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Fix to safari flexbox and merge

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This commit is contained in:
Carl Eberhard
2015-03-03 13:32:10 -05:00
parent 5f67895a00 d390ef2955
commit 83cc4361b7
16 changed files with 86 additions and 52 deletions
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client/galaxy/scripts/mvc/tools/tools-select-content.js
+1 -1
View File
@@ -217,7 +217,7 @@ var View = Backbone.View.extend({
}
// identify suitable select field
if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hcda') {
if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {
this.current = 'collection';
this.select_collection.value(list[0]);
} else {
lib/galaxy/tools/__init__.py
+5
View File
@@ -2316,6 +2316,11 @@ class Tool( object, Dictifiable ):
'id' : trans.security.encode_id(v.id),
'src' : 'hda'
}
elif isinstance(v, trans.app.model.HistoryDatasetCollectionAssociation):
return {
'id' : trans.security.encode_id(v.id),
'src' : 'hdca'
}
elif isinstance(v, bool):
if v is True:
return 'true'
lib/galaxy/tools/parameters/basic.py
+4
View File
@@ -2005,6 +2005,8 @@ class DataToolParameter( BaseDataToolParameter ):
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
else:
raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
elif isinstance( single_value, trans.app.model.HistoryDatasetAssociation ):
rval.append( single_value )
else:
rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
@@ -2021,6 +2023,8 @@ class DataToolParameter( BaseDataToolParameter ):
encoded_id = str( value )[ len( "__collection_reduce__|" ): ]
decoded_id = trans.app.security.decode_id( encoded_id )
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
rval = value
else:
rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value )
if isinstance( rval, list ):
static/scripts/mvc/tools/tools-select-content.js
+1 -1
View File
@@ -217,7 +217,7 @@ var View = Backbone.View.extend({
}
// identify suitable select field
if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hcda') {
if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {
this.current = 'collection';
this.select_collection.value(list[0]);
} else {
static/scripts/packed/mvc/tools/tools-select-content.js
+1 -1
View File
@@ -1 +1 @@
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(h){var f=this;function g(m,j){if(m){var n=[];for(var k in j){var l=j[k];n.push({label:l.hid+": "+l.name,value:l.id});f.app.history[l.id+"_"+l.src]=l}m.update(n)}}g(this.select_single,h.hda);g(this.select_multiple,h.hda);g(this.select_collection,h.hdca)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=_.findWhere(this.app.history,{id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=_.findWhere(this.app.history,{id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(h){var f=this;function g(m,j){if(m){var n=[];for(var k in j){var l=j[k];n.push({label:l.hid+": "+l.name,value:l.id});f.app.history[l.id+"_"+l.src]=l}m.update(n)}}g(this.select_single,h.hda);g(this.select_multiple,h.hda);g(this.select_collection,h.hdca)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hdca"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=_.findWhere(this.app.history,{id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=_.findWhere(this.app.history,{id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
static/style/blue/base.css
+2 -2
View File
@@ -2119,7 +2119,7 @@ div.permissionContainer{padding-left:20px}
.annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px}
.annotated-history-panel .empty-message{margin-top:8px}
.current-history-panel .list-item.history-content.current-content{border-left:5px solid #4E5777}
.multi-panel-history{display:flex;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
.multi-panel-history{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
.multi-panel-history .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column}
.multi-panel-history .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row}
.multi-panel-history .flex-row,.multi-panel-history .flex-column{-webkit-flex:1 1 auto;-ms-flex:1 1 auto;flex:1 1 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}
@@ -2142,7 +2142,7 @@ div.permissionContainer{padding-left:20px}
.multi-panel-history .history-column:nth-child(2){margin-left:320px}
.multi-panel-history .history-column:last-child{margin-right:0px}
.multi-panel-history .history-column .dropdown-menu{z-index:inherit}
.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;-webkit-flex:0 0 auto;-ms-flex:0 0 auto;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
.multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px}
.multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px}
.multi-panel-history .history-column .panel-controls .panel-menu{z-index:1}.multi-panel-history .history-column .panel-controls .panel-menu .dropdown-menu a{text-align:left}
static/style/src/less/history.less
+8
View File
@@ -584,7 +584,13 @@
// for some reason, .flex-row-container below won't be applied to multi-panel-history since it's the enclosing node
// re-apply here
display: -webkit-box;
display: -webkit-flex;
display: -ms-flexbox;
display: flex;
-webkit-flex-direction: column;
-ms-flex-direction: column;
flex-direction: column;
.flex-row-container,
@@ -770,6 +776,8 @@
background-color: white;
text-align: center;
-webkit-flex: 0 0 auto;
-ms-flex: 0 0 auto;
flex: 0 0 auto;
-webkit-align-self: auto;
test/api/test_jobs.py
+12 -3
View File
@@ -29,14 +29,23 @@ class JobsApiTestCase( api.ApiTestCase, TestsDatasets ):
def test_index_state_filter( self ):
# Initial number of ok jobs
original_count = len( self.__uploads_with_state( "ok" ) )
