1. Details
Return full configuration details.
1.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/' -X GET1.2. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of annotators |
|
|
list of bieEntity fields that are used by annotators |
|
|
when minerva platform was built |
|
|
git hash used to build minerva platform |
|
|
version of the minerva platform |
|
|
list of available export image formats |
|
|
list of supported frontend map engines |
|
|
list of submap types |
|
|
map of miriam types supported by minerva. Types are defined on https://identifiers.org/ |
|
|
list of map formats |
|
|
map with modification states |
|
|
list of configuration options |
|
|
list of overlay types |
|
|
map with privilege type available in the system |
|
|
list of reaction types |
|
|
list of basic unit types |
|
|
list of element types |
|
|
annotator name |
|
|
url address of assoiated database |
|
|
Java class responsible for annotating process |
|
|
Java classes that identify bioEntity types that can be annotated by the annotator |
|
|
short description of the annotator |
|
|
list of supported input fields, generated outputs that can be filled by annotator and configuration options |
|
|
identifier type. Either this or 'field' is required for INPUT/OUTPUT parameter |
|
|
bioEntity field. Either this or 'annotation_type' is required for INPUT/OUTPUT parameter |
|
|
name of the CONFIG parameter |
|
|
description of the parameter |
|
|
type of the CONFIG parameter |
|
|
name of the CONFIG parameter |
|
|
default value of the CONFIG parameter |
|
|
order position when listing parameters |
|
|
type of parameter (INPUT/OUTPUT/CONFIG) |
|
|
human readable name of the field |
|
|
unique name of the field |
|
|
Java class that identify type |
|
|
human readable name of the type |
|
|
Java class that identify parent type |
|
|
file extension |
|
|
human readable name of the format |
|
|
Java class that is responsible for export |
|
|
identifier of the map engine |
|
|
human readable name of the map engine |
|
|
identifier of the type |
|
|
human readable name of the submap type |
|
|
human readable name of the identifier type |
|
|
url to database homepage |
|
|
unique identifier used by identifiers.org to reference this type |
|
|
list of uris used by this identifier type |
|
|
human readable name of map format |
|
|
file extension |
|
|
Java class that is used for import/export from the map format |
|
|
human readable name of modification state type |
|
|
short name of the type |
|
|
human readable name of configuration option |
|
|
group of options where this configuration option belongs to |
|
|
TRUE/FALSE - is the option responsible for server side processing or frontend |
|
|
option type |
|
|
value of the configuration option |
|
|
type of the configuration option. Available options: BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, CUSTOM_CSS, DAPI_LOGIN, DAPI_PASSWORD, DEFAULT_CAN_CREATE_OVERLAYS, DEFAULT_MAP, DEFAULT_READ_PROJECT, DEFAULT_WRITE_PROJECT, EMAIL_ADDRESS, EMAIL_IMAP_SERVER, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, GOOGLE_ANALYTICS_IDENTIFIER, GOOGLE_MAPS_API_KEY, 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, MAX_COLOR_VAL, MAX_NUMBER_OF_MAP_LEVELS, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SEARCH_DISTANCE, SEARCH_RESULT_NUMBER, SESSION_LENGTH, SHOW_ELEMENT_ABBREVIATION, SHOW_ELEMENT_ANNOTATIONS, SHOW_ELEMENT_CHARGE, SHOW_ELEMENT_COMPARTMENT, SHOW_ELEMENT_DESCRIPTION, SHOW_ELEMENT_FORMER_SYMBOLS, SHOW_ELEMENT_FORMULA, SHOW_ELEMENT_FULL_NAME, SHOW_ELEMENT_GROUP_SIZE, SHOW_ELEMENT_ID, SHOW_ELEMENT_LINKED_SUBMAP, SHOW_ELEMENT_MODIFICATIONS, SHOW_ELEMENT_SYMBOL, SHOW_ELEMENT_SYNONYMS, SHOW_ELEMENT_TITLE, SHOW_ELEMENT_TYPE, SHOW_REACTION_ABBREVIATION, SHOW_REACTION_ANNOTATIONS, SHOW_REACTION_DESCRIPTION, SHOW_REACTION_FORMULA, SHOW_REACTION_GENE_PROTEIN_REACTION, SHOW_REACTION_LINKED_SUBMAP, SHOW_REACTION_LOWER_BOUND, SHOW_REACTION_MECHANICAL_CONFIDENCE_SCORE, SHOW_REACTION_NAME, SHOW_REACTION_SUBSYSTEM, SHOW_REACTION_SYMBOL, SHOW_REACTION_SYNONYMS, SHOW_REACTION_TITLE, SHOW_REACTION_TYPE, SHOW_REACTION_UPPER_BOUND, SIMPLE_COLOR_VAL, TERMS_OF_USE, USER_MANUAL_FILE, X_FRAME_DOMAIN |
