Legacy REST API Documentation

1. Details

Return full configuration details. The miriamTypes map contains every supported identifier type (several hundred); the sample response below is shortened to the first three entries.

1.1. CURL sample

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

1.2. Response Fields

Path Type Description

Path	Type	Description
`annotators`	`Array`	list of annotators
`bioEntityFields`	`Array`	list of bieEntity fields that are used by annotators
`buildDate`	`timestamp`	when minerva platform was built
`gitHash`	`String`	git hash used to build minerva platform
`version`	`String`	version of the minerva platform
`imageFormats`	`Array`	list of available export image formats
`miriamTypes`	`Object`	map of miriam types supported by minerva. Types are defined on https://identifiers.org/
`modelFormats`	`Array`	list of map formats
`modificationStateTypes`	`Object`	map with modification states
`options`	`Array`	list of configuration options
`overlayTypes`	`Array`	list of overlay types
`privilegeTypes`	`Object`	map with privilege type available in the system
`reactionTypes`	`Array`	list of reaction types
`unitTypes`	`Array`	list of basic unit types
`elementTypes`	`Array`	list of element types
`annotators[].name`	`String`	annotator name
`annotators[].url`	`String`	url address of assoiated database
`annotators[].className`	`String`	Java class responsible for annotating process
`annotators[].elementClassNames`	`array<string>`	Java classes that identify bioEntity types that can be annotated by the annotator
`annotators[].description`	`String`	short description of the annotator
`annotators[].parameters`	`array<object>`	list of supported input fields, generated outputs that can be filled by annotator and configuration options
`annotators[].parameters[].annotation_type`	`MiriamType`	identifier type. Either this or 'field' is required for INPUT/OUTPUT parameter
`annotators[].parameters[].field`	`String`	bioEntity field. Either this or 'annotation_type' is required for INPUT/OUTPUT parameter
`annotators[].parameters[].commonName`	`String`	name of the CONFIG parameter
`annotators[].parameters[].description`	`String`	description of the parameter
`annotators[].parameters[].inputType`	`String`	type of the CONFIG parameter
`annotators[].parameters[].name`	`String`	name of the CONFIG parameter
`annotators[].parameters[].value`	`String`	default value of the CONFIG parameter
`annotators[].parameters[].order`	`number`	order position when listing parameters
`annotators[].parameters[].type`	`String`	type of parameter (INPUT/OUTPUT/CONFIG)
`bioEntityFields[].commonName`	`String`	human readable name of the field
`bioEntityFields[].name`	`String`	unique name of the field
`elementTypes[].className`	`String`	Java class that identify type
`elementTypes[].name`	`String`	human readable name of the type
`elementTypes[].parentClass`	`String`	Java class that identify parent type
`imageFormats[].extension`	`String`	file extension
`imageFormats[].name`	`String`	human readable name of the format
`imageFormats[].handler`	`String`	Java class that is responsible for export
`miriamTypes[].commonName`	`String`	human readable name of the identifier type
`miriamTypes[].homepage`	`String`	url to database homepage
`miriamTypes[].registryIdentifier`	`String`	unique identifier used by identifiers.org to reference this type
`miriamTypes[].registryIdentifier`	`array<string>`	list of uris used by this identifier type
`modelFormats[].name`	`String`	human readable name of map format
`modelFormats[].extension`	`String`	default file extension
`modelFormats[].extensions`	`Array`	file extensions supported by parser
`modelFormats[].handler`	`String`	Java class that is used for import/export from the map format
`modificationStateTypes[].commonName`	`String`	human readable name of modification state type
`modificationStateTypes[].abbreviation`	`String`	short name of the type
`options[].commonName`	`String`	human readable name of configuration option
`options[].group`	`String`	group of options where this configuration option belongs to
`options[].isServerSide`	`boolean`	TRUE/FALSE - is the option responsible for server side processing or frontend
`options[].type`	`String`	option type
`options[].value`	`String`	value of the configuration option
`options[].valueType`	`String`	type of the configuration option. Available options: ALLOW_AUTO_REGISTER, BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, DEFAULT_MAP, EMAIL_ADDRESS, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, EMAIL_SSL_SERVER, LDAP_ADDRESS, LDAP_BASE_DN, LDAP_BIND_DN, LDAP_EMAIL_ATTRIBUTE, LDAP_FILTER, LDAP_FIRST_NAME_ATTRIBUTE, LDAP_LAST_NAME_ATTRIBUTE, LDAP_OBJECT_CLASS, LDAP_PASSWORD, LDAP_PORT, LDAP_SSL, LDAP_UID, LEFT_LOGO_IMG, LEFT_LOGO_LINK, LEFT_LOGO_TEXT, LEGEND_FILE_1, LEGEND_FILE_2, LEGEND_FILE_3, LEGEND_FILE_4, MATOMO_URL, MAX_COLOR_VAL, MCP_ENABLED, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SESSION_LENGTH, SIMPLE_COLOR_VAL, TERMS_OF_USE, X_FRAME_DOMAIN
`overlayTypes[].name`	`String`	name of the type
`privilegeTypes[].commonName`	`String`	human readable description of the privilege
`privilegeTypes[].objectType`	`String`	class of objects to which privilege applies
`privilegeTypes[].valueType`	`String`	type of the privilege value (ie. boolean)
`reactionTypes[].className`	`String`	Java class that identify type
`reactionTypes[].name`	`String`	human readable name of the type
`reactionTypes[].parentClass`	`String`	Java class that identify parent type
`unitTypes[].name`	`String`	human readable name of the type
`unitTypes[].id`	`String`	type identifier

