Rest API Documentation

1. List all users

1.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/' -i -X GET

1.2. Response Fields

Path Type Description

Path	Type	Description
`[]`	`array`	list of available input formats
`[].login`	`string`	user login
`[].connectedToLdap`	`boolean`	is user account connected to ldap
`[].ldapAccountAvailable`	`boolean`	does is account exist in ldap
`[].email`	`string`	email address
`[].id`	`number`	user unique id
`[].maxColor`	`color`	color used for drawing data overlays with max value
`[].minColor`	`color`	color used for drawing data overlays with min value
`[].neutralColor`	`color`	color used for drawing data overlays with 0 value
`[].simpleColor`	`color`	color used for drawing data overlays without value
`[].name`	`string`	first name
`[].surname`	`string`	last name
`[].removed`	`boolean`	is the account removed
`[].termsOfUseConsent`	`boolean`	did user agree to terms of use
`[].privileges`	`array`	list of user privileges
`[].privileges[].objectId`	`string`	object id to which project has privilege
`[].privileges[].privilegeType`	`string`	type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

[]

array

list of available input formats

[].login

string

user login

[].connectedToLdap

boolean

is user account connected to ldap

[].ldapAccountAvailable

boolean

does is account exist in ldap

[].email

string

email address

[].id

number

user unique id

[].maxColor

color

color used for drawing data overlays with max value

[].minColor

color

color used for drawing data overlays with min value

[].neutralColor

color

color used for drawing data overlays with 0 value

[].simpleColor

color

color used for drawing data overlays without value

[].name

string

first name

[].surname

string

last name

[].removed

boolean

is the account removed

[].termsOfUseConsent

boolean

did user agree to terms of use

[].privileges

array

list of user privileges

[].privileges[].objectId

string

object id to which project has privilege

[].privileges[].privilegeType

string

type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

1.3. Sample Response

[ {
  "connectedToLdap" : false,
  "email" : null,
  "id" : 898,
  "ldapAccountAvailable" : false,
  "login" : "test_user",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}, {
  "connectedToLdap" : false,
  "email" : null,
  "id" : 3,
  "ldapAccountAvailable" : false,
  "login" : "anonymous",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ {
    "objectId" : "empty",
    "privilegeType" : "READ_PROJECT"
  }, {
    "objectId" : "test_project",
    "privilegeType" : "READ_PROJECT"
  } ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}, {
  "connectedToLdap" : false,
  "email" : null,
  "id" : 1,
  "ldapAccountAvailable" : false,
  "login" : "admin",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ {
    "objectId" : "empty",
    "privilegeType" : "READ_PROJECT"
  }, {
    "objectId" : null,
    "privilegeType" : "IS_CURATOR"
  }, {
    "objectId" : null,
    "privilegeType" : "IS_ADMIN"
  }, {
    "objectId" : "empty",
    "privilegeType" : "WRITE_PROJECT"
  }, {
    "objectId" : "test_id2",
    "privilegeType" : "WRITE_PROJECT"
  } ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
} ]

2. Get specific user data

2.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user' -i -X GET

2.2. Path Parameters

Table 1. /users/{login}
Parameter	Description
`login`	user login

2.3. Response Fields

Path Type Description

Path	Type	Description
`login`	`string`	user login
`connectedToLdap`	`boolean`	is user account connected to ldap
`ldapAccountAvailable`	`boolean`	does is account exist in ldap
`email`	`string`	email address
`id`	`number`	user unique id
`maxColor`	`color`	color used for drawing data overlays with max value
`minColor`	`color`	color used for drawing data overlays with min value
`neutralColor`	`color`	color used for drawing data overlays with 0 value
`simpleColor`	`color`	color used for drawing data overlays without value
`name`	`string`	first name
`surname`	`string`	last name
`removed`	`boolean`	is the account removed
`termsOfUseConsent`	`boolean`	did user agree to terms of use
`privileges`	`array`	list of user privileges
`privileges[].objectId`	`string`	object id to which project has privilege
`privileges[].privilegeType`	`string`	type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

login

string

user login

connectedToLdap

boolean

is user account connected to ldap

ldapAccountAvailable

boolean

does is account exist in ldap

email

string

email address

id

number

user unique id

maxColor

color

color used for drawing data overlays with max value

minColor

color

color used for drawing data overlays with min value

neutralColor

color

color used for drawing data overlays with 0 value

simpleColor

color

color used for drawing data overlays without value

name

string

first name

surname

string

last name

removed

boolean

is the account removed

termsOfUseConsent

boolean

did user agree to terms of use

privileges

array

list of user privileges

privileges[].objectId

string

object id to which project has privilege

privileges[].privilegeType

string

type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

2.4. Sample Response

{
  "connectedToLdap" : false,
  "email" : null,
  "id" : 915,
  "ldapAccountAvailable" : false,
  "login" : "test_user",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}

