1. List data overlays

1.1. Path Parameters

Table 1. /minerva/api/projects/{projectId}/overlays/
Parameter Description

projectId

project identifier

1.2. Response Fields

Path Type Description

[].name

String

name

[].description

String

description

[].idObject

Number

identifier

[].publicOverlay

Boolean

is the data overlay publicly available to all users

[].order

Number

sort order

[].type

String

type; available options: GENERIC, GENETIC_VARIANT

[].genomeType

String

reference genome type; available options: UCSC

[].genomeVersion

String

reference genome version

[].creator

String

login of the user who uploaded data overlay

1.3. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

1.4. Sample Response 1

[ {
  "name" : "test title",
  "creator" : "admin",
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000137,
  "publicOverlay" : true,
  "type" : "GENERIC",
  "order" : 0
}, {
  "name" : "test title",
  "creator" : "test_user",
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000138,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 0
} ]

1.5. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/?creator=test_curator' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

1.6. Sample Response 2

[ {
  "name" : "test title",
  "creator" : "test_curator",
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000148,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 0
} ]

2. Get data overlay

2.1. Path Parameters

Table 2. /minerva/api/projects/{projectId}/overlays/{overlayId}/
Parameter Description

projectId

project identifier

overlayId

overlay identifier

2.2. Response Fields

Path Type Description

name

String

name

description

String

description

idObject

Number

identifier

publicOverlay

Boolean

is the data overlay publicly available to all users

order

Number

sort order

type

String

type; available options: GENERIC, GENETIC_VARIANT

genomeType

String

reference genome type; available options: UCSC

genomeVersion

String

reference genome version

creator

String

login of the user who uploaded data overlay

2.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000110/' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

2.4. Sample Response

{
  "name" : "test title",
  "creator" : "test_user",
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000110,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 0
}

3. Add overlay

3.1. Path Parameters

Table 3. /minerva/api/projects/{projectId}/overlays/
Parameter Description

projectId

project identifier

3.2. Request Parameters

Parameter Description

name

name of the data overlay

content

content of the file that is uploaded with definition what should be visible where (alternative to fileId)

fileId

uploaded file id that should be used as data overlay content content (alternative to content)

description

short description of the data overlay

filename

name of the file that should be used when downloading the source

type

type of the data overlay (default: GENERIC). Available options: GENERIC, GENETIC_VARIANT

3.3. Response Fields

Path Type Description

name

String

name

description

String

description

idObject

Number

identifier

publicOverlay

Boolean

is the data overlay publicly available to all users

order

Number

sort order

type

String

type; available options: GENERIC, GENETIC_VARIANT

genomeType

String

reference genome type; available options: UCSC

genomeVersion

String

reference genome version

creator

String

login of the user who uploaded data overlay

3.4. CURL sample from file

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/' -X POST \
    -d 'fileId=738&name=overlay+name&description=overlay+name&filename=overlay+name&type=GENERIC' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    -H 'Content-Type: application/x-www-form-urlencoded'

3.5. Sample Response from file

{
  "name" : "overlay name",
  "creator" : "admin",
  "description" : "overlay name",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000131,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 1
}

3.6. CURL sample from content

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/' -X POST \
    -d 'content=element_identifier%09value%0A%09-1&name=overlay+name&description=overlay+description&filename=source.txt&type=GENERIC' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    -H 'Content-Type: application/x-www-form-urlencoded'

3.7. Sample Response from content

{
  "name" : "overlay name",
  "creator" : "admin",
  "description" : "overlay description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000103,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 1
}

4. Update overlay

4.1. Path Parameters

Table 4. /minerva/api/projects/{projectId}/overlays/{overlayId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

4.2. Request Fields

Path Type Description

overlay.name

String

name

overlay.description

String

description

overlay.publicOverlay

Boolean

is the data overlay publicly available to all users

overlay.order

Number

sort order

overlay.type

String

type; available options: GENERIC, GENETIC_VARIANT

overlay.creator

String

login of the user who uploaded data overlay

4.3. Response Fields

Path Type Description

name

String

name

description

String

description

idObject

Number

identifier

publicOverlay

Boolean

is the data overlay publicly available to all users

order

Number

sort order

type

String

type; available options: GENERIC, GENETIC_VARIANT

genomeType

String

reference genome type; available options: UCSC

genomeVersion

String

reference genome version

creator

String

login of the user who uploaded data overlay

4.4. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000114' -X PATCH \
    -d '{"overlay":{"name":"test title","creator":"test_user","description":"test description","publicOverlay":false,"type":"GENERIC","order":0}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    -H 'Content-Type: application/json'

4.5. Sample Response

{
  "name" : "test title",
  "creator" : "test_user",
  "description" : "test description",
  "genomeType" : null,
  "genomeVersion" : null,
  "idObject" : 1000114,
  "publicOverlay" : false,
  "type" : "GENERIC",
  "order" : 0
}

5. Delete overlay

5.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000160' -X DELETE \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