annotators

Array

list of annotators

bioEntityFields

Array

list of bieEntity fields that are used by annotators

buildDate

timestamp

when minerva platform was built

gitHash

String

git hash used to build minerva platform

version

String

version of the minerva platform

imageFormats

Array

list of available export image formats

miriamTypes

Object

map of miriam types supported by minerva. Types are defined on https://identifiers.org/

modelFormats

Array

list of map formats

modificationStateTypes

Object

map with modification states

options

Array

list of configuration options

overlayTypes

Array

list of overlay types

privilegeTypes

Object

map with privilege type available in the system

reactionTypes

Array

list of reaction types

unitTypes

Array

list of basic unit types

elementTypes

Array

list of element types

annotators[].name

String

annotator name

annotators[].url

String

url address of assoiated database

annotators[].className

String

Java class responsible for annotating process

annotators[].elementClassNames

array<string>

Java classes that identify bioEntity types that can be annotated by the annotator

annotators[].description

String

short description of the annotator

annotators[].parameters

array<object>

list of supported input fields, generated outputs that can be filled by annotator and configuration options

annotators[].parameters[].annotation_type

MiriamType

identifier type. Either this or 'field' is required for INPUT/OUTPUT parameter

annotators[].parameters[].field

String

bioEntity field. Either this or 'annotation_type' is required for INPUT/OUTPUT parameter

annotators[].parameters[].commonName

String

name of the CONFIG parameter

annotators[].parameters[].description

String

description of the parameter

annotators[].parameters[].inputType

String

type of the CONFIG parameter

annotators[].parameters[].name

String

name of the CONFIG parameter

annotators[].parameters[].value

String

default value of the CONFIG parameter

annotators[].parameters[].order

number

order position when listing parameters

annotators[].parameters[].type

String

type of parameter (INPUT/OUTPUT/CONFIG)

bioEntityFields[].commonName

String

human readable name of the field

bioEntityFields[].name

String

unique name of the field

elementTypes[].className

String

Java class that identify type

elementTypes[].name

String

human readable name of the type

elementTypes[].parentClass

String

Java class that identify parent type

imageFormats[].extension

String

file extension

imageFormats[].name

String

human readable name of the format

imageFormats[].handler

String

Java class that is responsible for export

miriamTypes[].commonName

String

human readable name of the identifier type

miriamTypes[].homepage

String

url to database homepage

miriamTypes[].registryIdentifier

String

unique identifier used by identifiers.org to reference this type

miriamTypes[].registryIdentifier

array<string>

list of uris used by this identifier type

modelFormats[].name

String

human readable name of map format

modelFormats[].extension

String

default file extension

modelFormats[].extensions

Array

file extensions supported by parser

modelFormats[].handler

String

Java class that is used for import/export from the map format

modificationStateTypes[].commonName

String

human readable name of modification state type

modificationStateTypes[].abbreviation

String

short name of the type

options[].commonName

String

human readable name of configuration option

options[].group

String

group of options where this configuration option belongs to

options[].isServerSide

boolean

TRUE/FALSE - is the option responsible for server side processing or frontend

options[].type

String

option type

options[].value

String

value of the configuration option

options[].valueType

String

type of the configuration option. Available options: ALLOW_AUTO_REGISTER, BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, DEFAULT_MAP, EMAIL_ADDRESS, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, EMAIL_SSL_SERVER, LDAP_ADDRESS, LDAP_BASE_DN, LDAP_BIND_DN, LDAP_EMAIL_ATTRIBUTE, LDAP_FILTER, LDAP_FIRST_NAME_ATTRIBUTE, LDAP_LAST_NAME_ATTRIBUTE, LDAP_OBJECT_CLASS, LDAP_PASSWORD, LDAP_PORT, LDAP_SSL, LDAP_UID, LEFT_LOGO_IMG, LEFT_LOGO_LINK, LEFT_LOGO_TEXT, LEGEND_FILE_1, LEGEND_FILE_2, LEGEND_FILE_3, LEGEND_FILE_4, MATOMO_URL, MAX_COLOR_VAL, MCP_ENABLED, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SESSION_LENGTH, SIMPLE_COLOR_VAL, TERMS_OF_USE, X_FRAME_DOMAIN