3. Create user

3.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/xyz' -i -X POST \
    -H 'Content-Type: application/x-www-form-urlencoded' \
    -d 'name=FirstName&password=FirstName' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

3.2. Path Parameters

Table 2. /users/{login}
Parameter	Description
`login`	user login

3.3. Request Parameters

Parameter Description

Parameter	Description
`password`	user password
`connectedToLdap`	is user account connected to ldap
`ldapAccountAvailable`	does is account exist in ldap
`email`	email address
`maxColor`	color used for drawing data overlays with max value
`minColor`	color used for drawing data overlays with min value
`neutralColor`	color used for drawing data overlays with 0 value
`simpleColor`	color used for drawing data overlays without value
`name`	first name
`surname`	last name

password

user password

connectedToLdap

is user account connected to ldap

ldapAccountAvailable

does is account exist in ldap

email

email address

maxColor

color used for drawing data overlays with max value

minColor

color used for drawing data overlays with min value

neutralColor

color used for drawing data overlays with 0 value

simpleColor

color used for drawing data overlays without value

name

first name

surname

last name

3.4. Response Fields

Path Type Description

Path	Type	Description
`login`	`string`	user login
`connectedToLdap`	`boolean`	is user account connected to ldap
`ldapAccountAvailable`	`boolean`	does is account exist in ldap
`email`	`string`	email address
`id`	`number`	user unique id
`maxColor`	`color`	color used for drawing data overlays with max value
`minColor`	`color`	color used for drawing data overlays with min value
`neutralColor`	`color`	color used for drawing data overlays with 0 value
`simpleColor`	`color`	color used for drawing data overlays without value
`name`	`string`	first name
`surname`	`string`	last name
`removed`	`boolean`	is the account removed
`termsOfUseConsent`	`boolean`	did user agree to terms of use
`privileges`	`array`	list of user privileges
`privileges[].objectId`	`string`	object id to which project has privilege
`privileges[].privilegeType`	`string`	type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

login

string

user login

connectedToLdap

boolean

is user account connected to ldap

ldapAccountAvailable

boolean

does is account exist in ldap

email

string

email address

id

number

user unique id

maxColor

color

color used for drawing data overlays with max value

minColor

color

color used for drawing data overlays with min value

neutralColor

color

color used for drawing data overlays with 0 value

simpleColor

color

color used for drawing data overlays without value

name

string

first name

surname

string

last name

removed

boolean

is the account removed

termsOfUseConsent

boolean

did user agree to terms of use

privileges

array

list of user privileges

privileges[].objectId

string

object id to which project has privilege

privileges[].privilegeType

string

type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

3.5. Sample Response

{
  "connectedToLdap" : false,
  "email" : null,
  "id" : 901,
  "ldapAccountAvailable" : false,
  "login" : "xyz",
  "maxColor" : null,
  "minColor" : null,
  "name" : "FirstName",
  "neutralColor" : null,
  "privileges" : [ ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}

4. Update user

4.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user' -i -X PATCH \
    -d '{"user":{"password":"new pass"}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

4.2. Path Parameters

Table 3. /users/{login}
Parameter	Description
`login`	user login

4.3. Request Parameters

Parameter Description

Parameter	Description
`password`	user password
`connectedToLdap`	is user account connected to ldap
`ldapAccountAvailable`	does is account exist in ldap
`email`	email address
`maxColor`	color used for drawing data overlays with max value
`minColor`	color used for drawing data overlays with min value
`neutralColor`	color used for drawing data overlays with 0 value
`simpleColor`	color used for drawing data overlays without value
`name`	first name
`surname`	last name

password

user password

connectedToLdap

is user account connected to ldap

ldapAccountAvailable

does is account exist in ldap

email

email address

maxColor

color used for drawing data overlays with max value

minColor

color used for drawing data overlays with min value

neutralColor

color used for drawing data overlays with 0 value

simpleColor

color used for drawing data overlays without value

name

first name

surname

last name

4.4. Response Fields

Path Type Description

Path	Type	Description
`login`	`string`	user login
`connectedToLdap`	`boolean`	is user account connected to ldap
`ldapAccountAvailable`	`boolean`	does is account exist in ldap
`email`	`string`	email address
`id`	`number`	user unique id
`maxColor`	`color`	color used for drawing data overlays with max value
`minColor`	`color`	color used for drawing data overlays with min value
`neutralColor`	`color`	color used for drawing data overlays with 0 value
`simpleColor`	`color`	color used for drawing data overlays without value
`name`	`string`	first name
`surname`	`string`	last name
`removed`	`boolean`	is the account removed
`termsOfUseConsent`	`boolean`	did user agree to terms of use
`privileges`	`array`	list of user privileges
`privileges[].objectId`	`string`	object id to which project has privilege
`privileges[].privilegeType`	`string`	type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