5.2. Path Parameters

Table 5. /minerva/api/projects/{projectId}/overlays/{overlayId}
Parameter Description

projectId

project identifier

overlayId

overlay identifier

6. Download source data

6.1. Path Parameters

Table 6. /minerva/api/projects/{projectId}/overlays/{overlayId}:downloadSource
Parameter Description

projectId

project identifier

overlayId

overlay identifier

6.2. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000140:downloadSource' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.3. Sample Response

element_identifier	value
	-1

7. Download legend

7.1. Path Parameters

Unresolved directive in project_overlays.adoc - include::../../../target/generated-snippets/projects/project_legend/download_source/path-parameters.adoc[]

7.2. CURL sample

Unresolved directive in project_overlays.adoc - include::../../../target/generated-snippets/projects/project_legend/download_source/curl-request.adoc[]

8. Get list of associated bioEntites

8.1. Path Parameters

Table 7. /minerva/api/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/
Parameter Description

projectId

project identifier

mapId

map identifier

overlayId

overlay identifier

8.2. Response Fields

Path Type Description

[].type

String

type of bioEntity (ALIAS/REACTION)

[].overlayContent.idObject

String

identifier of the bioEntity

[].overlayContent.modelId

Number

map identifier where bioEntity is located

[].overlayContent.value

Number

normalized value assigned to the bioEntity from overlay

[].overlayContent.color

Object

color assigned to the bioEntity from overlay

[].overlayContent.description

String

description assigned to the bioEntity from overlay

[].overlayContent.sourceData

String

source data

[].overlayContent.geneVariations

Array

list of gene variants assigned to the bioEntity from overlay

[].overlayContent.width

Number

line width of reaction bioEntity assigned to the bioEntity from overlay

8.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000146/models/*/bioEntities/' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

8.4. Sample Response

[ {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1142,
    "idObject" : "2848",
    "value" : 1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 2848,
    "sourceData" : null
  }
}, {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1142,
    "idObject" : "2852",
    "value" : 1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 2852,
    "sourceData" : null
  }
}, {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1142,
    "idObject" : "2851",
    "value" : 1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 2851,
    "sourceData" : null
  }
}, {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1142,
    "idObject" : "2849",
    "value" : 1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 2849,
    "sourceData" : null
  }
}, {
  "type" : "REACTION",
  "overlayContent" : {
    "modelId" : 1142,
    "idObject" : "574",
    "value" : -1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 574,
    "sourceData" : null,
    "width" : null
  }
}, {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1143,
    "idObject" : "2850",
    "value" : 1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "uniqueId" : 2850,
    "sourceData" : null
  }
} ]

9. Get reaction data

9.1. Path Parameters

Table 8. /minerva/api/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/reactions/{reactionId}/
Parameter Description

projectId

project identifier

mapId

map identifier

overlayId

overlay identifier

reactionId

reaction identifier

9.2. Response Fields

Path Type Description

[].type

String

type of bioEntity (ALIAS/REACTION)

[].overlayContent.idObject

String

identifier of the bioEntity

[].overlayContent.modelId

Number

map identifier where bioEntity is located

[].overlayContent.value

Number

normalized value assigned to the bioEntity from overlay

[].overlayContent.color

Object

color assigned to the bioEntity from overlay

[].overlayContent.description

String

description assigned to the bioEntity from overlay

[].overlayContent.sourceData

String

source data

[].overlayContent.geneVariations

Array

list of gene variants assigned to the bioEntity from overlay

[].overlayContent.width

Number

line width of reaction bioEntity assigned to the bioEntity from overlay

9.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000100/models/1046/bioEntities/reactions/526/' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

9.4. Sample Response

[ {
  "type" : "REACTION",
  "overlayContent" : {
    "modelId" : 1046,
    "idObject" : "526",
    "value" : -1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "geneVariations" : [ ],
    "uniqueId" : 526,
    "sourceData" : null,
    "width" : null
  }
} ]

10. Get element data

10.1. Path Parameters

Table 9. /minerva/api/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/elements/{elementId}/
Parameter Description

projectId

project identifier

mapId

map identifier

overlayId

overlay identifier

elementId

element identifier

10.2. Response Fields

Path Type Description

[].type

String

type of bioEntity (ALIAS/REACTION)

[].overlayContent.idObject

String

identifier of the bioEntity

[].overlayContent.modelId

Number

map identifier where bioEntity is located

[].overlayContent.value

Number

normalized value assigned to the bioEntity from overlay

[].overlayContent.color

Object

color assigned to the bioEntity from overlay

[].overlayContent.description

String

description assigned to the bioEntity from overlay

[].overlayContent.sourceData

String

source data

[].overlayContent.geneVariations

Array

list of gene variants assigned to the bioEntity from overlay

[].overlayContent.width

Number

line width of reaction bioEntity assigned to the bioEntity from overlay

10.3. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/projects/test_project/overlays/1000152/models/1154/bioEntities/elements/2881/' -X GET \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

10.4. Sample Response

[ {
  "type" : "ALIAS",
  "overlayContent" : {
    "modelId" : 1154,
    "idObject" : "2881",
    "value" : -1.0,
    "color" : null,
    "description" : null,
    "type" : "GENERIC",
    "geneVariations" : [ ],
    "uniqueId" : 2881,
    "sourceData" : null
  }
} ]