overlayTypes[].name

String

name of the type

privilegeTypes[].commonName

String

human readable description of the privilege

privilegeTypes[].objectType

String

class of objects to which privilege applies

privilegeTypes[].valueType

String

type of the privilege value (ie. boolean)

reactionTypes[].className

String

Java class that identify type

reactionTypes[].name

String

human readable name of the type

reactionTypes[].parentClass

String

Java class that identify parent type

unitTypes[].name

String

human readable name of the type

unitTypes[].id

String

type identifier

1.3. Sample Response

{
  "options" : [ {
    "idObject" : 15,
    "type" : "DEFAULT_MAP",
    "valueType" : "STRING",
    "commonName" : "Default Project Id",
    "isServerSide" : false,
    "value" : "empty",
    "group" : "Server configuration"
  }, {
    "idObject" : 25,
    "type" : "LEFT_LOGO_IMG",
    "valueType" : "URL",
    "commonName" : "Left logo icon",
    "isServerSide" : false,
    "value" : "/minerva/images/udl.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 26,
    "type" : "LEFT_LOGO_LINK",
    "valueType" : "URL",
    "commonName" : "Left logo link (after click)",
    "isServerSide" : false,
    "value" : "http://wwwen.uni.lu/",
    "group" : "Legend and logo"
  }, {
    "idObject" : 27,
    "type" : "LEFT_LOGO_TEXT",
    "valueType" : "STRING",
    "commonName" : "Left logo description",
    "isServerSide" : false,
    "value" : "University of Luxembourg",
    "group" : "Legend and logo"
  }, {
    "idObject" : 28,
    "type" : "RIGHT_LOGO_IMG",
    "valueType" : "URL",
    "commonName" : "Right logo icon",
    "isServerSide" : false,
    "value" : "/minerva/images/lcsb.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 29,
    "type" : "RIGHT_LOGO_LINK",
    "valueType" : "URL",
    "commonName" : "Right logo link (after click)",
    "isServerSide" : false,
    "value" : "http://wwwen.uni.lu/lcsb/",
    "group" : "Legend and logo"
  }, {
    "idObject" : 30,
    "type" : "RIGHT_LOGO_TEXT",
    "valueType" : "STRING",
    "commonName" : "Right logo description",
    "isServerSide" : false,
    "value" : "LCSB - Luxembourg Centre for Systems Biomedicine",
    "group" : "Legend and logo"
  }, {
    "idObject" : 9,
    "type" : "REQUEST_ACCOUNT_EMAIL",
    "valueType" : "EMAIL",
    "commonName" : "Email used for requesting an account",
    "isServerSide" : false,
    "value" : "",
    "group" : "Email notification details"
  }, {
    "idObject" : 19,
    "type" : "X_FRAME_DOMAIN",
    "valueType" : "URL",
    "commonName" : "Domain allowed to connect via x-frame technology",
    "isServerSide" : false,
    "value" : "",
    "group" : "Server configuration"
  }, {
    "idObject" : 22,
    "type" : "CORS_DOMAIN",
    "valueType" : "BOOLEAN",
    "commonName" : "Disable CORS (when disabled 'ORIGIN' http header is required)",
    "isServerSide" : false,
    "value" : "false",
    "group" : "Server configuration"
  }, {
    "idObject" : 23,
    "type" : "BIG_FILE_STORAGE_DIR",
    "valueType" : "STRING",
    "commonName" : "Path to store big files",
    "isServerSide" : false,
    "value" : "minerva-big/",
    "group" : "Server configuration"
  }, {
    "idObject" : 31,
    "type" : "LEGEND_FILE_1",
    "valueType" : "URL",
    "commonName" : "Legend 1 image file",
    "isServerSide" : false,
    "value" : "/minerva/images/legend_a.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 32,
    "type" : "LEGEND_FILE_2",
    "valueType" : "URL",
    "commonName" : "Legend 2 image file",
    "isServerSide" : false,
    "value" : "/minerva/images/legend_b.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 33,
    "type" : "LEGEND_FILE_3",
    "valueType" : "URL",
    "commonName" : "Legend 3 image file",
    "isServerSide" : false,
    "value" : "/minerva/images/legend_c.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 34,
    "type" : "LEGEND_FILE_4",
    "valueType" : "URL",
    "commonName" : "Legend 4 image file",
    "isServerSide" : false,
    "value" : "/minerva/images/legend_d.png",
    "group" : "Legend and logo"
  }, {
    "idObject" : 39,
    "type" : "MIN_COLOR_VAL",
    "valueType" : "COLOR",
    "commonName" : "Overlay color for negative values",
    "isServerSide" : false,
    "value" : "FF0000",
    "group" : "Overlays"
  }, {
    "idObject" : 40,
    "type" : "MAX_COLOR_VAL",
    "valueType" : "COLOR",
    "commonName" : "Overlay color for positive values",
    "isServerSide" : false,
    "value" : "0000FF",
    "group" : "Overlays"
  }, {
    "idObject" : 41,
    "type" : "SIMPLE_COLOR_VAL",
    "valueType" : "COLOR",
    "commonName" : "Overlay color when no values are defined",
    "isServerSide" : false,
    "value" : "00FF00",
    "group" : "Overlays"
  }, {
    "idObject" : 42,
    "type" : "NEUTRAL_COLOR_VAL",
    "valueType" : "COLOR",
    "commonName" : "Overlay color for value=0",
    "isServerSide" : false,
    "value" : "FFFFFF",
    "group" : "Overlays"
  }, {
    "idObject" : 43,
    "type" : "OVERLAY_OPACITY",
