Rest New API Documentation - Element modifications

Modification residues (and other modification sites) of the element. The endpoints are served from /new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications.

1. List modifications

Returns all modifications of the element.

1.1. HTTP request

GET /minerva/new_api/projects/test_project/maps/248/bio_entities/elements/673/modifications/ HTTP/1.1

1.2. Path Parameters

Table 1. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications/
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`id`	unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file)

1.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/248/bio_entities/elements/673/modifications/' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

1.4. HTTP response

HTTP/1.1 200 OK

1.5. Sample Response

{
  "content" : [ {
    "id" : 51590,
    "idModificationResidue" : "r4",
    "name" : "",
    "x" : 10.0,
    "y" : 20.0,
    "z" : 13,
    "width" : 15.0,
    "height" : 15.0,
    "nameX" : 10.0,
    "nameY" : 20.0,
    "nameWidth" : 15.0,
    "nameHeight" : 15.0,
    "nameVerticalAlign" : "MIDDLE",
    "nameHorizontalAlign" : "CENTER",
    "species" : 673,
    "borderColor" : "#000000ff",
    "fillColor" : "#ffffffff",
    "fontSize" : 10.0,
    "fontWeight" : "NORMAL",
    "fontStyle" : "NORMAL",
    "state" : null,
    "sboTerm" : "SBO:0000493",
    "stateAbbreviation" : null,
    "size" : 225.0,
    "elementId" : "r4"
  }, {
    "id" : 51591,
    "idModificationResidue" : "",
    "name" : "X",
    "x" : 10.0,
    "y" : 20.0,
    "z" : 14,
    "width" : 10.0,
    "height" : 10.0,
    "nameX" : 10.0,
    "nameY" : 20.0,
    "nameWidth" : 10.0,
    "nameHeight" : 10.0,
    "nameVerticalAlign" : "MIDDLE",
    "nameHorizontalAlign" : "CENTER",
    "species" : 673,
    "borderColor" : "#000000ff",
    "fillColor" : "#ffffffff",
    "fontSize" : 12.0,
    "fontWeight" : "NORMAL",
    "fontStyle" : "NORMAL",
    "sboTerm" : "SBO:0000181",
    "size" : 100.0,
    "elementId" : ""
  }, {
    "id" : 51592,
    "idModificationResidue" : "b5",
    "name" : "",
    "x" : 60.0,
    "y" : 20.0,
    "z" : 15,
    "width" : 10.0,
    "height" : 10.0,
    "nameX" : 60.0,
    "nameY" : 20.0,
    "nameWidth" : 10.0,
    "nameHeight" : 10.0,
    "nameVerticalAlign" : "MIDDLE",
    "nameHorizontalAlign" : "CENTER",
    "species" : 673,
    "borderColor" : "#000000ff",
    "fillColor" : "#ffffffff",
    "fontSize" : 10.0,
    "fontWeight" : "NORMAL",
    "fontStyle" : "NORMAL",
    "sboTerm" : "SBO:0000494",
    "size" : 100.0,
    "elementId" : "b5"
  } ],
  "totalPages" : 1,
  "totalElements" : 3,
  "numberOfElements" : 3,
  "size" : 3,
  "number" : 0
}

2. Get modification

Returns a single modification of the element.

2.1. HTTP request

GET /minerva/new_api/projects/test_project/maps/250/bio_entities/elements/679/modifications/51597 HTTP/1.1

2.2. Path Parameters

Table 2. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications/{modificationId}
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`id`	unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file)
`modificationId`	modification residue identifier

2.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/250/bio_entities/elements/679/modifications/51597' -X GET \
    -H 'Authorization: Bearer xxxxxxxx'

2.4. HTTP response

HTTP/1.1 200 OK

2.5. Sample Response

{
  "id" : 51597,
  "idModificationResidue" : "b5",
  "name" : "",
  "x" : 60.0,
  "y" : 20.0,
  "z" : 15,
  "width" : 10.0,
  "height" : 10.0,
  "nameX" : 60.0,
  "nameY" : 20.0,
  "nameWidth" : 10.0,
  "nameHeight" : 10.0,
  "nameVerticalAlign" : "MIDDLE",
  "nameHorizontalAlign" : "CENTER",
  "species" : 679,
  "borderColor" : "#000000ff",
  "fillColor" : "#ffffffff",
  "fontSize" : 10.0,
  "fontWeight" : "NORMAL",
  "fontStyle" : "NORMAL",
  "sboTerm" : "SBO:0000494",
  "size" : 100.0,
  "elementId" : "b5"
}

3. Add modification

Adds a modification to the element. The sboTerm field decides which kind of modification is created.