|
|
name of the type |
|
|
human readable description of the privilege |
|
|
class of objects to which privilege applies |
|
|
type of the privilege value (ie. boolean) |
|
|
Java class that identify type |
|
|
human readable name of the type |
|
|
Java class that identify parent type |
|
|
human readable name of the type |
|
|
type identifier |
1.3. Sample Response
{
"options" : [ {
"idObject" : 7,
"type" : "DEFAULT_MAP",
"valueType" : "STRING",
"commonName" : "Default Project Id",
"isServerSide" : false,
"value" : "empty",
"group" : "Server configuration"
}, {
"idObject" : 19,
"type" : "LEFT_LOGO_IMG",
"valueType" : "URL",
"commonName" : "Left logo icon",
"isServerSide" : false,
"value" : "resources/images/udl.png",
"group" : "Legend and logo"
}, {
"idObject" : 20,
"type" : "LEFT_LOGO_LINK",
"valueType" : "URL",
"commonName" : "Left logo link (after click)",
"isServerSide" : false,
"value" : "http://wwwen.uni.lu/",
"group" : "Legend and logo"
}, {
"idObject" : 21,
"type" : "LEFT_LOGO_TEXT",
"valueType" : "STRING",
"commonName" : "Left logo description",
"isServerSide" : false,
"value" : "University of Luxembourg",
"group" : "Legend and logo"
}, {
"idObject" : 22,
"type" : "RIGHT_LOGO_IMG",
"valueType" : "URL",
"commonName" : "Right logo icon",
"isServerSide" : false,
"value" : "resources/images/lcsb.png",
"group" : "Legend and logo"
}, {
"idObject" : 23,
"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" : 24,
"type" : "RIGHT_LOGO_TEXT",
"valueType" : "STRING",
"commonName" : "Right logo description",
"isServerSide" : false,
"value" : "LCSB - Luxembourg Centre for Systems Biomedicine",
"group" : "Legend and logo"
}, {
"idObject" : 25,
"type" : "SEARCH_DISTANCE",
"valueType" : "DOUBLE",
"commonName" : "Max distance for clicking on element (px)",
"isServerSide" : false,
"value" : "10",
"group" : "Point and click"
}, {
"idObject" : 26,
"type" : "REQUEST_ACCOUNT_EMAIL",
"valueType" : "EMAIL",
"commonName" : "Email used for requesting an account",
"isServerSide" : false,
"value" : "",
"group" : "Email notification details"
}, {
"idObject" : 27,
"type" : "SEARCH_RESULT_NUMBER",
"valueType" : "INTEGER",
"commonName" : "Max number of results (this value indicates the max number of elements that will be returned from search - not the number of aggregated elements in the search box).",
"isServerSide" : false,
"value" : "100",
"group" : "Point and click"
}, {
"idObject" : 28,
"type" : "GOOGLE_ANALYTICS_IDENTIFIER",
"valueType" : "STRING",
"commonName" : "Google Analytics tracking ID used for statistics",
"isServerSide" : false,
"value" : "",
"group" : "Server configuration"
}, {
"idObject" : 1,
"type" : "X_FRAME_DOMAIN",
"valueType" : "URL",
"commonName" : "Domain allowed to connect via x-frame technology",
"isServerSide" : false,
"value" : "https://minerva.uni.lu",
"group" : "Server configuration"
}, {
"idObject" : 2,
"type" : "CORS_DOMAIN",
"valueType" : "BOOLEAN",
"commonName" : "Disable CORS (when disabled 'ORIGIN' http header is required)",
"isServerSide" : false,
"value" : "false",
"group" : "Server configuration"
}, {
"idObject" : 29,
"type" : "BIG_FILE_STORAGE_DIR",
"valueType" : "STRING",
"commonName" : "Path to store big files",
"isServerSide" : false,
"value" : "minerva-big/",
"group" : "Server configuration"
}, {
"idObject" : 30,
"type" : "LEGEND_FILE_1",
"valueType" : "URL",
"commonName" : "Legend 1 image file",
"isServerSide" : false,
"value" : "resources/images/legend_a.png",
"group" : "Legend and logo"
}, {
"idObject" : 31,
"type" : "LEGEND_FILE_2",
"valueType" : "URL",
"commonName" : "Legend 2 image file",
"isServerSide" : false,