    "valueType" : "DOUBLE",
    "commonName" : "Opacity used when drawing data overlays (value between 0.0-1.0)",
    "isServerSide" : false,
    "value" : "0.8",
    "group" : "Overlays"
  }, {
    "idObject" : 11,
    "type" : "REQUEST_ACCOUNT_DEFAULT_CONTENT",
    "valueType" : "TEXT",
    "commonName" : "Email content used for requesting an account",
    "isServerSide" : false,
    "value" : "Dear Disease map team,\nI would like to request an account in the system.\nKind regards",
    "group" : "Email notification details"
  }, {
    "idObject" : 12,
    "type" : "TERMS_OF_USE",
    "valueType" : "URL",
    "commonName" : "URL of platform's Terms of Service",
    "isServerSide" : false,
    "value" : "",
    "group" : "Legend and logo"
  }, {
    "idObject" : 14,
    "type" : "COOKIE_POLICY_URL",
    "valueType" : "URL",
    "commonName" : "Privacy policy (url)",
    "isServerSide" : false,
    "value" : "/minerva/default-cookie-policy.html",
    "group" : "Server configuration"
  }, {
    "idObject" : 1,
    "type" : "SESSION_LENGTH",
    "valueType" : "INTEGER",
    "commonName" : "Max session inactivity time (in seconds)",
    "isServerSide" : false,
    "value" : "7200",
    "group" : "Server configuration"
  }, {
    "idObject" : 16,
    "type" : "MINERVA_ROOT",
    "valueType" : "URL",
    "commonName" : "Minerva root url",
    "isServerSide" : false,
    "value" : "",
    "group" : "Server configuration"
  }, {
    "idObject" : 10,
    "type" : "REQUEST_ACCOUNT_DEFAULT_TITLE",
    "valueType" : "STRING",
    "commonName" : "Email title used for requesting an account",
    "isServerSide" : false,
    "value" : "MINERVA account request",
    "group" : "Email notification details"
  }, {
    "idObject" : 83,
    "type" : "ORCID_CLIENT_ID",
    "valueType" : "TEXT",
    "commonName" : "Orcid Client ID",
    "isServerSide" : false,
    "value" : "",
    "group" : "OAuth conifguration"
  }, {
    "idObject" : 84,
    "type" : "ORCID_CLIENT_SECRET",
    "valueType" : "PASSWORD",
    "commonName" : "Orcid Client Secret",
    "isServerSide" : false,
    "group" : "OAuth conifguration"
  }, {
    "idObject" : 20,
    "type" : "ALLOW_AUTO_REGISTER",
    "valueType" : "BOOLEAN",
    "commonName" : "Allow users to create accounts",
    "isServerSide" : false,
    "value" : "false",
    "group" : "Server configuration"
  }, {
    "idObject" : 21,
    "type" : "REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS",
    "valueType" : "BOOLEAN",
    "commonName" : "Require admin approval for auto-registered accounts",
    "isServerSide" : false,
    "value" : "true",
    "group" : "Server configuration"
  }, {
    "idObject" : 91,
    "type" : "MATOMO_URL",
    "valueType" : "URL",
    "commonName" : "Matomo tracking url (for example: https://cdn.matomo.cloud/atcomp.matomo.cloud/container_d9VKcbPg_dev_d48ac09b17cfa365367b6ce.js)",
    "isServerSide" : false,
    "value" : "",
    "group" : "Server configuration"
  } ],
  "imageFormats" : [ {
    "name" : "PNG image",
    "handler" : "lcsb.mapviewer.converter.graphics.PngImageGenerator",
    "extension" : "png"
  }, {
    "name" : "PDF image",
    "handler" : "lcsb.mapviewer.converter.graphics.PdfImageGenerator",
    "extension" : "pdf"
  }, {
    "name" : "SVG image",
    "handler" : "lcsb.mapviewer.converter.graphics.SvgImageGenerator",
    "extension" : "svg"
  } ],
  "modelFormats" : [ {
    "name" : "CellDesigner SBML",
    "handler" : "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
    "extension" : "xml",
    "extensions" : [ "xml" ]
  }, {
    "name" : "SBGN-ML",
    "handler" : "lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter",
    "extension" : "sbgn",
    "extensions" : [ "sbgn" ]
  }, {
    "name" : "GPML",
    "handler" : "lcsb.mapviewer.wikipathway.GpmlParser",
    "extension" : "gpml",
    "extensions" : [ "gpml" ]
  }, {
    "name" : "SBML",
    "handler" : "lcsb.mapviewer.converter.model.sbml.SbmlParser",
    "extension" : "xml",
    "extensions" : [ "xml", "sbml" ]
  } ],
  "overlayTypes" : [ {
    "name" : "GENERIC"
  }, {
    "name" : "GENETIC_VARIANT"
  } ],
  "elementTypes" : [ {
    "className" : "lcsb.mapviewer.model.map.species.Element",
    "name" : "Element",
    "parentClass" : "lcsb.mapviewer.model.map.BioEntity"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.Compartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.species.Element"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Species",
    "name" : "Species",
    "parentClass" : "lcsb.mapviewer.model.map.species.Element"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.RightSquareCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.TopSquareCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.SquareCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.OvalCompartment",
    "name" : "Compartment",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.compartment.PathwayCompartment",
    "name" : "Pathway",
    "parentClass" : "lcsb.mapviewer.model.map.compartment.Compartment"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.AntisenseRna",
