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MIRACUM
uc3
cbioportal-frontend
Commits
3d7f6db7
Commit
3d7f6db7
authored
3 years ago
by
Niklas Reimer
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3.7.21
parent
6a0a32c1
Changes
11
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11 changed files
end-to-end-test/local/specs/core/resultsviewDisabledTabs.spec.js
+52
-0
...end-test/local/specs/core/resultsviewDisabledTabs.spec.js
env/custom.sh
+0
-1
env/custom.sh
pom.xml
+1
-1
pom.xml
src/config/IAppConfig.ts
+0
-2
src/config/IAppConfig.ts
src/pages/patientView/PatientViewPage.tsx
+0
-13
src/pages/patientView/PatientViewPage.tsx
src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
+2
-1
...s/patientView/clinicalInformation/PatientViewPageStore.ts
src/pages/patientView/mutation/column/AlleleFreqColumnFormatter.tsx
+1
-1
...patientView/mutation/column/AlleleFreqColumnFormatter.tsx
src/shared/components/query/DataTypePrioritySelector.tsx
+4
-4
src/shared/components/query/DataTypePrioritySelector.tsx
src/shared/components/query/QueryStore.ts
+8
-7
src/shared/components/query/QueryStore.ts
src/shared/components/studyTagsTooltip/StudyTagsTooltip.tsx
+3
-4
src/shared/components/studyTagsTooltip/StudyTagsTooltip.tsx
src/shared/lib/StoreUtils.ts
+5
-8
src/shared/lib/StoreUtils.ts
with
76 additions
and
42 deletions
+76
-42
end-to-end-test/local/specs/core/resultsviewDisabledTabs.spec.js
0 → 100644
+
52
-
0
View file @
3d7f6db7
var
assert
=
require
(
'
assert
'
);
var
goToUrlAndSetLocalStorageWithProperty
=
require
(
'
../../../shared/specUtils
'
)
.
goToUrlAndSetLocalStorageWithProperty
;
var
{
waitForOncoprint
}
=
require
(
'
../../../shared/specUtils
'
);
var
goToUrlAndSetLocalStorage
=
require
(
'
../../../shared/specUtils
'
)
.
goToUrlAndSetLocalStorage
;
const
CBIOPORTAL_URL
=
process
.
env
.
CBIOPORTAL_URL
.
replace
(
/
\/
$/
,
''
);
const
url
=
`
${
CBIOPORTAL_URL
}
/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&data_priority=0&gene_list=ABLIM1%250ATMEM247&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&profileFilter=0&tab_index=tab_visualize`
;
describe
(
'
results view check possibility to disable tabs
'
,
function
()
{
it
(
'
check that all tabs can be disabled
'
,
()
=>
{
goToUrlAndSetLocalStorage
(
url
,
true
);
waitForOncoprint
();
const
tabsContainer
=
$
(
'
.mainTabs
'
);
tabsContainer
.
waitForDisplayed
();
const
tabs
=
getResultsViewTabNames
();
// test that each tab can be disabled
message
=
''
;
allTabsCanBeDisabled
=
true
;
tabs
.
forEach
(
tab
=>
{
goToUrlAndSetLocalStorageWithProperty
(
url
,
true
,
{
disabled_tabs
:
tab
,
});
tabsContainer
.
waitForDisplayed
();
const
tabAnchor
=
$
(
'
.tabAnchor.tabAnchor_
'
+
tab
);
if
(
tabAnchor
.
isDisplayed
())
{
message
=
message
+
'
Tab
'
+
tab
+
'
could not be disabled;
'
;
allTabsCanBeDisabled
=
false
;
}
});
assert
(
allTabsCanBeDisabled
,
message
);
});
});
function
getResultsViewTabNames
()
{
// getting all visible tabs, excluding the first one, oncoprint
const
tabs
=
$
(
'
.nav-tabs
'
)
.
$$
(
'
.tabAnchor
'
)
.
filter
(
tab
=>
tab
.
isDisplayed
())
.
filter
(
tab
=>
tab
.
getAttribute
(
'
class
'
)
!==
'
tabAnchor tabAnchor_oncoprint
'
)
.
map
(
tab
=>
tab
.
getAttribute
(
'
class
'
)
.
split
(
'
_
'
)
.
pop
()
);
return
tabs
;
}
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env/custom.sh
+
0
-
1
View file @
3d7f6db7
# set e.g.
export
CBIOPORTAL_URL
=
"https://www.cbioportal.org"
export
GENOME_NEXUS_URL
=
"https://www.genomenexus.org"
# export FHIRSPARK_HOST=localhost
...