login

string

user login

connectedToLdap

boolean

is user account connected to ldap

ldapAccountAvailable

boolean

does is account exist in ldap

email

string

email address

id

number

user unique id

maxColor

color

color used for drawing data overlays with max value

minColor

color

color used for drawing data overlays with min value

neutralColor

color

color used for drawing data overlays with 0 value

simpleColor

color

color used for drawing data overlays without value

name

string

first name

surname

string

last name

removed

boolean

is the account removed

termsOfUseConsent

boolean

did user agree to terms of use

privileges

array

list of user privileges

privileges[].objectId

string

object id to which project has privilege

privileges[].privilegeType

string

type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

4.5. Sample Response

{
  "connectedToLdap" : false,
  "email" : null,
  "id" : 918,
  "ldapAccountAvailable" : false,
  "login" : "test_user",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}

5. Update user privileges

5.1. Path Parameters

Table 4. /users/{login}:updatePrivileges
Parameter	Description
`login`	user login

5.2. Request Fields

Path Type Description

Path	Type	Description
`privileges.*`	`boolean`	should the privilege defined as PRIVILEGE_TYPE:ID_OBJECT be granted or not

privileges.*

boolean

should the privilege defined as PRIVILEGE_TYPE:ID_OBJECT be granted or not

5.3. Response Fields

Path Type Description

Path	Type	Description
`login`	`string`	user login
`connectedToLdap`	`boolean`	is user account connected to ldap
`ldapAccountAvailable`	`boolean`	does is account exist in ldap
`email`	`string`	email address
`id`	`number`	user unique id
`maxColor`	`color`	color used for drawing data overlays with max value
`minColor`	`color`	color used for drawing data overlays with min value
`neutralColor`	`color`	color used for drawing data overlays with 0 value
`simpleColor`	`color`	color used for drawing data overlays without value
`name`	`string`	first name
`surname`	`string`	last name
`removed`	`boolean`	is the account removed
`termsOfUseConsent`	`boolean`	did user agree to terms of use
`privileges`	`array`	list of user privileges
`privileges[].objectId`	`string`	object id to which project has privilege
`privileges[].privilegeType`	`string`	type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

login

string

user login

connectedToLdap

boolean

is user account connected to ldap

ldapAccountAvailable

boolean

does is account exist in ldap

email

string

email address

id

number

user unique id

maxColor

color

color used for drawing data overlays with max value

minColor

color

color used for drawing data overlays with min value

neutralColor

color

color used for drawing data overlays with 0 value

simpleColor

color

color used for drawing data overlays without value

name

string

first name

surname

string

last name

removed

boolean

is the account removed

termsOfUseConsent

boolean

did user agree to terms of use

privileges

array

list of user privileges

privileges[].objectId

string

object id to which project has privilege

privileges[].privilegeType

string

type of privilege, available values: CAN_CREATE_OVERLAYS, IS_ADMIN, IS_CURATOR, READ_PROJECT, WRITE_PROJECT

5.4. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePrivileges' -i -X PATCH \
    -d '{"privileges":{"IS_ADMIN":true}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

5.5. Sample Response 1

{
  "connectedToLdap" : false,
  "email" : null,
  "id" : 905,
  "ldapAccountAvailable" : false,
  "login" : "test_user",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ {
    "objectId" : null,
    "privilegeType" : "IS_ADMIN"
  } ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}

5.6. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePrivileges' -i -X PATCH \
    -d '{"privileges":{"READ_PROJECT:test_project":true}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

5.7. Sample Response 2

{
  "connectedToLdap" : false,
  "email" : null,
  "id" : 904,
  "ldapAccountAvailable" : false,
  "login" : "test_user",
  "maxColor" : null,
  "minColor" : null,
  "name" : null,
  "neutralColor" : null,
  "privileges" : [ {
    "objectId" : "test_project",
    "privilegeType" : "READ_PROJECT"
  } ],
  "removed" : false,
  "simpleColor" : null,
  "surname" : null,
  "termsOfUseConsent" : false
}