    "name" : "Antisense RNA",
    "parentClass" : "lcsb.mapviewer.model.map.species.Species"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Chemical",
    "name" : "Chemical",
    "parentClass" : "lcsb.mapviewer.model.map.species.Species"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Complex",
    "name" : "Complex",
    "parentClass" : "lcsb.mapviewer.model.map.species.Species"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Degraded",
    "name" : "Degraded",
    "parentClass" : "lcsb.mapviewer.model.map.species.Species"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Drug",
    "name" : "Drug",
    "parentClass" : "lcsb.mapviewer.model.map.species.Species"
  }, {
    "className" : "lcsb.mapviewer.model.map.species.Gene",
    "name" : "Gene",
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    "className" : "lcsb.mapviewer.annotation.services.annotators.KeggAnnotator",
    "name" : "KEGG",
    "description" : "Annotations extracted from KEGG ENZYME Database based on species EC numbers. Annotation include relevant publications and homologous genes for given EC numbers.",
    "url" : "https://www.genome.jp/kegg/",
    "elementClassNames" : [ "lcsb.mapviewer.model.map.species.GenericProtein", "lcsb.mapviewer.model.map.species.Gene", "lcsb.mapviewer.model.map.species.Rna" ],
    "parameters" : [ {
      "field" : null,
      "annotation_type" : "TAIR_LOCUS",
      "order" : 0,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "UNIPROT",
      "order" : 1,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "EC",
      "order" : 2,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "PUBMED",
      "order" : 3,
      "type" : "OUTPUT"
    }, {
      "field" : null,
      "annotation_type" : "TAIR_LOCUS",
      "order" : 4,
      "type" : "OUTPUT"
    }, {
      "type" : "CONFIG",
      "name" : "KEGG_ORGANISM_IDENTIFIER",
      "commonName" : "KEGG organism identifier",
      "inputType" : "java.lang.String",
      "description" : "Space-delimited list of organisms codes for which homologous genes (final GENE section in the KEGG enzyme record) should be imported. Currently only ATH (final Arabidopsis Thaliana) is supported.",
      "value" : "",
      "order" : 5
    } ]
  }, {
    "className" : "lcsb.mapviewer.annotation.services.annotators.PdbAnnotator",
    "name" : "Protein Data Bank",
    "description" : "",
    "url" : "http://www.pdbe.org/",
    "elementClassNames" : [ "lcsb.mapviewer.model.map.species.GenericProtein", "lcsb.mapviewer.model.map.species.Rna", "lcsb.mapviewer.model.map.species.Gene" ],
    "parameters" : [ {
      "field" : null,
      "annotation_type" : "UNIPROT",
      "order" : 0,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "PDB",
      "order" : 1,
      "type" : "OUTPUT"
    } ]
  }, {
    "className" : "lcsb.mapviewer.annotation.services.annotators.TairAnnotator",
    "name" : "TAIR",
    "description" : "",
    "url" : "http://arabidopsis.org/index.jsp",
    "elementClassNames" : [ "lcsb.mapviewer.model.map.species.GenericProtein", "lcsb.mapviewer.model.map.species.Gene", "lcsb.mapviewer.model.map.species.Rna" ],
    "parameters" : [ {
      "field" : null,
      "annotation_type" : "TAIR_LOCUS",
      "order" : 0,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "UNIPROT",
      "order" : 1,
      "type" : "OUTPUT"
    } ]
  }, {
    "className" : "lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator",
    "name" : "UniProt",
    "description" : "",
    "url" : "http://www.uniprot.org/",
    "elementClassNames" : [ "lcsb.mapviewer.model.map.species.GenericProtein", "lcsb.mapviewer.model.map.species.Gene", "lcsb.mapviewer.model.map.species.Rna" ],
    "parameters" : [ {
      "field" : null,
      "annotation_type" : "UNIPROT",
      "order" : 0,
      "type" : "INPUT"
    }, {
      "field" : "NAME",
      "annotation_type" : "UNIPROT",
      "order" : 1,
      "type" : "INPUT"
    }, {
      "field" : null,
      "annotation_type" : "HGNC_SYMBOL",
      "order" : 2,
      "type" : "OUTPUT"
    }, {
      "field" : null,
      "annotation_type" : "UNIPROT",
      "order" : 3,
      "type" : "OUTPUT"
    }, {
      "field" : null,
      "annotation_type" : "EC",
      "order" : 4,
      "type" : "OUTPUT"
    }, {
      "field" : null,
      "annotation_type" : "STRING",
      "order" : 5,
      "type" : "OUTPUT"
    }, {
      "field" : null,
      "annotation_type" : "ENTREZ",
      "order" : 6,
      "type" : "OUTPUT"
    } ]
  } ],
  "bioEntityFields" : [ {
    "commonName" : "Charge",
    "name" : "CHARGE"
  }, {
    "commonName" : "Description",
    "name" : "DESCRIPTION"
  }, {
    "commonName" : "Full name",
    "name" : "FULL_NAME"
  }, {
    "commonName" : "Name",
    "name" : "NAME"
  }, {
    "commonName" : "Previous Symbols",
    "name" : "PREVIOUS_SYMBOLS"
  }, {
    "commonName" : "Smiles",
    "name" : "SMILES"
  }, {
    "commonName" : "Symbol",
    "name" : "SYMBOL"
  }, {
    "commonName" : "Synonyms",
    "name" : "SYNONYMS"
  } ]
}