"value" : "resources/images/legend_b.png",
"group" : "Legend and logo"
}, {
"idObject" : 32,
"type" : "LEGEND_FILE_3",
"valueType" : "URL",
"commonName" : "Legend 3 image file",
"isServerSide" : false,
"value" : "resources/images/legend_c.png",
"group" : "Legend and logo"
}, {
"idObject" : 33,
"type" : "LEGEND_FILE_4",
"valueType" : "URL",
"commonName" : "Legend 4 image file",
"isServerSide" : false,
"value" : "resources/images/legend_d.png",
"group" : "Legend and logo"
}, {
"idObject" : 34,
"type" : "USER_MANUAL_FILE",
"valueType" : "URL",
"commonName" : "User manual file",
"isServerSide" : false,
"value" : "resources/other/user_guide.pdf",
"group" : "Legend and logo"
}, {
"idObject" : 10,
"type" : "MIN_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for negative values",
"isServerSide" : false,
"value" : "FF0000",
"group" : "Overlays"
}, {
"idObject" : 11,
"type" : "MAX_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for postive values",
"isServerSide" : false,
"value" : "0000FF",
"group" : "Overlays"
}, {
"idObject" : 12,
"type" : "SIMPLE_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color when no values are defined",
"isServerSide" : false,
"value" : "00FF00",
"group" : "Overlays"
}, {
"idObject" : 13,
"type" : "NEUTRAL_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for value=0",
"isServerSide" : false,
"value" : "FFFFFF",
"group" : "Overlays"
}, {
"idObject" : 35,
"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" : 36,
"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" : 37,
"type" : "DEFAULT_READ_PROJECT",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: View project",
"isServerSide" : false,
"value" : "true",
"group" : "Default user privileges"
}, {
"idObject" : 38,
"type" : "DEFAULT_WRITE_PROJECT",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: Modify project",
"isServerSide" : false,
"value" : "false",
"group" : "Default user privileges"
}, {
"idObject" : 39,
"type" : "DEFAULT_CAN_CREATE_OVERLAYS",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: Can create data overlays",
"isServerSide" : false,
"value" : "true",
"group" : "Default user privileges"
}, {
"idObject" : 40,
"type" : "SHOW_REACTION_TYPE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction type",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 41,
"type" : "GOOGLE_MAPS_API_KEY",
"valueType" : "STRING",
"commonName" : "By providing this Google Maps Platform API key I declare that I am aware that I am a Customer of the Google Maps Platform and I agree to the terms of the <a href=\"https://cloud.google.com/maps-platform/terms/\" target='_blank'>license of Google Maps Platform</a>.In particular, I warrant that neither any of the maps nor publicly available data overlays (\"General overlays\") on this MINERVA server contain Protected Health Information (as defined in and subject to HIPAA).",
"isServerSide" : false,
"value" : "",
"group" : "Server configuration"
}, {
"idObject" : 42,
"type" : "TERMS_OF_USE",
"valueType" : "URL",
"commonName" : "URL of platform's Terms of Service",
"isServerSide" : false,
"value" : "",
"group" : "Legend and logo"
}, {
"idObject" : 43,
"type" : "COOKIE_POLICY_URL",
"valueType" : "URL",
"commonName" : "Privacy policy (url)",
"isServerSide" : false,
"value" : "default-cookie-policy.xhtml",
"group" : "Server configuration"
}, {
"idObject" : 55,
"type" : "SHOW_REACTION_TITLE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction title",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 56,
"type" : "SHOW_REACTION_NAME",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction name",
"isServerSide" : false,
"value" : "false",
"group" : "Search panel options"
}, {
"idObject" : 57,
"type" : "SHOW_REACTION_LINKED_SUBMAP",
"valueType" : "BOOLEAN",
"commonName" : "Show linked submap for reaction",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 58,