6. Update user preferences

6.1. Path Parameters

Table 5. /users/{login}:updatePreferences
Parameter	Description
`login`	user login

6.2. Request Fields

Path Type Description

Path	Type	Description
`preferences`	`object`	information about default preferences
`preferences.project-upload`	`object`	definition of preferences for project-upload.
`preferences.project-upload.annotate-model`	`boolean`	annotate model after it is uploaded.
`preferences.project-upload.auto-resize`	`boolean`	auto resize map after parsing
`preferences.project-upload.cache-data`	`boolean`	cache all the data for project
`preferences.project-upload.sbgn`	`boolean`	visualize project in sbgn-like view
`preferences.project-upload.semantic-zooming-contains-multiple-overlays`	`boolean`	display each semantic zoom level in separate overlay.
`preferences.project-upload.validate-miriam`	`boolean`	validate all miriam annotations
`preferences.element-annotators`	`object`	definition of element annotators used by user
`preferences.element-annotators['*']`	`array`	list of annotators used for specific BioEntity type. Type of BioEntity is a class name that represents specific type in the system, for example: lcsb.mapviewer.model.map.BioEntity, lcsb.mapviewer.model.map.species.Complex
`preferences.element-annotators['*'][].id`	`number`	id
`preferences.element-annotators['*'][].annotatorClass`	`string`	type of annotator
`preferences.element-annotators['*'][].order`	`number`	defines order in which annotators should be used
`preferences.element-annotators['*'][].parameters`	`object`	list of parameters for the annotator
`preferences.element-annotators['*'][].parameters[].type`	`string`	is this parameter INPUT/OUTPUT/CONFIG type. INPUT types define what should be used to identify the element. OUTPUT parameter defines what should be written to the element.
`preferences.element-annotators['*'][].parameters[].annotation_type`	`string`	specifies annotation type to be used (if empty then field will be used)
`preferences.element-annotators['*'][].parameters[].field`	`string`	specifies field to be used
`preferences.element-annotators['*'][].parameters[].order`	`number`	input parameters are checked in order. First match identifies the element. This field defines what is the order of INPUT parameters.
`preferences.element-required-annotations`	`object`	definition of required annotation by BioEntity type.
`preferences.element-required-annotations['*']`	`object`	definition of required annotations for specific BioEntity type
`preferences.element-required-annotations['*'].require-at-least-one`	`boolean`	is at least one annotation required
`preferences.element-required-annotations['*'].annotation-list`	`array`	list of annotation types from which at least one is required
`preferences.element-valid-annotations`	`object`	definition of valid annotation by BioEntity type.
`preferences.element-valid-annotations['*'][]`	`array`	list of annotation types that is valid for specific BioEntity type
`preferences.gui-preferences`	`object`	definition of user gui preferences.
`preferences.gui-preferences.*`	`string`	key-value definition of gui preference used for remembering default sort order, default pagination, etc

preferences

object

information about default preferences

preferences.project-upload

object

definition of preferences for project-upload.

preferences.project-upload.annotate-model

boolean

annotate model after it is uploaded.

preferences.project-upload.auto-resize

boolean

auto resize map after parsing

preferences.project-upload.cache-data

boolean

cache all the data for project

preferences.project-upload.sbgn

boolean

visualize project in sbgn-like view

preferences.project-upload.semantic-zooming-contains-multiple-overlays

boolean

display each semantic zoom level in separate overlay.

preferences.project-upload.validate-miriam

boolean

validate all miriam annotations

preferences.element-annotators

object

definition of element annotators used by user

preferences.element-annotators['*']

array

list of annotators used for specific BioEntity type. Type of BioEntity is a class name that represents specific type in the system, for example: lcsb.mapviewer.model.map.BioEntity, lcsb.mapviewer.model.map.species.Complex

preferences.element-annotators['*'][].id

number

preferences.element-annotators['*'][].annotatorClass

string

type of annotator

preferences.element-annotators['*'][].order

number

defines order in which annotators should be used

preferences.element-annotators['*'][].parameters

object

list of parameters for the annotator

preferences.element-annotators['*'][].parameters[].type

string

is this parameter INPUT/OUTPUT/CONFIG type. INPUT types define what should be used to identify the element. OUTPUT parameter defines what should be written to the element.

preferences.element-annotators['*'][].parameters[].annotation_type

string

specifies annotation type to be used (if empty then field will be used)

preferences.element-annotators['*'][].parameters[].field

string

specifies field to be used

preferences.element-annotators['*'][].parameters[].order

number

input parameters are checked in order. First match identifies the element. This field defines what is the order of INPUT parameters.