2. List configuration options

List configuration options.

2.1. CURL sample

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

2.2. Response Fields

Path Type Description

Path	Type	Description
`[]`	`array<Option>`	list of options
`[].commonName`	`String`	human readable name of configuration option
`[].group`	`String`	group of options where this configuration option belongs to
`[].isServerSide`	`boolean`	TRUE/FALSE - is the option responsible for server side processing or frontend
`[].type`	`String`	option type
`[].value`	`String`	value of the configuration option
`[].valueType`	`String`	type of the configuration option. Available options: ALLOW_AUTO_REGISTER, BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, DEFAULT_MAP, EMAIL_ADDRESS, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, EMAIL_SSL_SERVER, LDAP_ADDRESS, LDAP_BASE_DN, LDAP_BIND_DN, LDAP_EMAIL_ATTRIBUTE, LDAP_FILTER, LDAP_FIRST_NAME_ATTRIBUTE, LDAP_LAST_NAME_ATTRIBUTE, LDAP_OBJECT_CLASS, LDAP_PASSWORD, LDAP_PORT, LDAP_SSL, LDAP_UID, LEFT_LOGO_IMG, LEFT_LOGO_LINK, LEFT_LOGO_TEXT, LEGEND_FILE_1, LEGEND_FILE_2, LEGEND_FILE_3, LEGEND_FILE_4, MATOMO_URL, MAX_COLOR_VAL, MCP_ENABLED, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SESSION_LENGTH, SIMPLE_COLOR_VAL, TERMS_OF_USE, X_FRAME_DOMAIN

[]

