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minerva
core
Commits
c337bf43
Commit
c337bf43
authored
Apr 05, 2018
by
Piotr Gawron
Browse files
copying annotators settings from other elemnts in tree and applying settings to subtree added
parent
fef90d5e
Pipeline
#4416
passed with stage
in 2 minutes and 28 seconds
Changes
7
Pipelines
1
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frontend-js/package-lock.json
View file @
c337bf43
...
...
@@ -45,30 +45,38 @@
"litemol"
:
"github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
},
"dependencies"
:
{
"ProtVista"
:
{
"version"
:
"git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e"
,
"dev"
:
true
,
"requires"
:
{
"d3"
:
"3.5.17"
,
"file-saver"
:
"1.3.3"
,
"jquery"
:
"2.2.4"
,
"jszip"
:
"3.1.4"
,
"underscore"
:
"1.8.3"
},
"dependencies"
:
{
"jquery"
:
{
"version"
:
"2.2.4"
,
"resolved"
:
"https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz"
,
"integrity"
:
"sha1-LInWiJterFIqfuoywUUhVZxsvwI="
,
"dev"
:
true
}
}
},
"jquery"
:
{
"version"
:
"3.3.1"
,
"resolved"
:
"https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz"
,
"integrity"
:
"sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg=="
,
"dev"
:
true
}
}
},
"ProtVista"
:
{
"version"
:
"git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e"
,
"dev"
:
true
,
"requires"
:
{
"d3"
:
"3.5.17"
,
"file-saver"
:
"1.3.3"
,
"jquery"
:
"2.2.4"
,
"jszip"
:
"3.1.4"
,
"underscore"
:
"1.8.3"
},
"dependencies"
:
{
"jquery"
:
{
"version"
:
"2.2.4"
,
"resolved"
:
"https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz"
,
"integrity"
:
"sha1-LInWiJterFIqfuoywUUhVZxsvwI="
,
"dev"
:
true
},
"litemol"
:
{
"version"
:
"github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
,
"dev"
:
true
,
"requires"
:
{
"@types/react"
:
"15.6.15"
,
"@types/react-dom"
:
"15.5.7"
}
}
}
},
...
...
@@ -2050,14 +2058,6 @@
"immediate"
:
"3.0.6"
}
},
"litemol"
:
{
"version"
:
"github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
,
"dev"
:
true
,
"requires"
:
{
"@types/react"
:
"15.6.15"
,
"@types/react-dom"
:
"15.5.7"
}
},
"lodash"
:
{
"version"
:
"4.17.4"
,
"resolved"
:
"https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz"
,
...
...
frontend-js/src/main/js/ServerConnector.js
View file @
c337bf43
...
...
@@ -1105,7 +1105,7 @@ ServerConnector.updateUserPreferences = function (params) {
var
obj
=
JSON
.
parse
(
content
);
var
user
=
new
User
(
obj
);
if
(
self
.
_usersByLogin
[
user
.
getLogin
()]
!==
undefined
)
{
self
.
_usersByLogin
[
user
.
getLogin
()].
update
(
user
);
self
.
_usersByLogin
[
user
.
getLogin
()].
getPreferences
().
update
(
user
.
getPreferences
()
);
}
else
{
self
.
_usersByLogin
[
user
.
getLogin
()]
=
user
;
}
...
...
frontend-js/src/main/js/gui/admin/AddProjectDialog.js
View file @
c337bf43
...
...
@@ -129,7 +129,8 @@ AddProjectDialog.prototype.showAnnotatorsDialog = function () {
if
(
self
.
_annotatorsDialog
===
undefined
)
{
self
.
_annotatorsDialog
=
new
ChooseAnnotatorsDialog
({
element
:
Functions
.
createElement
({
type
:
"
div
"
}),
customMap
:
null
customMap
:
null
,
configuration
:
self
.
getConfiguration
()
});
promise
=
self
.
_annotatorsDialog
.
init
();
}
else
{
...
...
frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
View file @
c337bf43
...
...
