state, change the request state to 'Complete' |
---|
| 653 | comments = "All samples of this request are in the last sample state (%s). " % request_type_state.name |
---|
| 654 | state = request.states.COMPLETE |
---|
| 655 | final_state = True |
---|
| 656 | else: |
---|
| 657 | comments = "All samples are in %s state. " % common_state.name |
---|
| 658 | state = request.states.SUBMITTED |
---|
| 659 | event = trans.model.RequestEvent(request, state, comments) |
---|
| 660 | trans.sa_session.add( event ) |
---|
| 661 | trans.sa_session.flush() |
---|
| 662 | # check if an email notification is configured to be sent when the samples |
---|
| 663 | # are in this state |
---|
| 664 | retval = request.send_email_notification( trans, common_state, final_state ) |
---|
| 665 | if retval: |
---|
| 666 | message = comments + retval |
---|
| 667 | else: |
---|
| 668 | message = comments |
---|
| 669 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 670 | action='manage_request', |
---|
| 671 | cntrller=cntrller, |
---|
| 672 | id=trans.security.encode_id(request.id), |
---|
| 673 | status='done', |
---|
| 674 | message=message ) ) |
---|
| 675 | def __save_sample( self, trans, cntrller, request, current_samples, **kwd ): |
---|
| 676 | # Save all the new/unsaved samples entered by the user |
---|
| 677 | params = util.Params( kwd ) |
---|
| 678 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 679 | status = params.get( 'status', 'done' ) |
---|
| 680 | managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) |
---|
| 681 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
---|
| 682 | selected_value = params.get( 'sample_operation', 'none' ) |
---|
| 683 | # Check for duplicate sample names |
---|
| 684 | message = '' |
---|
| 685 | for index in range( len( current_samples ) - len( request.samples ) ): |
---|
| 686 | sample_index = index + len( request.samples ) |
---|
| 687 | current_sample = current_samples[ sample_index ] |
---|
| 688 | sample_name = current_sample[ 'name' ] |
---|
| 689 | if not sample_name.strip(): |
---|
| 690 | message = 'Enter the name of sample number %i' % sample_index |
---|
| 691 | break |
---|
| 692 | count = 0 |
---|
| 693 | for i in range( len( current_samples ) ): |
---|
| 694 | if sample_name == current_samples[ i ][ 'name' ]: |
---|
| 695 | count += 1 |
---|
| 696 | if count > 1: |
---|
| 697 | message = "This request has %i samples with the name (%s). Samples belonging to a request must have unique names." % ( count, sample_name ) |
---|
| 698 | break |
---|
| 699 | if message: |
---|
| 700 | selected_samples = self.__get_selected_samples( trans, request, **kwd ) |
---|
| 701 | request_widgets = self.__get_request_widgets( trans, request.id ) |
---|
| 702 | sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) |
---|
| 703 | sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) |
---|
| 704 | status = 'error' |
---|
| 705 | return trans.fill_template( '/requests/common/manage_request.mako', |
---|
| 706 | cntrller=cntrller, |
---|
| 707 | request=request, |
---|
| 708 | selected_samples=selected_samples, |
---|
| 709 | request_widgets=request_widgets, |
---|
| 710 | current_samples=current_samples, |
---|
| 711 | sample_copy=sample_copy, |
---|
| 712 | managing_samples=managing_samples, |
---|
| 713 | sample_operation_select_field=sample_operation_select_field, |
---|
| 714 | status=status, |
---|
| 715 | message=message ) |
---|
| 716 | if not managing_samples: |
---|
| 717 | for index in range( len( current_samples ) - len( request.samples ) ): |
---|
| 718 | sample_index = len( request.samples ) |
---|
| 719 | current_sample = current_samples[ sample_index ] |
---|
| 720 | form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) |
---|
| 721 | trans.sa_session.add( form_values ) |
---|
| 722 | trans.sa_session.flush() |
---|
| 723 | s = trans.model.Sample( current_sample[ 'name' ], |
---|
| 724 | '', |
---|
| 725 | request, |
---|
| 726 | form_values, |
---|
| 727 | current_sample[ 'barcode' ], |
---|
| 728 | current_sample[ 'library' ], |
---|
| 729 | current_sample[ 'folder' ] ) |
---|
| 730 | trans.sa_session.add( s ) |
---|
| 731 | trans.sa_session.flush() |
---|
| 732 | else: |
---|
| 733 | message = 'Changes made to the samples are saved. ' |
---|
| 734 | for sample_index in range( len( current_samples ) ): |
---|
| 735 | sample = request.samples[ sample_index ] |
---|
| 736 | current_sample = current_samples[ sample_index ] |
---|
| 737 | sample.name = current_sample[ 'name' ] |
---|
| 738 | sample.library = current_sample[ 'library' ] |
---|
| 739 | sample.folder = current_sample[ 'folder' ] |
---|
| 740 | if request.is_submitted: |
---|
| 741 | bc_message = self.__validate_barcode( trans, sample, current_sample[ 'barcode' ] ) |
---|
| 742 | if bc_message: |
---|
| 743 | status = 'error' |
---|
| 744 | message += bc_message |
---|
