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Restrict the target history list to the users active hisstories when copying datasets between histories, clean up the relavent templates ( fixes ticket # 41 ), and add functional tests for copying history items between histories.

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This commit is contained in:
Greg Von Kuster
2009-06-11 12:06:29 -04:00
parent 5c1d1b1c78
commit d5ca0742ed
5 changed files with 154 additions and 73 deletions
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lib/galaxy/web/controllers/dataset.py
+4 -4
View File
@@ -159,7 +159,8 @@ class DatasetInterface( BaseController ):
raise "Error undeleting"
@web.expose
def copy_datasets( self, trans, source_dataset_ids = "", target_history_ids = "", new_history_name="", do_copy = False ):
def copy_datasets( self, trans, source_dataset_ids="", target_history_ids="", new_history_name="", do_copy=False, **kwd ):
params = util.Params( kwd )
user = trans.get_user()
history = trans.get_history()
create_new_history = False
@@ -202,7 +203,7 @@ class DatasetInterface( BaseController ):
error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) )
for data in map( trans.app.model.HistoryDatasetAssociation.get, source_dataset_ids ):
if data is None:
error_msg = error_msg + "You tried to copy a non-existant dataset. "
error_msg = error_msg + "You tried to copy a dataset that does not exist. "
invalid_datasets += 1
elif data.history != history:
error_msg = error_msg + "You tried to copy a dataset which is not in your current history. "
@@ -220,8 +221,7 @@ class DatasetInterface( BaseController ):
source_datasets = history.active_datasets
target_histories = [history]
if user:
target_histories = user.histories
target_histories = user.active_histories
return trans.fill_template( "/dataset/copy_view.mako",
source_dataset_ids = source_dataset_ids,
target_history_ids = target_history_ids,
templates/dataset/copy_view.mako
+56 -54
View File
@@ -5,65 +5,67 @@
${javascripts()}
%if error_msg:
<p>
<div class="errormessage">${error_msg}</div>
<div style="clear: both"></div>
</p>
<p>
<div class="errormessage">${error_msg}</div>
<div style="clear: both"></div>
</p>
%endif
%if done_msg:
<p>
<div class="donemessage">${done_msg}</div>
<div style="clear: both"></div>
</p>
<p>
<div class="donemessage">${done_msg}</div>
<div style="clear: both"></div>
</p>
%endif
<p>
<div class="toolForm">
<form>
<div style="float: left; width: 50%; padding: 0px 0px 0px 0px;">
<div class="toolFormTitle">Source History Items</div>
<div class="toolFormBody">
%for data in source_datasets:
<%
checked = ""
if data.id in source_dataset_ids:
checked = " checked"
%>
<div class="form-row"><input type="checkbox" name="source_dataset_ids" value="${data.id}"${checked}/> ${data.hid}: ${data.name}</div>
%endfor
</div>
</div>
<div style="float: right; width: 50%; padding: 0px 0px 0px 0px;">
<div class="toolFormTitle">Target Histories</div>
<div class="toolFormBody">
%for i, hist in enumerate( target_histories ):
<%
checked = ""
if hist.id in target_history_ids:
checked = " checked"
cur_history_text = ""
if hist == trans.get_history():
cur_history_text = " <strong>(current history)</strong>"
%>
<div class="form-row"><input type="checkbox" name="target_history_ids" value="${hist.id}"${checked}/> ${i + 1}${cur_history_text}: ${hist.name}</div>
%endfor
%if trans.get_user():
<%
checked = ""
if "create_new_history" in target_history_ids:
checked = " checked"
%>
<br>
<div class="form-row"><input type="checkbox" name="target_history_ids" value="create_new_history"${checked}/>New history named: <input type="textbox" name="new_history_name" value="${new_history_name}"/></div>
%endif
</div>
</div>
<div style="clear: both"></div>
<div class="form-row" align="center"><input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/></div>
</form>
</div>
<div class="toolForm">
<form>
<div style="float: left; width: 50%; padding: 0px 0px 0px 0px;">
<div class="toolFormTitle">Source History Items</div>
<div class="toolFormBody">
%for data in source_datasets:
<%
checked = ""
if data.id in source_dataset_ids:
checked = " checked"
%>
<div class="form-row"><input type="checkbox" name="source_dataset_ids" value="${data.id}"${checked}/> ${data.hid}: ${data.name}</div>
%endfor
</div>
</div>
<div style="float: right; width: 50%; padding: 0px 0px 0px 0px;">
<div class="toolFormTitle">Target Histories</div>
<div class="toolFormBody">
%for i, hist in enumerate( target_histories ):
<%
checked = ""
if hist.id in target_history_ids:
checked = " checked"
cur_history_text = ""
if hist == trans.get_history():
cur_history_text = " <strong>(current history)</strong>"
%>
<div class="form-row"><input type="checkbox" name="target_history_ids" value="${hist.id}"${checked}/> ${i + 1}${cur_history_text}: ${hist.name}</div>
%endfor
%if trans.get_user():
<%
checked = ""
if "create_new_history" in target_history_ids:
checked = " checked"
%>
<br/>
<div class="form-row"><input type="checkbox" name="target_history_ids" value="create_new_history"${checked}/>New history named: <input type="textbox" name="new_history_name" value="${new_history_name}"/></div>
%endif
</div>
</div>
<div style="clear: both"></div>
<div class="form-row" align="center">
<input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/>
</div>
</form>
</div>
</p>
<div style="clear: both"></div>
<p>
<div class="infomessage">Select any number of source history items and any number of target histories and click on "Copy History Items" to add a copy of each selected dataset to each selected history.</div>
<div style="clear: both"></div>
<div class="infomessage">Select any number of source history items and any number of target histories and click "Copy History Items" to add a copy of each selected history item to each selected target history.</div>
<div style="clear: both"></div>
</p>
templates/dataset/edit_attributes.mako
+12 -4
View File
@@ -157,8 +157,16 @@
%endif
<p/>
<div class="toolForm">
<div class="toolFormTitle">Copy History Item</div>
<div class="toolFormBody">
Click <a href="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" target="galaxy_main">here</a> to make a copy of this history item.