# Run through dataset upload to ensure num uplaods at least greater
# by 1.
self.__history_with_ok_dataset()
# Verify number of ok jobs is actually greater.
new_count = len( self.__uploads_with_state( "ok" ) )
assert original_count < new_count
count_increased = False
for i in range(10):
new_count = len( self.__uploads_with_state( "ok" ) )
if original_count < new_count:
count_increased = True
break
time.sleep(.1)
if not count_increased:
template = "Jobs in ok state did not increase (was %d, now %d)"
message = template % (original_count, new_count)
raise AssertionError(message)
def test_index_date_filter( self ):
self.__history_with_new_dataset()
test/api/test_tool_data.py
+28 -28
View File
@@ -1,11 +1,6 @@
""" Tests for the tool data API.
"""
import json
from base import api
from .helpers import DatasetPopulator
from requests import delete
import operator
@@ -40,7 +35,7 @@ class ToolDataApiTestCase( api.ApiTestCase ):
field = show_field_response.json()
self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" )
files = field[ "files" ]
assert len( files ) == 2
assert len( files ) == 2, "Length of files [%s] was not 2." % files
def test_download_field_file(self):
show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True )
@@ -48,27 +43,32 @@ class ToolDataApiTestCase( api.ApiTestCase ):
content = show_field_response.content
assert content == "This is data 1.", content
def test_delete_entry(self):
show_response = self._get( "tool_data/testbeta", admin=True )
original_count = len(show_response.json()["fields"])
# Following test case rendered invalid by the fix in
# https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020#diff-bfb557a99c1f7d646d4968d8d680b885R154.
# TODO: Restore the test case when test framework allows actions from
# admin users.
dataset_populator = DatasetPopulator( self.galaxy_interactor )
history_id = dataset_populator.new_history()
payload = dataset_populator.run_tool_payload(
tool_id="data_manager",
inputs={"ignored_value": "moo"},
history_id=history_id,
)
create_response = self._post( "tools", data=payload )
self._assert_status_code_is( create_response, 200 )
dataset_populator.wait_for_history( history_id, assert_ok=True )
show_response = self._get( "tool_data/testbeta", admin=True )
updated_fields = show_response.json()["fields"]
assert len(updated_fields) == original_count + 1
field0 = updated_fields[0]
url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
delete( url, data=json.dumps({"values": "\t".join(field0)}) )
# def test_delete_entry(self):
# show_response = self._get( "tool_data/testbeta", admin=True )
# original_count = len(show_response.json()["fields"])
show_response = self._get( "tool_data/testbeta", admin=True )
updated_fields = show_response.json()["fields"]
assert len(updated_fields) == original_count
# dataset_populator = DatasetPopulator( self.galaxy_interactor )
# history_id = dataset_populator.new_history()
# payload = dataset_populator.run_tool_payload(
# tool_id="data_manager",
# inputs={"ignored_value": "moo"},
# history_id=history_id,
# )
# create_response = self._post( "tools", data=payload )
# self._assert_status_code_is( create_response, 200 )
# dataset_populator.wait_for_history( history_id, assert_ok=True )
# show_response = self._get( "tool_data/testbeta", admin=True )
# updated_fields = show_response.json()["fields"]
# assert len(updated_fields) == original_count + 1
# field0 = updated_fields[0]
# url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
# delete( url, data=json.dumps({"values": "\t".join(field0)}) )
# show_response = self._get( "tool_data/testbeta", admin=True )
# updated_fields = show_response.json()["fields"]
# assert len(updated_fields) == original_count
test/api/test_tools.py
+3 -2
View File
@@ -219,8 +219,9 @@ class ToolsTestCase( api.ApiTestCase ):
'col': "' ; echo 'moo",
}
response = self._run( "column_param", history_id, inputs )