| 745 | else: |
---|
| 746 | if not sample.bar_code: |
---|
| 747 | # If this is a 'new' (still in its first state) sample |
---|
| 748 | # change the state to the next |
---|
| 749 | if sample.state.id == request.type.states[0].id: |
---|
| 750 | event = trans.model.SampleEvent( sample, |
---|
| 751 | request.type.states[1], |
---|
| 752 | 'Sample added to the system' ) |
---|
| 753 | trans.sa_session.add( event ) |
---|
| 754 | trans.sa_session.flush() |
---|
| 755 | # Now check if all the samples' barcode has been entered. |
---|
| 756 | # If yes then send notification email if configured |
---|
| 757 | common_state = request.samples_have_common_state |
---|
| 758 | if common_state: |
---|
| 759 | if common_state.id == request.type.states[1].id: |
---|
| 760 | event = trans.model.RequestEvent( request, |
---|
| 761 | request.states.SUBMITTED, |
---|
| 762 | "All samples are in %s state." % common_state.name ) |
---|
| 763 | trans.sa_session.add( event ) |
---|
| 764 | trans.sa_session.flush() |
---|
| 765 | request.send_email_notification( trans, request.type.states[1] ) |
---|
| 766 | sample.bar_code = current_samples[sample_index]['barcode'] |
---|
| 767 | trans.sa_session.add( sample ) |
---|
| 768 | trans.sa_session.flush() |
---|
| 769 | form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) |
---|
| 770 | form_values.content = current_sample[ 'field_values' ] |
---|
| 771 | trans.sa_session.add( form_values ) |
---|
| 772 | trans.sa_session.flush() |
---|
| 773 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 774 | action='manage_request', |
---|
| 775 | cntrller=cntrller, |
---|
| 776 | id=trans.security.encode_id( request.id ), |
---|
| 777 | status=status, |
---|
| 778 | message=message ) ) |
---|
| 779 | @web.expose |
---|
| 780 | @web.require_login( "find samples" ) |
---|
| 781 | def find_samples( self, trans, cntrller, **kwd ): |
---|
| 782 | params = util.Params( kwd ) |
---|
| 783 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 784 | status = params.get( 'status', 'done' ) |
---|
| 785 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
---|
| 786 | samples_list = [] |
---|
| 787 | results = '' |
---|
| 788 | if params.get( 'find_samples_button', False ): |
---|
| 789 | search_string = kwd.get( 'search_box', '' ) |
---|
| 790 | search_type = params.get( 'search_type', '' ) |
---|
| 791 | request_states = util.listify( params.get( 'request_states', '' ) ) |
---|
| 792 | samples = [] |
---|
| 793 | if search_type == 'barcode': |
---|
| 794 | samples = trans.sa_session.query( trans.model.Sample ) \ |
---|
| 795 | .filter( and_( trans.model.Sample.table.c.deleted==False, |
---|
| 796 | func.lower( trans.model.Sample.table.c.bar_code ).like( "%" + search_string.lower() + "%" ) ) ) \ |
---|
| 797 | .order_by( trans.model.Sample.table.c.create_time.desc() ) |
---|
| 798 | elif search_type == 'sample name': |
---|
| 799 | samples = trans.sa_session.query( trans.model.Sample ) \ |
---|
| 800 | .filter( and_( trans.model.Sample.table.c.deleted==False, |
---|
| 801 | func.lower( trans.model.Sample.table.c.name ).like( "%" + search_string.lower() + "%" ) ) ) \ |
---|
| 802 | .order_by( trans.model.Sample.table.c.create_time.desc() ) |
---|
| 803 | elif search_type == 'dataset': |
---|
| 804 | samples = trans.sa_session.query( trans.model.Sample ) \ |
---|
| 805 | .filter( and_( trans.model.Sample.table.c.deleted==False, |
---|
| 806 | trans.model.SampleDataset.table.c.sample_id==trans.model.Sample.table.c.id, |
---|
| 807 | func.lower( trans.model.SampleDataset.table.c.name ).like( "%" + search_string.lower() + "%" ) ) ) \ |
---|
| 808 | .order_by( trans.model.Sample.table.c.create_time.desc() ) |
---|
| 809 | if is_admin: |
---|
| 810 | for s in samples: |
---|
| 811 | if not s.request.deleted and s.request.state in request_states: |
---|
| 812 | samples_list.append( s ) |
---|
| 813 | else: |
---|
| 814 | for s in samples: |
---|
| 815 | if s.request.user.id == trans.user.id and s.request.state in request_states and not s.request.deleted: |
---|
| 816 | samples_list.append( s ) |
---|
| 817 | results = 'There are %i samples matching the search parameters.' % len( samples_list ) |
---|
| 818 | # Build the request_states SelectField |
---|
| 819 | selected_value = kwd.get( 'request_states', trans.model.Request.states.SUBMITTED ) |
---|
| 820 | states = [ v for k, v in trans.model.Request.states.items() ] |
---|
| 821 | request_states = build_select_field( trans, |
---|
| 822 | states, |
---|
| 823 | 'self', |
---|
| 824 | 'request_states', |
---|
| 825 | selected_value=selected_value, |
---|
| 826 | refresh_on_change=False, |
---|
| 827 | multiple=True, |
---|
| 828 | display='checkboxes' ) |
---|
| 829 | # Build the search_type SelectField |
---|
| 830 | selected_value = kwd.get( 'search_type', 'sample name' ) |
---|
| 831 | types = [ 'sample name', 'barcode', 'dataset' ] |
---|