array<Option>

list of options

[].commonName

String

human readable name of configuration option

[].group

String

group of options where this configuration option belongs to

[].isServerSide

boolean

TRUE/FALSE - is the option responsible for server side processing or frontend

[].type

String

option type

[].value

String

value of the configuration option

[].valueType

String

2.3. Sample Response

[ {
  "idObject" : 15,
  "type" : "DEFAULT_MAP",
  "valueType" : "STRING",
  "commonName" : "Default Project Id",
  "isServerSide" : false,
  "value" : "empty",
  "group" : "Server configuration"
}, {
  "idObject" : 25,
  "type" : "LEFT_LOGO_IMG",
  "valueType" : "URL",
  "commonName" : "Left logo icon",
  "isServerSide" : false,
  "value" : "/minerva/images/udl.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 26,
  "type" : "LEFT_LOGO_LINK",
  "valueType" : "URL",
  "commonName" : "Left logo link (after click)",
  "isServerSide" : false,
  "value" : "http://wwwen.uni.lu/",
  "group" : "Legend and logo"
}, {
  "idObject" : 27,
  "type" : "LEFT_LOGO_TEXT",
  "valueType" : "STRING",
  "commonName" : "Left logo description",
  "isServerSide" : false,
  "value" : "University of Luxembourg",
  "group" : "Legend and logo"
}, {
  "idObject" : 28,
  "type" : "RIGHT_LOGO_IMG",
  "valueType" : "URL",
  "commonName" : "Right logo icon",
  "isServerSide" : false,
  "value" : "/minerva/images/lcsb.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 29,
  "type" : "RIGHT_LOGO_LINK",
  "valueType" : "URL",
  "commonName" : "Right logo link (after click)",
  "isServerSide" : false,
  "value" : "http://wwwen.uni.lu/lcsb/",
  "group" : "Legend and logo"
}, {
  "idObject" : 30,
  "type" : "RIGHT_LOGO_TEXT",
  "valueType" : "STRING",
  "commonName" : "Right logo description",
  "isServerSide" : false,
  "value" : "LCSB - Luxembourg Centre for Systems Biomedicine",
  "group" : "Legend and logo"
}, {
  "idObject" : 9,
  "type" : "REQUEST_ACCOUNT_EMAIL",
  "valueType" : "EMAIL",
  "commonName" : "Email used for requesting an account",
  "isServerSide" : false,
  "value" : "",
  "group" : "Email notification details"
}, {
  "idObject" : 19,
  "type" : "X_FRAME_DOMAIN",
  "valueType" : "URL",
  "commonName" : "Domain allowed to connect via x-frame technology",
  "isServerSide" : false,
  "value" : "",
  "group" : "Server configuration"
}, {
  "idObject" : 22,
  "type" : "CORS_DOMAIN",
  "valueType" : "BOOLEAN",
  "commonName" : "Disable CORS (when disabled 'ORIGIN' http header is required)",
  "isServerSide" : false,
  "value" : "false",
  "group" : "Server configuration"
}, {
  "idObject" : 23,
  "type" : "BIG_FILE_STORAGE_DIR",
  "valueType" : "STRING",
  "commonName" : "Path to store big files",
  "isServerSide" : false,
  "value" : "minerva-big/",
  "group" : "Server configuration"
}, {
  "idObject" : 31,
  "type" : "LEGEND_FILE_1",
  "valueType" : "URL",
  "commonName" : "Legend 1 image file",
  "isServerSide" : false,
  "value" : "/minerva/images/legend_a.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 32,
  "type" : "LEGEND_FILE_2",
  "valueType" : "URL",
  "commonName" : "Legend 2 image file",
  "isServerSide" : false,
  "value" : "/minerva/images/legend_b.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 33,
  "type" : "LEGEND_FILE_3",
  "valueType" : "URL",
  "commonName" : "Legend 3 image file",
  "isServerSide" : false,
  "value" : "/minerva/images/legend_c.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 34,
  "type" : "LEGEND_FILE_4",
  "valueType" : "URL",
  "commonName" : "Legend 4 image file",
  "isServerSide" : false,
  "value" : "/minerva/images/legend_d.png",
  "group" : "Legend and logo"
}, {
  "idObject" : 39,
  "type" : "MIN_COLOR_VAL",
  "valueType" : "COLOR",
  "commonName" : "Overlay color for negative values",
  "isServerSide" : false,
  "value" : "FF0000",
  "group" : "Overlays"
}, {
  "idObject" : 40,
  "type" : "MAX_COLOR_VAL",
  "valueType" : "COLOR",
  "commonName" : "Overlay color for positive values",
  "isServerSide" : false,
  "value" : "0000FF",
  "group" : "Overlays"
}, {
  "idObject" : 41,
  "type" : "SIMPLE_COLOR_VAL",
  "valueType" : "COLOR",
  "commonName" : "Overlay color when no values are defined",
  "isServerSide" : false,
  "value" : "00FF00",
  "group" : "Overlays"
}, {
  "idObject" : 42,
  "type" : "NEUTRAL_COLOR_VAL",
  "valueType" : "COLOR",
  "commonName" : "Overlay color for value=0",
  "isServerSide" : false,
  "value" : "FFFFFF",
  "group" : "Overlays"
}, {
  "idObject" : 43,
  "type" : "OVERLAY_OPACITY",
  "valueType" : "DOUBLE",
  "commonName" : "Opacity used when drawing data overlays (value between 0.0-1.0)",
  "isServerSide" : false,
  "value" : "0.8",
  "group" : "Overlays"
}, {
  "idObject" : 11,
  "type" : "REQUEST_ACCOUNT_DEFAULT_CONTENT",
  "valueType" : "TEXT",
  "commonName" : "Email content used for requesting an account",
  "isServerSide" : false,
  "value" : "Dear Disease map team,\nI would like to request an account in the system.\nKind regards",
  "group" : "Email notification details"
}, {
  "idObject" : 12,
  "type" : "TERMS_OF_USE",
  "valueType" : "URL",
  "commonName" : "URL of platform's Terms of Service",
  "isServerSide" : false,
  "value" : "",
  "group" : "Legend and logo"
}, {
  "idObject" : 14,
  "type" : "COOKIE_POLICY_URL",
  "valueType" : "URL",
  "commonName" : "Privacy policy (url)",
  "isServerSide" : false,
  "value" : "/minerva/default-cookie-policy.html",
  "group" : "Server configuration"
}, {
  "idObject" : 1,
  "type" : "SESSION_LENGTH",
  "valueType" : "INTEGER",
  "commonName" : "Max session inactivity time (in seconds)",
  "isServerSide" : false,
  "value" : "7200",
  "group" : "Server configuration"
}, {
  "idObject" : 16,
  "type" : "MINERVA_ROOT",
  "valueType" : "URL",
  "commonName" : "Minerva root url",
  "isServerSide" : false,
  "value" : "",
  "group" : "Server configuration"
}, {
  "idObject" : 10,
  "type" : "REQUEST_ACCOUNT_DEFAULT_TITLE",
  "valueType" : "STRING",
  "commonName" : "Email title used for requesting an account",
  "isServerSide" : false,
  "value" : "MINERVA account request",
  "group" : "Email notification details"
}, {
  "idObject" : 83,
  "type" : "ORCID_CLIENT_ID",
  "valueType" : "TEXT",
  "commonName" : "Orcid Client ID",
  "isServerSide" : false,
  "value" : "",
  "group" : "OAuth conifguration"
}, {
  "idObject" : 84,
  "type" : "ORCID_CLIENT_SECRET",
  "valueType" : "PASSWORD",
  "commonName" : "Orcid Client Secret",
  "isServerSide" : false,
  "group" : "OAuth conifguration"
}, {
  "idObject" : 20,
  "type" : "ALLOW_AUTO_REGISTER",
  "valueType" : "BOOLEAN",
  "commonName" : "Allow users to create accounts",
  "isServerSide" : false,
  "value" : "false",
  "group" : "Server configuration"
}, {
  "idObject" : 21,
  "type" : "REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS",
  "valueType" : "BOOLEAN",
  "commonName" : "Require admin approval for auto-registered accounts",
  "isServerSide" : false,
  "value" : "true",
  "group" : "Server configuration"
}, {
  "idObject" : 91,
  "type" : "MATOMO_URL",
  "valueType" : "URL",
  "commonName" : "Matomo tracking url (for example: https://cdn.matomo.cloud/atcomp.matomo.cloud/container_d9VKcbPg_dev_d48ac09b17cfa365367b6ce.js)",
  "isServerSide" : false,
  "value" : "",
  "group" : "Server configuration"
} ]