preferences.element-required-annotations

object

definition of required annotation by BioEntity type.

preferences.element-required-annotations['*']

object

definition of required annotations for specific BioEntity type

preferences.element-required-annotations['*'].require-at-least-one

boolean

is at least one annotation required

preferences.element-required-annotations['*'].annotation-list

array

list of annotation types from which at least one is required

preferences.element-valid-annotations

object

definition of valid annotation by BioEntity type.

preferences.element-valid-annotations['*'][]

array

list of annotation types that is valid for specific BioEntity type

preferences.gui-preferences

object

definition of user gui preferences.

preferences.gui-preferences.*

string

key-value definition of gui preference used for remembering default sort order, default pagination, etc

6.3. Response Fields

Path Type Description

Path	Type	Description
`preferences`	`object`	set of user preferences
`preferences.element-annotators`	`object`	definition of element annotators used by user
`preferences.element-annotators['*']`	`array`	list of annotators used for specific BioEntity type. Type of BioEntity is a class name that represents specific type in the system, for example: lcsb.mapviewer.model.map.BioEntity, lcsb.mapviewer.model.map.species.Complex
`preferences.element-annotators['*'][].annotatorClass`	`string`	type of annotator
`preferences.element-annotators['*'][].order`	`number`	defines order in which annotators should be used
`preferences.element-annotators['*'][].parameters`	`object`	list of parameters for the annotator
`preferences.element-annotators['*'][].parameters[].type`	`string`	is this parameter INPUT/OUTPUT/CONFIG type. INPUT types define what should be used to identify the element. OUTPUT parameter defines what should be written to the element.
`preferences.element-annotators['*'][].parameters[].annotation_type`	`string`	specifies annotation type to be used (if empty then field will be used)
`preferences.element-annotators['*'][].parameters[].field`	`string`	specifies field to be used
`preferences.element-annotators['*'][].parameters[].order`	`number`	input parameters are checked in order. First match identifies the element. This field defines what is the order of INPUT parameters.
`preferences.element-required-annotations`	`object`	definition of required annotation by BioEntity type.
`preferences.element-required-annotations['*']`	`object`	definition of required annotations for specific BioEntity type
`preferences.element-required-annotations['*'].require-at-least-one`	`boolean`	is at least one annotation required
`preferences.element-required-annotations['*'].annotation-list`	`array`	list of annotation types from which at least one is required
`preferences.element-valid-annotations`	`object`	definition of valid annotation by BioEntity type.
`preferences.element-valid-annotations['*'][]`	`array`	list of annotation types that is valid for specific BioEntity type
`preferences.gui-preferences`	`object`	definition of user gui preferences.
`preferences.gui-preferences.*`	`string`	key-value definition of gui preference used for remembering default sort order, default pagination, etc
`preferences.project-upload`	`object`	definition of preferences for project-upload.
`preferences.project-upload.annotate-model`	`boolean`	annotate model after it is uploaded.
`preferences.project-upload.auto-resize`	`boolean`	auto resize map after parsing
`preferences.project-upload.cache-data`	`boolean`	cache all the data for project
`preferences.project-upload.sbgn`	`boolean`	visualize project in sbgn-like view
`preferences.project-upload.semantic-zooming-contains-multiple-overlays`	`boolean`	display each semantic zoom level in separate overlay.
`preferences.project-upload.validate-miriam`	`boolean`	validate all miriam annotations

preferences

object

set of user preferences

preferences.element-annotators

object

definition of element annotators used by user

preferences.element-annotators['*']

array

preferences.element-annotators['*'][].annotatorClass

string

type of annotator

preferences.element-annotators['*'][].order

number

defines order in which annotators should be used

preferences.element-annotators['*'][].parameters

object

list of parameters for the annotator

preferences.element-annotators['*'][].parameters[].type

string

is this parameter INPUT/OUTPUT/CONFIG type. INPUT types define what should be used to identify the element. OUTPUT parameter defines what should be written to the element.

preferences.element-annotators['*'][].parameters[].annotation_type

string

specifies annotation type to be used (if empty then field will be used)

preferences.element-annotators['*'][].parameters[].field

string

specifies field to be used

preferences.element-annotators['*'][].parameters[].order

number

input parameters are checked in order. First match identifies the element. This field defines what is the order of INPUT parameters.

preferences.element-required-annotations

object

definition of required annotation by BioEntity type.