| 832 | search_type = build_select_field( trans, types, 'self', 'search_type', selected_value=selected_value, refresh_on_change=False ) |
---|
| 833 | # Build the search_box TextField |
---|
| 834 | search_box = TextField( 'search_box', 50, kwd.get('search_box', '' ) ) |
---|
| 835 | return trans.fill_template( '/requests/common/find_samples.mako', |
---|
| 836 | cntrller=cntrller, |
---|
| 837 | request_states=request_states, |
---|
| 838 | samples=samples_list, |
---|
| 839 | search_type=search_type, |
---|
| 840 | results=results, |
---|
| 841 | search_box=search_box ) |
---|
| 842 | @web.expose |
---|
| 843 | @web.require_login( "sample events" ) |
---|
| 844 | def sample_events( self, trans, cntrller, **kwd ): |
---|
| 845 | params = util.Params( kwd ) |
---|
| 846 | status = params.get( 'status', 'done' ) |
---|
| 847 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 848 | sample_id = params.get( 'sample_id', None ) |
---|
| 849 | try: |
---|
| 850 | sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) |
---|
| 851 | except: |
---|
| 852 | return invalid_id_redirect( trans, cntrller, sample_id ) |
---|
| 853 | events_list = [] |
---|
| 854 | for event in sample.events: |
---|
| 855 | events_list.append( ( event.state.name, |
---|
| 856 | event.state.desc, |
---|
| 857 | time_ago( event.update_time ), |
---|
| 858 | event.comment ) ) |
---|
| 859 | return trans.fill_template( '/requests/common/sample_events.mako', |
---|
| 860 | cntrller=cntrller, |
---|
| 861 | events_list=events_list, |
---|
| 862 | sample=sample ) |
---|
| 863 | def __add_sample( self, trans, cntrller, request, **kwd ): |
---|
| 864 | params = util.Params( kwd ) |
---|
| 865 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 866 | status = params.get( 'status', 'done' ) |
---|
| 867 | managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) |
---|
| 868 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
---|
| 869 | # Get the widgets for rendering the request form |
---|
| 870 | request_widgets = self.__get_request_widgets( trans, request.id ) |
---|
| 871 | current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) |
---|
| 872 | if not current_samples: |
---|
| 873 | # Form field names are zero-based. |
---|
| 874 | sample_index = 0 |
---|
| 875 | else: |
---|
| 876 | sample_index = len( current_samples ) |
---|
| 877 | if params.get( 'add_sample_button', False ): |
---|
| 878 | num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) |
---|
| 879 | # See if the user has selected a sample to copy. |
---|
| 880 | copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) |
---|
| 881 | for index in range( num_samples_to_add ): |
---|
| 882 | if copy_sample_index != -1: |
---|
| 883 | # The user has selected a sample to copy. |
---|
| 884 | library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) |
---|
| 885 | folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) |
---|
| 886 | name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) |
---|
| 887 | field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] |
---|
| 888 | else: |
---|
| 889 | # The user has not selected a sample to copy (may just be adding a sample). |
---|
| 890 | library_id = None |
---|
| 891 | folder_id = None |
---|
| 892 | name = 'Sample_%i' % ( len( current_samples ) + 1 ) |
---|
| 893 | field_values = [ '' for field in request.type.sample_form.fields ] |
---|
| 894 | # Build the library_select_field and folder_select_field for the new sample being added. |
---|
| 895 | library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, |
---|
| 896 | user=request.user, |
---|
| 897 | sample_index=len( current_samples ), |
---|
| 898 | libraries=libraries, |
---|
| 899 | sample=None, |
---|
| 900 | library_id=library_id, |
---|
| 901 | folder_id=folder_id, |
---|
| 902 | **kwd ) |
---|
| 903 | # Append the new sample to the current list of samples for the request |
---|
| 904 | current_samples.append( dict( name=name, |
---|
| 905 | barcode='', |
---|
| 906 | library=None, |
---|
| 907 | library_id=library_id, |
---|
| 908 | folder=None, |
---|
| 909 | folder_id=folder_id, |
---|
| 910 | field_values=field_values, |
---|
| 911 | library_select_field=library_select_field, |
---|
| 912 | folder_select_field=folder_select_field ) ) |
---|
| 913 | selected_samples = self.__get_selected_samples( trans, request, **kwd ) |
---|
| 914 | selected_value = params.get( 'sample_operation', 'none' ) |
---|
| 915 | sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, selected_value ) |
---|
| 916 | sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) |
---|
| 917 | return trans.fill_template( '/requests/common/manage_request.mako', |
---|
| 918 | cntrller=cntrller, |
---|
| 919 | request=request, |
---|
| 920 | selected_samples=selected_samples, |
---|
| 921 | request_widgets=request_widgets, |
---|
| 922 | current_samples=current_samples, |