@@ -62,15 +62,53 @@ function onChangeParameterValue(element, user) {
return
ServerConnector
.
updateUserPreferences
({
user
:
user
,
preferences
:
data
}).
then
(
null
,
GuiConnector
.
alert
);
}
ChooseAnnotatorsDialog
.
prototype
.
saveAnnotatorsInfo
=
function
(
elementTypes
,
selectedAnnotators
)
{
selectedAnnotators
=
selectedAnnotators
.
slice
();
return
ServerConnector
.
getLoggedUser
().
then
(
function
(
user
)
{
var
data
=
new
UserPreferences
();
var
elementAnnotators
=
{};
for
(
var
i
=
0
;
i
<
elementTypes
.
length
;
i
++
)
{
elementAnnotators
[
elementTypes
[
i
].
className
]
=
selectedAnnotators
;
var
userAnnotators
=
user
.
getPreferences
().
getElementAnnotators
(
elementTypes
[
i
].
className
);
userAnnotators
.
length
=
0
;
userAnnotators
.
push
.
apply
(
userAnnotators
,
selectedAnnotators
);
}
data
.
setElementAnnotators
(
elementAnnotators
);
return
ServerConnector
.
updateUserPreferences
({
user
:
user
,
preferences
:
data
});
}).
catch
(
GuiConnector
.
alert
);
};
ChooseAnnotatorsDialog
.
prototype
.
getAllChildrenTypesIfNeeded
=
function
(
elementType
,
includeChildren
)
{
var
result
=
[
elementType
];
if
(
includeChildren
)
{
var
queue
=
[
elementType
];
var
elementTypes
=
this
.
getConfiguration
().
getElementTypes
();
while
(
queue
.
length
>
0
)
{
var
type
=
queue
.
shift
();
for
(
var
i
=
0
;
i
<
elementTypes
.
length
;
i
++
)
{
if
(
type
.
className
===
elementTypes
[
i
].
parentClass
)
{
queue
.
push
(
elementTypes
[
i
]);
result
.
push
(
elementTypes
[
i
]);
}
}
}
}
return
result
;
};
ChooseAnnotatorsDialog
.
prototype
.
setElementType
=
function
(
elementType
)
{
var
self
=
this
;
var
configuration
;
var
configuration
=
self
.
getConfiguration
()
;
return
ServerConnector
.
getConfiguration
().
then
(
function
(
result
)
{
configuration
=
result
;
return
ServerConnector
.
getLoggedUser
();
}).
then
(
function
(
user
)
{
return
ServerConnector
.
getLoggedUser
().
then
(
function
(
user
)
{
var
element
=
$
(
"
[name='annotatorListBox']
"
,
self
.
getElement
())[
0
];
var
annotatorsParams
=
$
(
"
.minerva-annotators-params
"
,
self
.
getElement
())[
0
];
Functions
.
removeChildren
(
element
);
...
...
@@ -81,6 +119,52 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
});
element
.
appendChild
(
selectElement
);
var
includeChildrenCheckbox
=
Functions
.
createElement
({
type
:
"
input
"
,
inputType
:
"
checkbox
"
});
element
.
appendChild
(
includeChildrenCheckbox
);
element
.
appendChild
(
Functions
.
createElement
({
type
:
"
span
"
,
content
:
"
Apply to all in subtree
"
}));
element
.
appendChild
(
Functions
.
createElement
({
type
:
"
br
"
}));
var
copyFromButton
=
Functions
.
createElement
({
type
:
"
button
"
,
content
:
"
Copy from
"
,
onclick
:
function
()
{
var
typeClassName
=
copyFromSelect
.
value
;
var
annotators
;
for
(
var
i
=
0
;
i
<
configuration
.
getElementTypes
().
length
;
i
++
)
{
var
type
=
configuration
.
getElementTypes
()[
i
];
if
(
typeClassName
===
type
.
className
)
{
annotators
=
user
.
getPreferences
().
getElementAnnotators
(
typeClassName
);
}
}
if
(
annotators
===
undefined
)
{
return
GuiConnector
.
alert
(
"
Invalid element type:
"
+
copyFromSelect
.
value
);
}
else
{
var
includeChildren
=
includeChildrenCheckbox
.
checked
;
return
self
.