...
This diff is collapsed.
Click to expand it.
pom.xml
+
1
-
1
View file @
3d7f6db7
...
...
@@ -4,7 +4,7 @@
<modelVersion>
4.0.0
</modelVersion>
<groupId>
com.github.cbioportal
</groupId>
<artifactId>
cbioportal
-frontend
</artifactId>
<artifactId>
frontend-
cbioportal
</artifactId>
<version>
0.3.0
</version>
<packaging>
jar
</packaging>
...
...
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Click to expand it.
src/config/IAppConfig.ts
+
0
-
2
View file @
3d7f6db7
...
...
@@ -151,8 +151,6 @@ export interface IServerConfig {
enable_request_body_gzip_compression
:
boolean
;
enable_treatment_groups
:
boolean
;
referenceGenomeVersion
:
string
;
skin_show_unauthorized_studies
:
boolean
;
skin_global_message_for_unauthorized_studies
:
string
;
skin_home_page_show_unauthorized_studies
:
boolean
;
skin_home_page_unauthorized_studies_global_message
:
string
;
fhirspark
?:
IFhirsparkConfig
;
...
...
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Click to expand it.
src/pages/patientView/PatientViewPage.tsx
+
0
-
13
View file @
3d7f6db7
...
...
@@ -1712,19 +1712,6 @@ export default class PatientViewPage extends React.Component<
}
/>
</
MSKTab
>
{
/*<MSKTab key={5} id={{PatientViewPageTabs.MutationalSignatures}} linkText="Mutational Signature Data" hide={true}>*/
}
{
/*<div className="clearfix">*/
}
{
/*<FeatureTitle title="Mutational Signatures" isLoading={ this.patientViewPageStore.clinicalDataGroupedBySample.isPending } className="pull-left" />*/
}
{
/*<LoadingIndicator isLoading={this.patientViewPageStore.mutationalSignatureData.isPending}/>*/
}
{
/*{*/
}
{
/*(this.patientViewPageStore.clinicalDataGroupedBySample.isComplete && this.patientViewPageStore.mutationalSignatureData.isComplete) && (*/
}
{
/*<ClinicalInformationMutationalSignatureTable data={this.patientViewPageStore.mutationalSignatureData.result} showTitleBar={true}/>*/
}
{
/*)*/
}
{
/*}*/
}
{
/*</div>*/
}
{
/*</MSKTab>*/
}
{
this
.
patientViewPageStore
.
hasMutationalSignatureData
.
result
&&
(
<
MSKTab
...
...
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Click to expand it.
src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
+
2
-
1
View file @
3d7f6db7
...
...
@@ -471,7 +471,8 @@ export class PatientViewPageStore {
invoke
:
async
()
=>
findMutationMolecularProfile
(
this
.
molecularProfilesInStudy
,
this
.
studyId
this
.
studyId
,
AlterationTypeConstants
.
MUTATION_EXTENDED
),
});
...
...
This diff is collapsed.
Click to expand it.
src/pages/patientView/mutation/column/AlleleFreqColumnFormatter.tsx
+
1
-
1
View file @
3d7f6db7
...
...
@@ -264,7 +264,7 @@ export default class AlleleFreqColumnFormatter {
return
result
;
}
p
ublic
static
calcFrequency
(
mutation
:
Mutation
):
number
|
null
{
p
rotected
static
calcFrequency
(
mutation
:
Mutation
):
number
|
null
{
if
(
!
mutation
)
{
return
null
;
}
...
...
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src/shared/components/query/DataTypePrioritySelector.tsx
+
4
-
4
View file @
3d7f6db7
...
...