3.1. HTTP request

POST /minerva/new_api/projects/test_project/maps/252/bio_entities/elements/685/modifications/ HTTP/1.1

3.2. Path Parameters

Table 3. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications/
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`id`	unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file)

3.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/252/bio_entities/elements/685/modifications/' -X POST \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"sboTerm":"SBO:0000493","modificationResidueId":"zz","x":12.0,"y":13.0,"z":2,"width":1.0,"height":1.0,"fontSize":10.0,"borderColor":"#00ffffff","fillColor":"#ff00ffff","name":"xy","nameX":12.0,"nameY":13.0,"nameWidth":1.0,"nameHeight":1.0,"nameHorizontalAlign":"CENTER","nameVerticalAlign":"MIDDLE","state":"phosphorylated","direction":null,"active":null}' \
    -H 'Content-Type: application/json'

3.4. HTTP response

HTTP/1.1 201 Created

3.5. Sample Response

{
  "id" : 51603,
  "idModificationResidue" : "zz",
  "name" : "xy",
  "x" : 12.0,
  "y" : 13.0,
  "z" : 2,
  "width" : 1.0,
  "height" : 1.0,
  "nameX" : 12.0,
  "nameY" : 13.0,
  "nameWidth" : 1.0,
  "nameHeight" : 1.0,
  "nameVerticalAlign" : "MIDDLE",
  "nameHorizontalAlign" : "CENTER",
  "species" : 685,
  "borderColor" : "#00ffffff",
  "fillColor" : "#ff00ffff",
  "fontSize" : 10.0,
  "fontWeight" : "NORMAL",
  "fontStyle" : "NORMAL",
  "state" : "PHOSPHORYLATED",
  "sboTerm" : "SBO:0000493",
  "stateAbbreviation" : "P",
  "size" : 1.0,
  "elementId" : "zz"
}

4. Update modification

A full replacement of the modification: every geometry and label field has to be sent, as omitted ones are cleared, and neither sboTerm nor modificationResidueId may be changed. state is only stored for modifications that can carry one (such as a phosphorylated residue), direction and active only for transcription sites.

Note	Supports optimistic locking via the `If-Match` header.

4.1. HTTP request

PUT /minerva/new_api/projects/test_project/maps/256/bio_entities/elements/698/modifications/51613 HTTP/1.1

4.2. Path Parameters

Table 4. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications/{modificationId}
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`id`	unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file)
`modificationId`	modification residue identifier

4.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/256/bio_entities/elements/698/modifications/51613' -X PUT \
    -H 'Authorization: Bearer xxxxxxxx' \
    -d '{"sboTerm":"SBO:0000494","modificationResidueId":"b5","x":60.0,"y":20.0,"z":15,"width":10.0,"height":10.0,"fontSize":10.0,"borderColor":"#000000ff","fillColor":"#ffffffff","name":"","nameX":60.0,"nameY":20.0,"nameWidth":10.0,"nameHeight":10.0,"nameHorizontalAlign":"CENTER","nameVerticalAlign":"MIDDLE","state":null,"direction":null,"active":null}' \
    -H 'Content-Type: application/json'

4.4. HTTP response

HTTP/1.1 200 OK

4.5. Sample Response

{
  "id" : 51613,
  "idModificationResidue" : "b5",
  "name" : "",
  "x" : 60.0,
  "y" : 20.0,
  "z" : 15,
  "width" : 10.0,
  "height" : 10.0,
  "nameX" : 60.0,
  "nameY" : 20.0,
  "nameWidth" : 10.0,
  "nameHeight" : 10.0,
  "nameVerticalAlign" : "MIDDLE",
  "nameHorizontalAlign" : "CENTER",
  "species" : 698,
  "borderColor" : "#000000ff",
  "fillColor" : "#ffffffff",
  "fontSize" : 10.0,
  "fontWeight" : "NORMAL",
  "fontStyle" : "NORMAL",
  "sboTerm" : "SBO:0000494",
  "size" : 100.0,
  "elementId" : "b5"
}

5. Delete modification

Removes one modification site from the element, for instance a phosphorylation residue together with its state, position and label; the element itself and its remaining modifications are left in place.

Note	Supports optimistic locking via the `If-Match` header.

5.1. HTTP request

DELETE /minerva/new_api/projects/test_project/maps/254/bio_entities/elements/691/modifications/51608 HTTP/1.1

5.2. Path Parameters

Table 5. /minerva/new_api/projects/{projectId}/maps/{mapId}/bio_entities/elements/{id}/modifications/{modificationId}
Parameter	Description
`projectId`	project identifier
`mapId`	map identifier
`id`	unique element identifier (the numeric "id" field of the element, not the "elementId" taken from the source file)
`modificationId`	modification residue identifier

5.3. CURL sample

$ curl 'https://minerva-dev.lcsb.uni.lu/minerva/new_api/projects/test_project/maps/254/bio_entities/elements/691/modifications/51608' -X DELETE \
    -H 'Authorization: Bearer xxxxxxxx'

5.4. HTTP response

HTTP/1.1 200 OK