</div>
<div class="toolFormTitle">Copy History Item</div>
<div class="toolFormBody">
<form name="copy_hda" action="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" method="post">
<div class="form-row">
<input type="submit" name="change" value="Copy history item"/>
</div>
<div class="toolParamHelp" style="clear: both;">
Make a copy of this history item in your current history or any of your active histories.
</div>
</form>
</div>
</div>
</div>
test/base/twilltestcase.py
+28 -4
View File
@@ -181,8 +181,9 @@ class TwillTestCase( unittest.TestCase ):
self.home()
def new_history( self, name=None ):
"""Creates a new, empty history"""
self.home()
if name:
self.visit_url( "%s/history_new?name=%s" % ( self.url, str( name ) ) )
self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) )
else:
self.visit_url( "%s/history_new" % self.url )
self.check_history_for_string('Your history is empty')
@@ -191,7 +192,7 @@ class TwillTestCase( unittest.TestCase ):
"""Rename an existing history"""
self.home()
self.visit_page( "history/rename?id=%s&name=%s" %( id, new_name ) )
check_str = 'History: %s renamed to: %s' % ( old_name, new_name )
check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) )
self.check_page_for_string( check_str )
self.home()
def set_history( self ):
@@ -330,7 +331,7 @@ class TwillTestCase( unittest.TestCase ):
self.check_page_for_string( 'Attributes updated' )
self.home()
def convert_format( self, hda_id, target_type ):
"""Auto-detect history_dataset_association metadata"""
"""Convert format of history_dataset_association"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
self.check_page_for_string( 'This will inspect the dataset and attempt' )
@@ -339,7 +340,7 @@ class TwillTestCase( unittest.TestCase ):
self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' )
self.home()
def change_datatype( self, hda_id, datatype ):
"""Auto-detect history_dataset_association metadata"""
"""Change format of history_dataset_association"""
self.home()
self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) )
self.check_page_for_string( 'This will change the datatype of the existing dataset but' )
@@ -347,6 +348,29 @@ class TwillTestCase( unittest.TestCase ):
tc.submit( 'change' )
self.check_page_for_string( 'Edit Attributes' )
self.home()
def copy_history_item( self, source_dataset_ids='', target_history_ids=[], all_target_history_ids=[], deleted_history_ids=[] ):
"""Copy 1 or more history_dataset_associations to 1 or more histories"""
self.home()
self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_ids ) )
self.check_page_for_string( 'Source History Items' )
# Make sure all of users active histories are displayed
for id in all_target_history_ids:
self.check_page_for_string( id )
# Make sure only active histories are displayed
for id in deleted_history_ids:
try:
self.check_page_for_string( id )
raise AssertionError, "deleted history id %d displayed in list of target histories" % id
except:
pass
# Check each history to which we want to copy the item
for id in target_history_ids:
tc.fv( '1', 'target_history_ids', id )
tc.submit( 'do_copy' )
no_source_ids = len( source_dataset_ids.split( ',' ) )
check_str = '%d datasets copied to %d histories.' % ( no_source_ids, len( target_history_ids ) )
self.check_page_for_string( check_str )
self.home()
def get_dataset_ids_in_history( self ):
"""Returns the ids of datasets in a history"""
data_list = self.get_history()
test/functional/test_history_functions.py
+54 -7
View File
@@ -1,3 +1,4 @@
import urllib
import galaxy.model
from galaxy.model.orm import *
from base.twilltestcase import *
@@ -55,7 +56,7 @@ class TestHistory( TwillTestCase ):
history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history1 is not None, "Problem retrieving history1 from database"
self.upload_file( '1.bed', dbkey='hg18' )
self.new_history( name='history2' )
self.new_history( name=urllib.quote( 'history2' ) )
global history2
history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history2 is not None, "Problem retrieving history2 from database"
@@ -96,7 +97,7 @@ class TestHistory( TwillTestCase ):
assert history3 is not None, "Problem retrieving history3 from database"
if history3.deleted:
raise AssertionError, "History id %d deleted when it should not be" % latest_history.id
self.rename_history( str( history3.id ), history3.name, new_name='history3' )
self.rename_history( str( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) )
def test_020_history_list( self ):
"""Testing viewing previously stored histories"""
self.view_stored_active_histories()
@@ -131,7 +132,7 @@ class TestHistory( TwillTestCase ):
global history4