preferences.element-required-annotations['*']

object

definition of required annotations for specific BioEntity type

preferences.element-required-annotations['*'].require-at-least-one

boolean

is at least one annotation required

preferences.element-required-annotations['*'].annotation-list

array

list of annotation types from which at least one is required

preferences.element-valid-annotations

object

definition of valid annotation by BioEntity type.

preferences.element-valid-annotations['*'][]

array

list of annotation types that is valid for specific BioEntity type

preferences.gui-preferences

object

definition of user gui preferences.

preferences.gui-preferences.*

string

key-value definition of gui preference used for remembering default sort order, default pagination, etc

preferences.project-upload

object

definition of preferences for project-upload.

preferences.project-upload.annotate-model

boolean

annotate model after it is uploaded.

preferences.project-upload.auto-resize

boolean

auto resize map after parsing

preferences.project-upload.cache-data

boolean

cache all the data for project

preferences.project-upload.sbgn

boolean

visualize project in sbgn-like view

preferences.project-upload.semantic-zooming-contains-multiple-overlays

boolean

display each semantic zoom level in separate overlay.

preferences.project-upload.validate-miriam

boolean

validate all miriam annotations

6.4. CURL sample 1

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePreferences' -i -X PATCH \
    -d '{"preferences":{"project-upload":{"semantic-zooming-contains-multiple-overlays":true,"auto-resize":true,"sbgn":true,"cache-data":true,"annotate-model":true,"validate-miriam":true}}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.5. CURL sample 2

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePreferences' -i -X PATCH \
    -d '{"preferences":{"element-annotators":{"lcsb.mapviewer.model.map.species.Gene":[{"annotatorClass":"lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator","parameters":[{"annotation_type":"UNIPROT","type":"INPUT","order":0},{"field":"NAME","annotation_type":"UNIPROT","type":"INPUT","order":1},{"annotation_type":"HGNC_SYMBOL","type":"OUTPUT","order":2},{"annotation_type":"UNIPROT","type":"OUTPUT","order":3},{"annotation_type":"EC","type":"OUTPUT","order":4},{"annotation_type":"ENTREZ","type":"OUTPUT","order":5}]}]}}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.6. CURL sample 3

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePreferences' -i -X PATCH \
    -d '{"preferences":{"element-required-annotations":{"lcsb.mapviewer.model.map.species.Protein":{"require-at-least-one":true,"annotation-list":["HGNC","HGNC_SYMBOL"]}}}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.7. CURL sample 4

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePreferences' -i -X PATCH \
    -d '{"preferences":{"element-valid-annotations":{"lcsb.mapviewer.model.map.species.Gene":["HGNC"]}}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.8. CURL sample 5

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:updatePreferences' -i -X PATCH \
    -d '{"preferences":{"gui-preferences":{"admin-projects-datatable-order":"1-asc"}}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