---|
| 923 | sample_operation_select_field=sample_operation_select_field, |
---|
| 924 | sample_copy=sample_copy, |
---|
| 925 | managing_samples=managing_samples, |
---|
| 926 | message=message, |
---|
| 927 | status=status ) |
---|
| 928 | def __get_sample_info( self, trans, request, **kwd ): |
---|
| 929 | """ |
---|
| 930 | Retrieves all user entered sample information and returns a |
---|
| 931 | list of all the samples and their field values. |
---|
| 932 | """ |
---|
| 933 | params = util.Params( kwd ) |
---|
| 934 | managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) |
---|
| 935 | # Bet all data libraries accessible to this user |
---|
| 936 | libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) |
---|
| 937 | # Build the list of widgets which will be used to render each sample row on the request page |
---|
| 938 | current_samples = [] |
---|
| 939 | for index, sample in enumerate( request.samples ): |
---|
| 940 | library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, |
---|
| 941 | request.user, |
---|
| 942 | index, |
---|
| 943 | libraries, |
---|
| 944 | sample, |
---|
| 945 | **kwd ) |
---|
| 946 | current_samples.append( dict( name=sample.name, |
---|
| 947 | barcode=sample.bar_code, |
---|
| 948 | library=sample.library, |
---|
| 949 | folder=sample.folder, |
---|
| 950 | field_values=sample.values.content, |
---|
| 951 | library_select_field=library_select_field, |
---|
| 952 | folder_select_field=folder_select_field ) ) |
---|
| 953 | if not managing_samples: |
---|
| 954 | sample_index = len( request.samples ) |
---|
| 955 | else: |
---|
| 956 | sample_index = 0 |
---|
| 957 | while True: |
---|
| 958 | library_id = params.get( 'sample_%i_library_id' % sample_index, None ) |
---|
| 959 | folder_id = params.get( 'sample_%i_folder_id' % sample_index, None ) |
---|
| 960 | if params.get( 'sample_%i_name' % sample_index, False ): |
---|
| 961 | # Data library |
---|
| 962 | try: |
---|
| 963 | library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) |
---|
| 964 | #library_id = library.id |
---|
| 965 | except: |
---|
| 966 | library = None |
---|
| 967 | if library is not None: |
---|
| 968 | # Folder |
---|
| 969 | try: |
---|
| 970 | folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) |
---|
| 971 | #folder_id = folder.id |
---|
| 972 | except: |
---|
| 973 | if library: |
---|
| 974 | folder = library.root_folder |
---|
| 975 | else: |
---|
| 976 | folder = None |
---|
| 977 | else: |
---|
| 978 | folder = None |
---|
| 979 | sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ), |
---|
| 980 | barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, '' ) ), |
---|
| 981 | library=library, |
---|
| 982 | folder=folder) |
---|
| 983 | sample_info[ 'field_values' ] = [] |
---|
| 984 | for field_index in range( len( request.type.sample_form.fields ) ): |
---|
| 985 | sample_info[ 'field_values' ].append( util.restore_text( params.get( 'sample_%i_field_%i' % ( sample_index, field_index ), '' ) ) ) |
---|
| 986 | if not managing_samples: |
---|
| 987 | sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans, |
---|
| 988 | request.user, |
---|
| 989 | sample_index, |
---|
| 990 | libraries, |
---|
| 991 | None, |
---|
| 992 | library_id, |
---|
| 993 | folder_id, |
---|
| 994 | **kwd ) |
---|
| 995 | current_samples.append( sample_info ) |
---|
| 996 | else: |
---|
| 997 | sample_info[ 'library_select_field' ], sample_info[ 'folder_select_field' ] = self.__build_library_and_folder_select_fields( trans, |
---|
| 998 | request.user, |
---|
| 999 | sample_index, |
---|
| 1000 | libraries, |
---|
| 1001 | request.samples[ sample_index ], |
---|
| 1002 | **kwd ) |
---|
| 1003 | current_samples[ sample_index ] = sample_info |
---|
| 1004 | sample_index += 1 |
---|
| 1005 | else: |
---|
| 1006 | break |
---|
| 1007 | return current_samples, managing_samples, libraries |
---|
| 1008 | @web.expose |
---|
| 1009 | @web.require_login( "delete sample from sequencing request" ) |
---|
| 1010 | def delete_sample( self, trans, cntrller, **kwd ): |
---|
| 1011 | params = util.Params( kwd ) |
---|
| 1012 | status = params.get( 'status', 'done' ) |
---|
| 1013 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 1014 | request_id = params.get( 'request_id', None ) |
---|
| 1015 | try: |
---|
| 1016 | request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) |
---|
| 1017 | except: |
---|
| 1018 | return invalid_id_redirect( trans, cntrller, request_id ) |
---|
| 1019 | current_samples, managing_samples, libraries = self.__get_sample_info( trans, request, **kwd ) |
---|
| 1020 | sample_index = int( params.get( 'sample_id', 0 ) ) |
---|
| 1021 | sample_name = current_samples[sample_index]['name'] |
---|
| 1022 | sample = request.has_sample( sample_name ) |
---|
| 1023 | if sample: |
---|
| 1024 | trans.sa_session.delete( sample.values ) |
---|