history4 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history4 is not None, "Problem retrieving history4 from database"
self.rename_history( str( history4.id ), history4.name, new_name='history4' )
self.rename_history( str( history4.id ), history4.name, new_name=urllib.quote( 'history 4' ) )
history4.refresh()
self.upload_file( '2.bed', dbkey='hg18' )
id = '%s,%s' % ( str( history3.id ), str( history4.id ) )
@@ -195,7 +196,7 @@ class TestHistory( TwillTestCase ):
global history5
history5 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history5 is not None, "Problem retrieving history5 from database"
self.rename_history( str( history5.id ), history5.name, new_name='history5' )
self.rename_history( str( history5.id ), history5.name, new_name=urllib.quote( 'history5' ) )
history5.refresh()
# Due to the limitations of twill ( not functional with the permissions forms ), we're forced
# to do this manually. At this point, we just want to restrict the access permission on history5
@@ -377,7 +378,7 @@ class TestHistory( TwillTestCase ):
action='no_share' )
def test_055_history_show_and_hide_deleted_datasets( self ):
"""Testing displaying deleted history items"""
self.new_history( name='temp_history1' )
self.new_history( name=urllib.quote( 'show hide deleted datasets' ) )
self.upload_file('1.bed', dbkey='hg18')
latest_hda = galaxy.model.HistoryDatasetAssociation.query() \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
@@ -393,7 +394,7 @@ class TestHistory( TwillTestCase ):
self.check_page_for_string( 'Your history is empty' )
def test_060_deleting_and_undeleting_history_items( self ):
"""Testing deleting and un-deleting history items"""
self.new_history( name='temp_history2' )
self.new_history( name=urllib.quote( 'delete undelete history items' ) )
# Add a new history item
self.upload_file( '1.bed', dbkey='hg15' )
self.home()
@@ -416,8 +417,54 @@ class TestHistory( TwillTestCase ):
self.visit_url( "%s/history/?show_deleted=False" % self.url )
self.check_page_for_string( '1.bed' )
self.check_page_for_string( 'hg15' )
def test_065_reset_data_for_later_test_runs( self ):
def test_065_copying_history_items_between_histories( self ):
"""Testing copying history items between histories"""
self.new_history( name=urllib.quote( 'copy history items' ) )
global history6
history6 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history6 is not None, "Problem retrieving history6 from database"
self.upload_file( '1.bed', dbkey='hg18' )
hda1 = galaxy.model.HistoryDatasetAssociation.query() \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
assert hda1 is not None, "Problem retrieving hda1 from database"
# We'll just test copying 1 hda
source_dataset_ids=str( hda1.id )
# The valid list of target histories is only the user's active histories
all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ]
# Since history1 and history2 have been deleted, they should not be displayed in the list of target histories
# on the copy_view.mako form
deleted_history_ids = [ str( history1.id ), str( history2.id ) ]
# Test copying to the current history
target_history_ids=[ str( history6.id ) ]
self.copy_history_item( source_dataset_ids=source_dataset_ids,
target_history_ids=target_history_ids,
all_target_history_ids=all_target_history_ids,
deleted_history_ids=deleted_history_ids )
history6.refresh()
if len( history6.datasets ) != 2:
raise AssertionError, "Copying hda1 to the current history failed"
# Test copying 1 hda to another history
self.new_history( name=urllib.quote( 'copy history items - 2' ) )
global history7
history7 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
assert history7 is not None, "Problem retrieving history7 from database"
# Switch back to our history from which we want to copy
self.switch_history( id=str( history6.id ), name=history6.name )
target_history_ids=[ str( history7.id ) ]
all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ]
# Test copying to the a history that is not the current history
target_history_ids=[ str( history7.id ) ]
self.copy_history_item( source_dataset_ids=source_dataset_ids,
target_history_ids=target_history_ids,
all_target_history_ids=all_target_history_ids,
deleted_history_ids=deleted_history_ids )
# Switch to the history to which we copied
self.switch_history( id=str( history7.id ), name=history7.name )
self.check_history_for_string( hda1.name )
def test_070_reset_data_for_later_test_runs( self ):
"""Reseting data to enable later test runs to pass"""
self.delete_history( id=str( history3.id ) )
self.delete_history( id=str( history4.id ) )
self.delete_history( id=str( history5.id ) )
self.delete_history( id=str( history6.id ) )
self.delete_history( id=str( history7.id ) )