saveAnnotatorsInfo
(
self
.
getAllChildrenTypesIfNeeded
(
elementType
,
includeChildren
),
annotators
).
then
(
function
()
{
return
self
.
setElementType
(
elementType
);
});
}
}
});
element
.
appendChild
(
copyFromButton
);
var
copyFromSelect
=
Functions
.
createElement
({
type
:
"
select
"
,
style
:
"
margin:5px
"
});
element
.
appendChild
(
copyFromSelect
);
var
options
=
[],
i
;
for
(
i
=
0
;
i
<
configuration
.
getElementTypes
().
length
;
i
++
)
{
var
type
=
configuration
.
getElementTypes
()[
i
];
var
name
=
type
.
className
;
if
(
name
.
indexOf
(
"
.
"
)
>
0
)
{
name
=
name
.
substr
(
name
.
lastIndexOf
(
"
.
"
)
+
1
);
}
options
.
push
(
Functions
.
createElement
({
type
:
"
option
"
,
value
:
type
.
className
,
content
:
name
}));
}
options
.
sort
(
function
(
a
,
b
)
{
return
a
.
text
===
b
.
text
?
0
:
a
.
text
<
b
.
text
?
-
1
:
1
});
for
(
i
=
0
;
i
<
options
.
length
;
i
++
)
{
copyFromSelect
.
appendChild
(
options
[
i
]);
}
var
annotators
=
configuration
.
getElementAnnotators
(
elementType
);
...
...
@@ -90,7 +174,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var
entries
=
[];
for
(
var
i
=
0
;
i
<
annotators
.
length
;
i
++
)
{
for
(
i
=
0
;
i
<
annotators
.
length
;
i
++
)
{
var
annotator
=
annotators
[
i
];
var
entry
=
{
name
:
annotator
.
getName
(),
value
:
annotator
.
getClassName
(),
selected
:
false
};
for
(
var
j
=
0
;
j
<
selectedAnnotators
.
length
;
j
++
)
{
...
...
@@ -115,9 +199,6 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
annotator
=
annotators
[
i
];
}
}
var
data
=
new
UserPreferences
();
var
elementAnnotators
=
{};
if
(
selected
)
{
selectedAnnotators
.
push
(
annotator
.
getName
());
}
else
{
...
...
@@ -127,13 +208,12 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}
}
createAnnotatorsParams
();
elementAnnotators
[
elementType
.
className
]
=
selectedAnnotators
;
data
.
setElementAnnotators
(
elementAnnotators
);
return
ServerConnector
.
updateUserPreferences
({
user
:
user
,
preferences
:
data
}).
then
(
null
,
GuiConnector
.
alert
);
var
includeChildren
=
includeChildrenCheckbox
.
checked
;
return
self
.
saveAnnotatorsInfo
(
self
.
getAllChildrenTypesIfNeeded
(
elementType
,
includeChildren
),
selectedAnnotators
);
};
includeChildrenCheckbox
.
onchange
=
function
()
{
var
includeChildren
=
includeChildrenCheckbox
.
checked
;
return
self
.
saveAnnotatorsInfo
(
self
.
getAllChildrenTypesIfNeeded
(
elementType
,
includeChildren
),
selectedAnnotators
);
};
checkboxList
.
addListener
(
"
select
"
,
function
(
element
)
{
...
...
@@ -295,7 +375,7 @@ ChooseAnnotatorsDialog.prototype.open = function () {
});
}
$
(
div
).
dialog
(
"
open
"
);
$
(
div
).
css
(
"
overflow
"
,
"
hidden
"
);
$
(
div
).
css
(
"
overflow
"
,
"
hidden
"
);
};
module
.
exports
=
ChooseAnnotatorsDialog
;
frontend-js/src/main/js/map/data/UserPreferences.js
View file @
c337bf43
...
...
@@ -81,7 +81,8 @@ UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
UserPreferences
.
prototype
.
getElementAnnotators
=
function
(
className
)
{
var
result
=
this
.
_elementAnnotators
[
className
];
if
(
result
===
undefined
)
{
result
=
[];
this
.
_elementAnnotators
[
className
]
=
[];
result
=
this
.