| 1025 | trans.sa_session.delete( sample ) |
---|
| 1026 | trans.sa_session.flush() |
---|
| 1027 | message = 'Sample (%s) has been deleted.' % sample_name |
---|
| 1028 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 1029 | action='manage_request', |
---|
| 1030 | cntrller=cntrller, |
---|
| 1031 | id=trans.security.encode_id( request.id ), |
---|
| 1032 | status=status, |
---|
| 1033 | message=message ) ) |
---|
| 1034 | @web.expose |
---|
| 1035 | @web.require_login( "view data transfer page" ) |
---|
| 1036 | def view_dataset_transfer( self, trans, cntrller, **kwd ): |
---|
| 1037 | params = util.Params( kwd ) |
---|
| 1038 | message = util.restore_text( params.get( 'message', '' ) ) |
---|
| 1039 | status = params.get( 'status', 'done' ) |
---|
| 1040 | is_admin = cntrller == 'requests_admin' and trans.user_is_admin() |
---|
| 1041 | sample_id = params.get( 'sample_id', None ) |
---|
| 1042 | try: |
---|
| 1043 | sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) |
---|
| 1044 | except: |
---|
| 1045 | return invalid_id_redirect( trans, cntrller, sample_id ) |
---|
| 1046 | # check if a library and folder has been set for this sample yet. |
---|
| 1047 | if not sample.library or not sample.folder: |
---|
| 1048 | status = 'error' |
---|
| 1049 | message = "Set a data library and folder for sequencing request (%s) to transfer datasets." % sample.name |
---|
| 1050 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 1051 | action='manage_request', |
---|
| 1052 | cntrller=cntrller, |
---|
| 1053 | id=trans.security.encode_id( sample.request.id ), |
---|
| 1054 | status=status, |
---|
| 1055 | message=message ) ) |
---|
| 1056 | if is_admin: |
---|
| 1057 | return trans.response.send_redirect( web.url_for( controller='requests_admin', |
---|
| 1058 | action='manage_datasets', |
---|
| 1059 | sample_id=sample_id ) ) |
---|
| 1060 | |
---|
| 1061 | folder_path = util.restore_text( params.get( 'folder_path', '' ) ) |
---|
| 1062 | if not folder_path: |
---|
| 1063 | if len( sample.datasets ): |
---|
| 1064 | folder_path = os.path.dirname( sample.datasets[-1].file_path[:-1] ) |
---|
| 1065 | else: |
---|
| 1066 | folder_path = util.restore_text( sample.request.type.datatx_info.get( 'data_dir', '' ) ) |
---|
| 1067 | if folder_path and folder_path[-1] != os.sep: |
---|
| 1068 | folder_path += os.sep |
---|
| 1069 | if not sample.request.type.datatx_info['host'] \ |
---|
| 1070 | or not sample.request.type.datatx_info['username'] \ |
---|
| 1071 | or not sample.request.type.datatx_info['password']: |
---|
| 1072 | status = 'error' |
---|
| 1073 | message = 'The sequencer login information is incomplete. Click on sequencer information to add login details.' |
---|
| 1074 | return trans.fill_template( '/requests/common/dataset_transfer.mako', |
---|
| 1075 | cntrller=cntrller, |
---|
| 1076 | sample=sample, |
---|
| 1077 | dataset_files=sample.datasets, |
---|
| 1078 | message=message, |
---|
| 1079 | status=status, |
---|
| 1080 | files=[], |
---|
| 1081 | folder_path=folder_path ) |
---|
| 1082 | def __import_samples( self, trans, cntrller, request, current_samples, libraries, **kwd ): |
---|
| 1083 | """ |
---|
| 1084 | Reads the samples csv file and imports all the samples. The format of the csv file is: |
---|
| 1085 | SampleName,DataLibrary,DataLibraryFolder,Field1,Field2.... |
---|
| 1086 | """ |
---|
| 1087 | params = util.Params( kwd ) |
---|
| 1088 | managing_samples = util.string_as_bool( params.get( 'managing_samples', False ) ) |
---|
| 1089 | file_obj = params.get( 'file_data', '' ) |
---|
| 1090 | try: |
---|
| 1091 | reader = csv.reader( file_obj.file ) |
---|
| 1092 | for row in reader: |
---|
| 1093 | library_id = None |
---|
| 1094 | folder_id = None |
---|
| 1095 | # FIXME: this is bad - what happens when multiple libraries have the same name?? |
---|
| 1096 | lib = trans.sa_session.query( trans.model.Library ) \ |
---|
| 1097 | .filter( and_( trans.model.Library.table.c.name==row[1], |
---|
| 1098 | trans.model.Library.table.c.deleted==False ) ) \ |
---|
| 1099 | .first() |
---|
| 1100 | if lib: |
---|
| 1101 | folder = trans.sa_session.query( trans.model.LibraryFolder ) \ |
---|
| 1102 | .filter( and_( trans.model.LibraryFolder.table.c.name==row[2], |
---|
| 1103 | trans.model.LibraryFolder.table.c.deleted==False ) ) \ |
---|
| 1104 | .first() |
---|
| 1105 | if folder: |
---|
| 1106 | library_id = lib.id |
---|
| 1107 | folder_id = folder.id |
---|
| 1108 | library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, |
---|
| 1109 | request.user, |
---|
| 1110 | len( current_samples ), |
---|
| 1111 | libraries, |
---|
| 1112 | None, |
---|
| 1113 | library_id, |
---|
| 1114 | folder_id, |
---|
| 1115 | **kwd ) |
---|
| 1116 | current_samples.append( dict( name=row[0], |
---|
| 1117 | barcode='', |
---|
| 1118 | library=None, |
---|
| 1119 | folder=None, |
---|