6.9. Sample Response 5

{
  "preferences" : {
    "element-annotators" : {
      "lcsb.mapviewer.model.map.BioEntity" : [ ],
      "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment" : [ {
        "id" : 142,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.Compartment" : [ {
        "id" : 159,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment" : [ {
        "id" : 148,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.OvalCompartment" : [ {
        "id" : 149,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.PathwayCompartment" : [ {
        "id" : 150,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.RightSquareCompartment" : [ {
        "id" : 153,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.SquareCompartment" : [ {
        "id" : 156,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.compartment.TopSquareCompartment" : [ {
        "id" : 157,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.reaction.Reaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.CatalysisReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.DissociationReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.InhibitionReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.ModulationReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction" : [ ],
      "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.TriggerReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.TruncationReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction" : [ ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction" : [ ],
      "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" : [ {
        "id" : 160,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator",
        "parameters" : [ {
          "annotation_type" : "CHEBI",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "NAME",
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 2,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "INCHI",
          "order" : 3,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "INCHI_KEY",
          "order" : 4,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SMILE",
          "order" : 5,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYNONYMS",
          "order" : 6,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.Complex" : [ {
        "id" : 143,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.Degraded" : [ ],
      "lcsb.mapviewer.model.map.species.Drug" : [ ],
      "lcsb.mapviewer.model.map.species.Element" : [ ],
      "lcsb.mapviewer.model.map.species.Gene" : [ {
        "id" : 144,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.HgncAnnotator",
        "parameters" : [ {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : "NAME",
          "order" : 2,
          "type" : "INPUT"
        }, {
          "annotation_type" : "ENSEMBL",
          "field" : null,
          "order" : 3,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "ENTREZ",
          "field" : null,
          "order" : 4,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 5,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 6,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "REFSEQ",
          "field" : null,
          "order" : 7,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "UNIPROT",
          "field" : null,
          "order" : 8,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYMBOL",
          "order" : 9,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYNONYMS",
          "order" : 10,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "NAME",
          "order" : 11,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 12,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.GenericProtein" : [ {
        "id" : 145,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.HgncAnnotator",
        "parameters" : [ {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : "NAME",
          "order" : 2,
          "type" : "INPUT"
        }, {
          "annotation_type" : "ENSEMBL",
          "field" : null,
          "order" : 3,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "ENTREZ",
          "field" : null,
          "order" : 4,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 5,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 6,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "REFSEQ",
          "field" : null,
          "order" : 7,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "UNIPROT",
          "field" : null,
          "order" : 8,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYMBOL",
          "order" : 9,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYNONYMS",
          "order" : 10,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "NAME",
          "order" : 11,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 12,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.Ion" : [ {
        "id" : 146,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator",
        "parameters" : [ {
          "annotation_type" : "CHEBI",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "NAME",
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 2,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "INCHI",
          "order" : 3,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "INCHI_KEY",
          "order" : 4,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SMILE",
          "order" : 5,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYNONYMS",
          "order" : 6,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.IonChannelProtein" : [ {
        "id" : 147,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.HgncAnnotator",
        "parameters" : [ {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : "NAME",
          "order" : 2,
          "type" : "INPUT"
        }, {
          "annotation_type" : "ENSEMBL",
          "field" : null,
          "order" : 3,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "ENTREZ",
          "field" : null,
          "order" : 4,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 5,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 6,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "REFSEQ",
          "field" : null,
          "order" : 7,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : "UNIPROT",
          "field" : null,
          "order" : 8,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYMBOL",
          "order" : 9,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "SYNONYMS",
          "order" : 10,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "NAME",
          "order" : 11,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 12,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.Phenotype" : [ {
        "id" : 151,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
        "parameters" : [ {
          "annotation_type" : "GO",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : null,
          "field" : "FULL_NAME",
          "order" : 1,
          "type" : "OUTPUT"
        }, {
          "annotation_type" : null,
          "field" : "DESCRIPTION",
          "order" : 2,
          "type" : "OUTPUT"
        } ],
        "order" : 0
      } ],
      "lcsb.mapviewer.model.map.species.Protein" : [ {
        "id" : 161,
        "annotatorClass" : "lcsb.mapviewer.annotation.services.annotators.HgncAnnotator",
        "parameters" : [ {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : null,
          "order" : 0,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC",
          "field" : null,
          "order" : 1,
          "type" : "INPUT"
        }, {
          "annotation_type" : "HGNC_SYMBOL",
          "field" : "NAME",
          "order" : 2,
          "type" : "INPUT"
        }, {
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      "lcsb.mapviewer.model.map.reaction.type.TransportReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.TriggerReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.TruncationReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction" : [ "DOI", "KEGG_PATHWAY", "PUBMED", "RHEA", "VMH_REACTION", "COG", "RGD", "REACTOME", "KEGG_REACTION" ],
      "lcsb.mapviewer.model.map.species.AntisenseRna" : [ "PUBMED" ],
      "lcsb.mapviewer.model.map.species.Chemical" : [ "VMH_METABOLITE", "PUBMED", "KEGG_COMPOUND", "CHEBI", "HMDB", "CHEM_ID_PLUS", "PUBCHEM", "PUBCHEM_SUBSTANCE" ],
      "lcsb.mapviewer.model.map.species.Complex" : [ "GO", "EC", "PUBMED", "MESH_2012", "INTERPRO", "CHEMBL_TARGET" ],
      "lcsb.mapviewer.model.map.species.Degraded" : [ "PUBMED" ],
      "lcsb.mapviewer.model.map.species.Drug" : [ "PUBMED", "CHEBI", "CHEMBL_COMPOUND", "HMDB", "DRUGBANK", "CHEM_ID_PLUS" ],
      "lcsb.mapviewer.model.map.species.Element" : [ "PUBMED" ],
      "lcsb.mapviewer.model.map.species.Gene" : [ "HGNC", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "ENSEMBL", "UNIPROT", "ECO", "REFSEQ", "MGD", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.GenericProtein" : [ "EC", "CHEMBL_TARGET", "UNIPROT", "MGD", "HGNC", "UNIPROT_ISOFORM", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "INTERPRO", "ENSEMBL", "ECO", "REFSEQ", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.Ion" : [ "VMH_METABOLITE", "PUBMED", "KEGG_COMPOUND", "CHEBI", "HMDB", "CHEM_ID_PLUS", "PUBCHEM", "PUBCHEM_SUBSTANCE" ],
      "lcsb.mapviewer.model.map.species.IonChannelProtein" : [ "EC", "CHEMBL_TARGET", "UNIPROT", "MGD", "HGNC", "UNIPROT_ISOFORM", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "INTERPRO", "ENSEMBL", "ECO", "REFSEQ", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.Phenotype" : [ "GO", "PUBMED", "MESH_2012", "OMIM" ],
      "lcsb.mapviewer.model.map.species.Protein" : [ "EC", "CHEMBL_TARGET", "UNIPROT", "MGD", "HGNC", "UNIPROT_ISOFORM", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "INTERPRO", "ENSEMBL", "ECO", "REFSEQ", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.ReceptorProtein" : [ "EC", "CHEMBL_TARGET", "UNIPROT", "MGD", "HGNC", "UNIPROT_ISOFORM", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "INTERPRO", "ENSEMBL", "ECO", "REFSEQ", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.Rna" : [ "HGNC", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "ENSEMBL", "UNIPROT", "ECO", "REFSEQ", "MGD", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.SimpleMolecule" : [ "VMH_METABOLITE", "PUBMED", "KEGG_COMPOUND", "CHEBI", "HMDB", "CHEM_ID_PLUS", "PUBCHEM", "PUBCHEM_SUBSTANCE" ],
      "lcsb.mapviewer.model.map.species.Species" : [ "PUBMED" ],
      "lcsb.mapviewer.model.map.species.TruncatedProtein" : [ "EC", "CHEMBL_TARGET", "UNIPROT", "MGD", "HGNC", "UNIPROT_ISOFORM", "PANTHER", "PUBMED", "KEGG_GENES", "ENTREZ", "INTERPRO", "ENSEMBL", "ECO", "REFSEQ", "HGNC_SYMBOL", "PDB" ],
      "lcsb.mapviewer.model.map.species.Unknown" : [ "PUBMED" ]
    },
    "gui-preferences" : {
      "admin-projects-datatable-order" : "1-asc"
    },
    "project-upload" : {
      "annotate-model" : false,
      "auto-resize" : true,
      "cache-data" : true,
      "sbgn" : false,
      "semantic-zooming-contains-multiple-overlays" : false,
      "validate-miriam" : false
    }
  }
}