_elementAnnotators
[
className
];
}
return
result
;
};
...
...
frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js
View file @
c337bf43
...
...
@@ -10,23 +10,50 @@ var chai = require('chai');
var
assert
=
chai
.
assert
;
describe
(
'
ChooseAnnotatorsDialog
'
,
function
()
{
it
(
'
init
'
,
function
()
{
var
dialog
=
new
ChooseAnnotatorsDialog
({
function
createDialog
()
{
return
new
ChooseAnnotatorsDialog
({
element
:
testDiv
,
customMap
:
null
customMap
:
null
,
configuration
:
helper
.
getConfiguration
()
});
}
it
(
'
init
'
,
function
()
{
var
dialog
=
createDialog
();
assert
.
equal
(
0
,
logger
.
getWarnings
().
length
);
return
dialog
.
init
();
});
it
(
'
setElementType
'
,
function
()
{
var
dialog
=
new
ChooseAnnotatorsDialog
({
element
:
testDiv
,
customMap
:
null
});
var
dialog
=
createDialog
();
return
ServerConnector
.
getConfiguration
().
then
(
function
(
configuration
)
{
return
dialog
.
setElementType
(
configuration
.
getReactionTypes
()[
0
]);
})
});
it
(
'
saveAnnotatorsInfo
'
,
function
()
{
var
dialog
=
createDialog
();
var
user
;
return
ServerConnector
.
getLoggedUser
().
then
(
function
(
result
)
{
user
=
result
;
return
ServerConnector
.
getConfiguration
();
}).
then
(
function
(
configuration
)
{
var
elementTypes
=
configuration
.
getElementTypes
();
return
dialog
.
saveAnnotatorsInfo
(
elementTypes
,
[]);
});
});
it
(
'
getAllChildrenTypesIfNeeded
'
,
function
()
{
var
dialog
=
createDialog
();
var
configuration
=
helper
.
getConfiguration
();
var
elementTypes
=
configuration
.
getElementTypes
();
var
elementType
;
for
(
var
i
=
0
;
i
<
elementTypes
.
length
;
i
++
)
{
if
(
elementTypes
[
i
].
className
===
"
lcsb.mapviewer.model.map.species.Protein
"
)
{
elementType
=
elementTypes
[
i
];
}
}
assert
.
equal
(
1
,
dialog
.
getAllChildrenTypesIfNeeded
(
elementType
,
false
).
length
);
assert
.
ok
(
dialog
.
getAllChildrenTypesIfNeeded
(
elementType
,
true
).
length
>=
5
);
});
});
frontend-js/testFiles/apiCalls/users/anonymous.updatePreferences/PATCH_token=MOCK_TOKEN_ID&
0 → 100644
View file @
c337bf43
{"preferences":{"annotators-parameters":{},"element-annotators":{"lcsb.mapviewer.model.map.BioEntity":[],"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.Compartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.OvalCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.PathwayCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.RightSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.SquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.TopSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.reaction.Reaction":[],"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction":[],"lcsb.mapviewer.model.map.reaction.type.DissociationReaction":[],"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction":[],"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction":[],"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction":[],"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction":[],"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction":[],"lcsb.mapviewer.model.map.reaction.type.TranslationReaction":[],"lcsb.mapviewer.model.map.reaction.type.TransportReaction":[],"lcsb.mapviewer.model.map.reaction.type.TruncationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction":[],"lcsb.mapviewer.model.map.species.AntisenseRna":[],"lcsb.mapviewer.model.map.species.Chemical":["Chebi"],"lcsb.mapviewer.model.map.species.Complex":["Gene Ontology"],"lcsb.mapviewer.model.map.species.Degraded":[],"lcsb.mapviewer.model.map.species.Drug":[],"lcsb.mapviewer.model.map.species.Element":[],"lcsb.mapviewer.model.map.species.Gene":["HGNC"],"lcsb.mapviewer.model.map.species.GenericProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Ion":["Chebi"],"lcsb.mapviewer.model.map.species.IonChannelProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Phenotype":["Gene 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\ No newline at end of file
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