| 1120 | library_select_field=library_select_field, |
---|
| 1121 | folder_select_field=folder_select_field, |
---|
| 1122 | field_values=row[3:] ) ) |
---|
| 1123 | except Exception, e: |
---|
| 1124 | status = 'error' |
---|
| 1125 | message = 'Error thrown when importing samples file: %s' % str( e ) |
---|
| 1126 | return trans.response.send_redirect( web.url_for( controller='requests_common', |
---|
| 1127 | action='manage_request', |
---|
| 1128 | cntrller=cntrller, |
---|
| 1129 | id=trans.security.encode_id( request.id ), |
---|
| 1130 | status=status, |
---|
| 1131 | message=message ) ) |
---|
| 1132 | request_widgets = self.__get_request_widgets( trans, request.id ) |
---|
| 1133 | sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) |
---|
| 1134 | return trans.fill_template( '/requests/common/manage_request.mako', |
---|
| 1135 | cntrller=cntrller, |
---|
| 1136 | request=request, |
---|
| 1137 | request_widgets=request_widgets, |
---|
| 1138 | current_samples=current_samples, |
---|
| 1139 | sample_copy=sample_copy, |
---|
| 1140 | managing_samples=managing_samples ) |
---|
| 1141 | # ===== Methods for handling form definition widgets ===== |
---|
| 1142 | def __get_request_widgets( self, trans, id ): |
---|
| 1143 | """Get the widgets for the request""" |
---|
| 1144 | request = trans.sa_session.query( trans.model.Request ).get( id ) |
---|
| 1145 | # The request_widgets list is a list of dictionaries |
---|
| 1146 | request_widgets = [] |
---|
| 1147 | for index, field in enumerate( request.type.request_form.fields ): |
---|
| 1148 | if field[ 'required' ]: |
---|
| 1149 | required_label = 'Required' |
---|
| 1150 | else: |
---|
| 1151 | required_label = 'Optional' |
---|
| 1152 | if field[ 'type' ] == 'AddressField': |
---|
| 1153 | if request.values.content[ index ]: |
---|
| 1154 | request_widgets.append( dict( label=field[ 'label' ], |
---|
| 1155 | value=trans.sa_session.query( trans.model.UserAddress ).get( int( request.values.content[ index ] ) ).get_html(), |
---|
| 1156 | helptext=field[ 'helptext' ] + ' (' + required_label + ')' ) ) |
---|
| 1157 | else: |
---|
| 1158 | request_widgets.append( dict( label=field[ 'label' ], |
---|
| 1159 | value=None, |
---|
| 1160 | helptext=field[ 'helptext' ] + ' (' + required_label + ')' ) ) |
---|
| 1161 | else: |
---|
| 1162 | request_widgets.append( dict( label=field[ 'label' ], |
---|
| 1163 | value=request.values.content[ index ], |
---|
| 1164 | helptext=field[ 'helptext' ] + ' (' + required_label + ')' ) ) |
---|
| 1165 | return request_widgets |
---|
| 1166 | def __get_samples_widgets( self, trans, request, libraries, **kwd ): |
---|
| 1167 | """Get the widgets for all of the samples currently associated with the request""" |
---|
| 1168 | # The current_samples_widgets list is a list of dictionaries |
---|
| 1169 | current_samples_widgets = [] |
---|
| 1170 | for index, sample in enumerate( request.samples ): |
---|
| 1171 | # Build the library_select_field and folder_select_field for each existing sample |
---|
| 1172 | library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, |
---|
| 1173 | user=request.user, |
---|
| 1174 | sample_index=index, |
---|
| 1175 | libraries=libraries, |
---|
| 1176 | sample=sample, |
---|
| 1177 | **kwd ) |
---|
| 1178 | # Append the dictionary for the current sample to the current_samples_widgets list |
---|
| 1179 | current_samples_widgets.append( dict( name=sample.name, |
---|
| 1180 | barcode=sample.bar_code, |
---|
| 1181 | library=sample.library, |
---|
| 1182 | folder=sample.folder, |
---|
| 1183 | field_values=sample.values.content, |
---|
| 1184 | library_select_field=library_select_field, |
---|
| 1185 | folder_select_field=folder_select_field ) ) |
---|
| 1186 | return current_samples_widgets |
---|
| 1187 | # ===== Methods for building SelectFields used on various request forms ===== |
---|
| 1188 | def __build_copy_sample_select_field( self, trans, current_samples ): |
---|
| 1189 | copy_sample_index_select_field = SelectField( 'copy_sample_index' ) |
---|
| 1190 | copy_sample_index_select_field.add_option( 'None', -1, selected=True ) |
---|
| 1191 | for index, sample_dict in enumerate( current_samples ): |
---|
| 1192 | copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) |
---|
| 1193 | return copy_sample_index_select_field |
---|
| 1194 | def __build_request_type_id_select_field( self, trans, selected_value='none' ): |
---|
| 1195 | accessible_request_types = trans.user.accessible_request_types( trans ) |
---|
| 1196 | return build_select_field( trans, accessible_request_types, 'name', 'request_type_id', selected_value=selected_value, refresh_on_change=True ) |
---|
| 1197 | def __build_user_id_select_field( self, trans, selected_value='none' ): |
---|
| 1198 | active_users = trans.sa_session.query( trans.model.User ) \ |
---|
| 1199 | .filter( trans.model.User.table.c.deleted == False ) \ |