# TODO: make this test pass...
self._assert_status_code_is( response, 400 )
if response.status_code == 200:
message = "Known, high priority issue. Column parameters are sanitized but invalid values should prevent execution and doesn't."
raise AssertionError(message)
@skip_without_tool( "collection_paired_test" )
def test_collection_parameter( self ):
test/api/test_workflows.py
+17 -11
View File
@@ -168,6 +168,7 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase ):
return RunJobsSummary(
history_id=history_id,
workflow_id=workflow_id,
invocation_id=invocation_id,
inputs=inputs,
jobs=jobs,
)
@@ -570,11 +571,13 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
'0': self._ds_entry(hda1),
'1': self._ds_entry(hda2),
}
self.__invoke_workflow( history_id, workflow_id, inputs )
# TODO: wait on workflow invocations
time.sleep(10)
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
self.assertEquals("10.0\n30.0\n20.0\n40.0\n", self.dataset_populator.get_history_dataset_content( history_id, hid=0 ) )
invocation_id = self.__invoke_workflow( history_id, workflow_id, inputs )
self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
details = self.dataset_populator.get_history_dataset_details( history_id, hid=0 )
last_item_hid = details["hid"]
assert last_item_hid == 7, "Expected 7 history items, got %s" % last_item_hid
content = self.dataset_populator.get_history_dataset_content( history_id, hid=0 )
self.assertEquals("10.0\n30.0\n20.0\n40.0\n", content )
def test_workflow_request( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
@@ -731,7 +734,7 @@ test_data:
time.sleep( 2 )
history_id = run_summary.history_id
workflow_id = run_summary.workflow_id
invocation_id = run_summary.workflow_id
invocation_id = run_summary.invocation_id
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
invocation = self._invocation_details( workflow_id, invocation_id )
assert invocation[ 'state' ] != 'scheduled'
@@ -740,12 +743,15 @@ test_data:
assert len( self._history_jobs( history_id ) ) == 2
self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True )
self.wait_for_invocation( workflow_id, invocation_id )
time.sleep(1)
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
time.sleep(1)
self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
assert len( self._history_jobs( history_id ) ) == 4
def wait_for_invocation_and_jobs( self, history_id, workflow_id, invocation_id, assert_ok=True ):
self.wait_for_invocation( workflow_id, invocation_id )
time.sleep(.5)
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
time.sleep(.5)
def test_cannot_run_inaccessible_workflow( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -1169,4 +1175,4 @@ test_data:
'input_steps',
)
RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'invocation_id', 'inputs', 'jobs'])
test/api/test_workflows_from_yaml.py
-3
View File
@@ -100,8 +100,6 @@ test_data:
$link: the_pause
""")
print self._get("workflows/%s/download" % workflow_id).json()
assert False
# TODO: fill out test...
def test_implicit_connections( self ):
workflow_id = self._upload_yaml_workflow("""
@@ -132,4 +130,3 @@ test_data:
""")
workflow = self._get("workflows/%s/download" % workflow_id).json()
print workflow
assert False
test/functional/tool-data/data1/entry.txt
+1
View File
@@ -0,0 +1 @@
This is data 1.
test/functional/tool-data/data1/entry.txt.index
+1
View File
@@ -0,0 +1 @@
fancy compressed map built with cool algorithms...
test/functional/tool-data/data2/entry.txt
+1
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@@ -0,0 +1 @@
This is data 2.
test/functional/tool-data/data2/entry.txt.index
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fancy compressed map built with cool algorithms...2