7. Delete user

7.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user' -i -X PATCH \
    -d '{"user":{"password":"new pass"}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

7.2. Path Parameters

Table 6. /users/{login}
Parameter	Description
`login`	user login

8. Request password reset over email

8.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users/test_user:requestResetPassword' -i -X POST

8.2. Path Parameters

Table 7. /users/{login}:requestResetPassword
Parameter	Description
`login`	user login

9. Reset password using token obtained over email

9.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/users:resetPassword' -i -X POST \
    -H 'Content-Type: application/x-www-form-urlencoded' \
    -d 'token=82b153eb-9635-4aa5-93c3-2b3b98423288&password=pass2' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"

9.2. Request Parameters

Parameter Description

Parameter	Description
`password`	new password
`token`	reset poassowrd token obtained using email

password

new password

token

reset poassowrd token obtained using email

Rest API Documentation - Users

1. List all users

1.1. CURL sample

1.2. Response Fields

1.3. Sample Response

2. Get specific user data

2.1. CURL sample

2.2. Path Parameters

2.3. Response Fields

2.4. Sample Response

3. Create user

3.1. CURL sample

3.2. Path Parameters

3.3. Request Parameters

3.4. Response Fields

3.5. Sample Response

4. Update user

4.1. CURL sample

4.2. Path Parameters

4.3. Request Parameters

4.4. Response Fields

4.5. Sample Response

5. Update user privileges

5.1. Path Parameters

5.2. Request Fields

5.3. Response Fields

5.4. CURL sample 1

5.5. Sample Response 1

5.6. CURL sample 2

5.7. Sample Response 2

6. Update user preferences

6.1. Path Parameters

6.2. Request Fields

6.3. Response Fields

6.4. CURL sample 1

6.5. CURL sample 2

6.6. CURL sample 3

6.7. CURL sample 4

6.8. CURL sample 5

6.9. Sample Response 5

7. Delete user

7.1. CURL sample

7.2. Path Parameters

8. Request password reset over email

8.1. CURL sample

8.2. Path Parameters

9. Reset password using token obtained over email

9.1. CURL sample

9.2. Request Parameters