---|
| 1200 | .order_by( trans.model.User.email.asc() ) |
---|
| 1201 | # A refresh_on_change is required so the user's set of addresses can be displayed. |
---|
| 1202 | return build_select_field( trans, active_users, 'email', 'user_id', selected_value=selected_value, refresh_on_change=True ) |
---|
| 1203 | def __build_sample_operation_select_field( self, trans, is_admin, request, selected_value ): |
---|
| 1204 | # The sample_operation SelectField is displayed only after the request has been submitted. |
---|
| 1205 | # It's label is "For selected samples" |
---|
| 1206 | if is_admin: |
---|
| 1207 | if request.is_complete: |
---|
| 1208 | bulk_operations = [ trans.model.Sample.bulk_operations.CHANGE_STATE ] |
---|
| 1209 | if request.is_rejected: |
---|
| 1210 | bulk_operations = [ trans.model.Sample.bulk_operations.SELECT_LIBRARY ] |
---|
| 1211 | else: |
---|
| 1212 | bulk_operations = [ s for i, s in trans.model.Sample.bulk_operations.items() ] |
---|
| 1213 | else: |
---|
| 1214 | if request.is_complete: |
---|
| 1215 | bulk_operations = [] |
---|
| 1216 | else: |
---|
| 1217 | bulk_operations = [ trans.model.Sample.bulk_operations.SELECT_LIBRARY ] |
---|
| 1218 | return build_select_field( trans, bulk_operations, 'self', 'sample_operation', selected_value=selected_value, refresh_on_change=True ) |
---|
| 1219 | def __build_library_and_folder_select_fields( self, trans, user, sample_index, libraries, sample=None, library_id=None, folder_id=None, **kwd ): |
---|
| 1220 | # Create the library_id SelectField for a specific sample. The received libraries param is a list of all the libraries |
---|
| 1221 | # accessible to the current user, and we add them as options to the library_select_field. If the user has selected an |
---|
| 1222 | # existing library then display all the accessible folders of the selected library in the folder_select_field. |
---|
| 1223 | # |
---|
| 1224 | # The libraries dictionary looks like: { library : '1,2' }, library : '3' }. Its keys are the libraries that |
---|
| 1225 | # should be displayed for the current user and its values are strings of comma-separated folder ids that should |
---|
| 1226 | # NOT be displayed. |
---|
| 1227 | # |
---|
| 1228 | # TODO: all object ids received in the params must be encoded. |
---|
| 1229 | params = util.Params( kwd ) |
---|
| 1230 | library_select_field_name= "sample_%i_library_id" % sample_index |
---|
| 1231 | folder_select_field_name = "sample_%i_folder_id" % sample_index |
---|
| 1232 | if not library_id: |
---|
| 1233 | library_id = params.get( library_select_field_name, 'none' ) |
---|
| 1234 | selected_library = None |
---|
| 1235 | selected_hidden_folder_ids = [] |
---|
| 1236 | showable_folders = [] |
---|
| 1237 | if sample and sample.library and library_id == 'none': |
---|
| 1238 | library_id = str( sample.library.id ) |
---|
| 1239 | selected_library = sample.library |
---|
| 1240 | # If we have a selected library, get the list of it's folders that are not accessible to the current user |
---|
| 1241 | for library, hidden_folder_ids in libraries.items(): |
---|
| 1242 | encoded_id = trans.security.encode_id( library.id ) |
---|
| 1243 | if encoded_id == str( library_id ): |
---|
| 1244 | selected_library = library |
---|
| 1245 | selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) |
---|
| 1246 | break |
---|
| 1247 | # sample_%i_library_id SelectField with refresh on change enabled |
---|
| 1248 | library_select_field = build_select_field( trans, |
---|
| 1249 | libraries.keys(), |
---|
| 1250 | 'name', |
---|
| 1251 | library_select_field_name, |
---|
| 1252 | initial_value='none', |
---|
| 1253 | selected_value=str( library_id ).lower(), |
---|
| 1254 | refresh_on_change=True ) |
---|
| 1255 | # Get all accessible folders for the selected library, if one is indeed selected |
---|
| 1256 | if selected_library: |
---|
| 1257 | showable_folders = trans.app.security_agent.get_showable_folders( user, |
---|
| 1258 | user.all_roles(), |
---|
| 1259 | selected_library, |
---|
| 1260 | [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], |
---|
| 1261 | selected_hidden_folder_ids ) |
---|
| 1262 | if sample: |
---|
| 1263 | # The user is editing the request, and may have previously selected a folder |
---|
| 1264 | if sample.folder: |
---|
| 1265 | selected_folder_id = sample.folder.id |
---|
| 1266 | else: |
---|
| 1267 | # If a library is selected but not a folder, use the library's root folder |
---|
| 1268 | if sample.library: |
---|
| 1269 | selected_folder_id = sample.library.root_folder.id |
---|
| 1270 | else: |
---|
| 1271 | # The user just selected a folder |
---|
| 1272 | selected_folder_id = params.get( folder_select_field_name, 'none' ) |
---|
| 1273 | elif folder_id: |
---|
| 1274 | # TODO: not sure when this would be passed |
---|
| 1275 | selected_folder_id = folder_id |