3. Modify configuration option

Modify configuration option.

3.1. CURL sample

$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/options/EMAIL_SMTP_PORT' -X PATCH \
    -d '{"option":{"value":"25"}}' \
    --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
    -H 'Content-Type: application/json'

3.2. Path Parameters

Table 1. /minerva/api/configuration/options/{option}
Parameter	Description
`option`	option type

3.3. Request Fields

Path Type Description

Path	Type	Description
`option.value`	`String`	new option value

option.value

String

new option value

3.4. Response Fields

Path Type Description

Path	Type	Description
`commonName`	`String`	human readable name of configuration option
`group`	`String`	group of options where this configuration option belongs to
`isServerSide`	`boolean`	TRUE/FALSE - is the option responsible for server side processing or frontend
`type`	`String`	option type
`value`	`String`	value of the configuration option
`valueType`	`String`	type of the configuration option. Available options: ALLOW_AUTO_REGISTER, BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, DEFAULT_MAP, EMAIL_ADDRESS, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, EMAIL_SSL_SERVER, LDAP_ADDRESS, LDAP_BASE_DN, LDAP_BIND_DN, LDAP_EMAIL_ATTRIBUTE, LDAP_FILTER, LDAP_FIRST_NAME_ATTRIBUTE, LDAP_LAST_NAME_ATTRIBUTE, LDAP_OBJECT_CLASS, LDAP_PASSWORD, LDAP_PORT, LDAP_SSL, LDAP_UID, LEFT_LOGO_IMG, LEFT_LOGO_LINK, LEFT_LOGO_TEXT, LEGEND_FILE_1, LEGEND_FILE_2, LEGEND_FILE_3, LEGEND_FILE_4, MATOMO_URL, MAX_COLOR_VAL, MCP_ENABLED, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, REQUIRE_APPROVAL_FOR_AUTO_REGISTERED_USERS, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SESSION_LENGTH, SIMPLE_COLOR_VAL, TERMS_OF_USE, X_FRAME_DOMAIN

commonName

String

human readable name of configuration option

group

String

group of options where this configuration option belongs to

isServerSide

boolean

TRUE/FALSE - is the option responsible for server side processing or frontend

type

String

option type

value

String

value of the configuration option

valueType

String

3.5. Sample Response

{
  "idObject" : 8,
  "type" : "EMAIL_SMTP_PORT",
  "valueType" : "INTEGER",
  "commonName" : "SMTP port",
  "isServerSide" : true,
  "value" : "25",
  "group" : "Email notification details"
}

Legacy REST API Documentation - Configuration

1. Details

1.1. CURL sample

1.2. Response Fields

1.3. Sample Response

2. List configuration options

2.1. CURL sample

2.2. Response Fields

2.3. Sample Response

3. Modify configuration option

3.1. CURL sample

3.2. Path Parameters

3.3. Request Fields

3.4. Response Fields

3.5. Sample Response