@@ -78,10 +78,10 @@ export const DataTypePriorityCheckBox = observer(
profileTypes
:
string
[];
store
:
QueryStore
;
})
=>
{
let
isS
elected
=
true
;
props
.
profileTypes
.
forEach
(
profileType
=>
{
isSelected
=
isSelected
&&
props
.
store
.
isProfileTypeSelected
(
profileType
);
// as long as a profile type matches any s
elected
profile
// we consider it selected
let
isSelected
=
props
.
profileTypes
.
some
(
profileType
=>
{
return
props
.
store
.
isProfileTypeSelected
(
profileType
);
});
return
(
...
...
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Click to expand it.
src/shared/components/query/QueryStore.ts
+
8
-
7
View file @
3d7f6db7
...
...
@@ -982,14 +982,15 @@ export class QueryStore {
profile
.
molecularAlterationType
+
profile
.
datatype
)
.
map
(
alterationTypeProfiles
=>
{
// A study can have multiple profiles for same
alteration
t
ype
and datatpye.
// we need just one profile of each
return
getSuffixOfMolecularProfile
(
alterationTypeProfiles
[
0
]
.
reduce
((
agg
:
string
[],
alterationTypeProfiles
)
=>
{
const
profileTypes
=
alteration
T
ype
Profiles
.
map
(
p
=>
{
return
getSuffixOfMolecularProfile
(
p
);
}
);
})
.
value
();
agg
.
push
(...
profileTypes
);
return
agg
;
},
[]);
})
.
value
();
...
...
This diff is collapsed.
Click to expand it.
src/shared/components/studyTagsTooltip/StudyTagsTooltip.tsx
+
3
-
4
View file @
3d7f6db7
...
...
@@ -131,9 +131,9 @@ class StudyInfoOverlay extends React.Component<
)
:
(
<
div
style
=
{
{
maxWidth
:
300
}
}
dangerouslySetInnerHTML
=
{
{
__html
:
`
${
message
}
`
,
}
}
dangerouslySetInnerHTML
=
{
this
.
addHTMLDescription
(
message
.
toString
()
)
}
/>
);
}
...
...
@@ -154,7 +154,6 @@ export default class StudyTagsTooltip extends React.Component<
renderTooltip
()
{
return
(
<
DefaultTooltip
key
=
{
this
.
props
.
key
}
mouseEnterDelay
=
{
this
.
props
.
mouseEnterDelay
}
placement
=
{
this
.
props
.
placement
}
overlay
=
{
...
...
This diff is collapsed.
Click to expand it.
src/shared/lib/StoreUtils.ts
+
5
-
8
View file @
3d7f6db7
...
...
@@ -1079,16 +1079,14 @@ export function isMutationProfile(profile: MolecularProfile): boolean {
export
function
findMutationMolecularProfile
(
molecularProfilesInStudy
:
MobxPromise
<
MolecularProfile
[]
>
,
studyId
:
string
,
suffix
:
string
=
MOLECULAR_PROFILE_MUTATIONS_SUFFIX
type
:
string
)
{
if
(
!
molecularProfilesInStudy
.
result
)
{
return
undefined
;
}
const
profile
=
molecularProfilesInStudy
.
result
.
find
(
(
p
:
MolecularProfile
)
=>
{
return
p
.
molecularProfileId
===
`
${
studyId
}${
suffix
}
`
;
}
const
profile
=
molecularProfilesInStudy
.
result
!
.
find
(
(
profile
:
MolecularProfile
)
=>
profile
.
molecularAlterationType
===
type
);
return
profile
;
...
...
@@ -1096,13 +1094,12 @@ export function findMutationMolecularProfile(
export
function
findUncalledMutationMolecularProfileId
(
molecularProfilesInStudy
:
MobxPromise
<
MolecularProfile
[]
>
,
studyId
:
string
,
suffix
:
string
=
MOLECULAR_PROFILE_UNCALLED_MUTATIONS_SUFFIX
studyId
:
string
)
{
const
profile
=
findMutationMolecularProfile
(
molecularProfilesInStudy
,
studyId
,
suffix
AlterationTypeConstants
.
MUTATION_UNCALLED
);
if
(
profile
)
{
return
profile
.
molecularProfileId
;
...
...
This diff is collapsed.
Click to expand it.
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