---|
| 1276 | else: |
---|
| 1277 | selected_folder_id = 'none' |
---|
| 1278 | # TODO: Change the name of the library root folder to "Library root" to clarify to the |
---|
| 1279 | # user that it is the root folder. We probably should just change this in the Library code, |
---|
| 1280 | # and update the data in the db. |
---|
| 1281 | folder_select_field = build_select_field( trans, |
---|
| 1282 | showable_folders, |
---|
| 1283 | 'name', |
---|
| 1284 | folder_select_field_name, |
---|
| 1285 | initial_value='none', |
---|
| 1286 | selected_value=selected_folder_id ) |
---|
| 1287 | return library_select_field, folder_select_field |
---|
| 1288 | def __build_sample_state_id_select_field( self, trans, request, selected_value ): |
---|
| 1289 | if selected_value == 'none': |
---|
| 1290 | if request.samples: |
---|
| 1291 | selected_value = trans.security.encode_id( request.samples[0].state.id ) |
---|
| 1292 | else: |
---|
| 1293 | selected_value = trans.security.encode_id( request.type.states[0].id ) |
---|
| 1294 | return build_select_field( trans, |
---|
| 1295 | objs=request.type.states, |
---|
| 1296 | label_attr='name', |
---|
| 1297 | select_field_name='sample_state_id', |
---|
| 1298 | selected_value=selected_value, |
---|
| 1299 | refresh_on_change=False ) |
---|
| 1300 | # ===== Methods for validation forms and fields ===== |
---|
| 1301 | def __validate_request( self, trans, cntrller, request ): |
---|
| 1302 | """Validates the request entered by the user""" |
---|
| 1303 | # TODO: Add checks for required sample fields here. |
---|
| 1304 | empty_fields = [] |
---|
| 1305 | # Make sure required form fields are filled in. |
---|
| 1306 | for index, field in enumerate( request.type.request_form.fields ): |
---|
| 1307 | if field[ 'required' ] == 'required' and request.values.content[ index ] in [ '', None ]: |
---|
| 1308 | empty_fields.append( field[ 'label' ] ) |
---|
| 1309 | if empty_fields: |
---|
| 1310 | message = 'Complete the following fields of the request before submitting: ' |
---|
| 1311 | for ef in empty_fields: |
---|
| 1312 | message += '<b>' + ef + '</b> ' |
---|
| 1313 | return message |
---|
| 1314 | return None |
---|
| 1315 | def __validate_barcode( self, trans, sample, barcode ): |
---|
| 1316 | """ |
---|
| 1317 | Makes sure that the barcode about to be assigned to a sample is gobally unique. |
---|
| 1318 | That is, barcodes must be unique across requests in Galaxy sample tracking. |
---|
| 1319 | """ |
---|
| 1320 | message = '' |
---|
| 1321 | unique = True |
---|
| 1322 | for index in range( len( sample.request.samples ) ): |
---|
| 1323 | # Check for empty bar code |
---|
| 1324 | if not barcode.strip(): |
---|
| 1325 | message = 'Fill in the barcode for sample (%s).' % sample.name |
---|
| 1326 | break |
---|
| 1327 | # TODO: Add a unique constraint to sample.bar_code table column |
---|
| 1328 | # Make sure bar code is unique |
---|
| 1329 | for sample_has_bar_code in trans.sa_session.query( trans.model.Sample ) \ |
---|
| 1330 | .filter( trans.model.Sample.table.c.bar_code == barcode ): |
---|
| 1331 | if sample_has_bar_code and sample_has_bar_code.id != sample.id: |
---|
| 1332 | message = '''The bar code (%s) associated with the sample (%s) belongs to another sample. |
---|
| 1333 | Bar codes must be unique across all samples, so use a different bar code |
---|
| 1334 | for this sample.''' % ( barcode, sample.name ) |
---|
| 1335 | unique = False |
---|
| 1336 | break |
---|
| 1337 | if not unique: |
---|
| 1338 | break |
---|
| 1339 | return message |
---|
| 1340 | def __validate_email( self, email ): |
---|
| 1341 | error = '' |
---|
| 1342 | if len( email ) == 0 or "@" not in email or "." not in email: |
---|
| 1343 | error = "(%s) is not a valid email address. " % str( email ) |
---|
| 1344 | elif len( email ) > 255: |
---|
| 1345 | error = "(%s) exceeds maximum allowable length. " % str( email ) |
---|
| 1346 | return error |
---|
| 1347 | # ===== Other miscellaneoud utility methods ===== |
---|
| 1348 | def __get_selected_samples( self, trans, request, **kwd ): |
---|
| 1349 | selected_samples = [] |
---|
| 1350 | for sample in request.samples: |
---|
| 1351 | if CheckboxField.is_checked( kwd.get( 'select_sample_%i' % sample.id, '' ) ): |
---|
| 1352 | selected_samples.append( trans.security.encode_id( sample.id ) ) |
---|
| 1353 | return selected_samples |
---|
| 1354 | |
---|
| 1355 | # ===== Miscellaneoud utility methods outside of the RequestsCommon class ===== |
---|
| 1356 | def invalid_id_redirect( trans, cntrller, obj_id, action='browse_requests' ): |
---|
| 1357 | status = 'error' |
---|
| 1358 | message = "Invalid request id (%s)" % str( obj_id ) |
---|
| 1359 | return trans.response.send_redirect( web.url_for( controller=cntrller, |
---|
| 1360 | action=action, |
---|
| 1361 | status=status, |
---|
| 1362 | message=message ) ) |
---|