"type" : "SHOW_REACTION_SYMBOL",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 59,
"type" : "SHOW_REACTION_ABBREVIATION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction abbreviation",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 60,
"type" : "SHOW_REACTION_FORMULA",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction formula",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 61,
"type" : "SHOW_REACTION_MECHANICAL_CONFIDENCE_SCORE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction mechanical confidence score",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 62,
"type" : "SHOW_REACTION_LOWER_BOUND",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction lower bound",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 63,
"type" : "SHOW_REACTION_UPPER_BOUND",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction upper bound",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 64,
"type" : "SHOW_REACTION_GENE_PROTEIN_REACTION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction gene protein reaction",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 65,
"type" : "SHOW_REACTION_SUBSYSTEM",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction subsystem",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 66,
"type" : "SHOW_REACTION_SYNONYMS",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction synonyms",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 67,
"type" : "SHOW_REACTION_DESCRIPTION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction description",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 68,
"type" : "SHOW_REACTION_ANNOTATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction annotations",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 69,
"type" : "SHOW_ELEMENT_TYPE",
"valueType" : "BOOLEAN",
"commonName" : "Show element type",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 70,
"type" : "SHOW_ELEMENT_TITLE",
"valueType" : "BOOLEAN",
"commonName" : "Show element title",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 71,
"type" : "SHOW_ELEMENT_LINKED_SUBMAP",
"valueType" : "BOOLEAN",
"commonName" : "Show linked submap for element",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 72,
"type" : "SHOW_ELEMENT_GROUP_SIZE",
"valueType" : "BOOLEAN",
"commonName" : "Show element group size",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 73,
"type" : "SHOW_ELEMENT_COMPARTMENT",
"valueType" : "BOOLEAN",
"commonName" : "Show element compartment",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 74,
"type" : "SHOW_ELEMENT_FULL_NAME",
"valueType" : "BOOLEAN",
"commonName" : "Show element full name",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 75,
"type" : "SHOW_ELEMENT_SYMBOL",
"valueType" : "BOOLEAN",
"commonName" : "Show element symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 76,
"type" : "SHOW_ELEMENT_ABBREVIATION",
"valueType" : "BOOLEAN",
"commonName" : "Show element abbreviation",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 77,
"type" : "SHOW_ELEMENT_FORMULA",
"valueType" : "BOOLEAN",
"commonName" : "Show element formula",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 78,
"type" : "SHOW_ELEMENT_FORMER_SYMBOLS",
"valueType" : "BOOLEAN",
"commonName" : "Show element former symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 79,
"type" : "SHOW_ELEMENT_MODIFICATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show element modifications",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 80,
"type" : "SHOW_ELEMENT_CHARGE",
"valueType" : "BOOLEAN",
"commonName" : "Show element charge",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 81,
"type" : "SHOW_ELEMENT_SYNONYMS",
"valueType" : "BOOLEAN",
"commonName" : "Show element synonyms",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 82,
"type" : "SHOW_ELEMENT_DESCRIPTION",
"valueType" : "BOOLEAN",
"commonName" : "Show element description",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 83,
"type" : "SHOW_ELEMENT_ANNOTATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show element annotations",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 84,
"type" : "SHOW_ELEMENT_ID",
"valueType" : "BOOLEAN",
"commonName" : "Show element id",
"isServerSide" : false,
"value" : "false",
"group" : "Search panel options"
}, {
"idObject" : 3,
"type" : "SESSION_LENGTH",
"valueType" : "INTEGER",
"commonName" : "Max session inactivity time (in seconds)",
"isServerSide" : false,
"value" : "7200",
"group" : "Server configuration"
}, {
"idObject" : 85,
"type" : "MAX_NUMBER_OF_MAP_LEVELS",
"valueType" : "INTEGER",
"commonName" : "Max number of map zoom levels",
"isServerSide" : false,
"value" : "10",
"group" : "Point and click"
}, {
"idObject" : 86,
"type" : "DAPI_LOGIN",
"valueType" : "STRING",
"commonName" : "Login to Data-API system",
"isServerSide" : false,
"value" : "",
"group" : "Data-API configuration"
}, {
"idObject" : 87,
"type" : "DAPI_PASSWORD",
"valueType" : "PASSWORD",
"commonName" : "Password to Data-API system",
"isServerSide" : false,
"group" : "Data-API configuration"
}, {
"idObject" : 4,
"type" : "MINERVA_ROOT",
"valueType" : "URL",
"commonName" : "Minerva root url",
"isServerSide" : false,
"value" : "https://minerva-dev.lcsb.uni.lu/minerva/",
"group" : "Server configuration"
}, {
"idObject" : 88,
"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" : 89,
"type" : "CUSTOM_CSS",
"valueType" : "TEXT",
"commonName" : "Custom CSS",
"isServerSide" : false,
"value" : "",
"group" : "Legend and logo"
} ],
"imageFormats" : [ {
"name" : "PNG image",
"handler" : "lcsb.mapviewer.converter.graphics.PngImageGenerator",
"extension" : "png"
}, {
"name" : "PDF",
"handler" : "lcsb.mapviewer.converter.graphics.PdfImageGenerator",
"extension" : "pdf"
}, {
"name" : "SVG image",
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"annotation_type" : null,
"order" : 25,
"type" : "OUTPUT"
}, {
"field" : "SYNONYMS",
"annotation_type" : null,
"order" : 26,
"type" : "OUTPUT"
}, {
"field" : "INCHI_KEY",
"annotation_type" : null,
"order" : 27,
"type" : "OUTPUT"
}, {
"field" : "SMILE",
"annotation_type" : null,
"order" : 28,
"type" : "OUTPUT"
} ]
}, {
"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.Protein", "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.ChebiAnnotator",
"name" : "Chebi",
"description" : "",
"url" : "http://www.ebi.ac.uk/chebi/",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Chemical" ],
"parameters" : [ {
"field" : null,
"annotation_type" : "CHEBI",
"order" : 0,
"type" : "INPUT"
}, {
"field" : "NAME",
"annotation_type" : null,
"order" : 1,
"type" : "INPUT"
}, {
"field" : "FULL_NAME",
"annotation_type" : null,
"order" : 2,
"type" : "OUTPUT"
}, {
"field" : "INCHI",
"annotation_type" : null,
"order" : 3,
"type" : "OUTPUT"
}, {
"field" : "INCHI_KEY",
"annotation_type" : null,
"order" : 4,
"type" : "OUTPUT"
}, {
"field" : "SMILE",
"annotation_type" : null,
"order" : 5,
"type" : "OUTPUT"
}, {
"field" : "SYNONYMS",
"annotation_type" : null,
"order" : 6,
"type" : "OUTPUT"
} ]
}, {
"className" : "lcsb.mapviewer.annotation.services.annotators.GoAnnotator",
"name" : "Gene Ontology",
"description" : "",
"url" : "http://amigo.geneontology.org/amigo",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Phenotype", "lcsb.mapviewer.model.map.compartment.Compartment", "lcsb.mapviewer.model.map.species.Complex" ],
"parameters" : [ {
"field" : null,
"annotation_type" : "GO",
"order" : 0,
"type" : "INPUT"
}, {
"field" : "FULL_NAME",
"annotation_type" : null,
"order" : 1,
"type" : "OUTPUT"
}, {
"field" : "DESCRIPTION",
"annotation_type" : null,
"order" : 2,
"type" : "OUTPUT"
} ]
}, {
"className" : "lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator",
"name" : "Ensembl",
"description" : "",
"url" : "https://www.ensembl.org/",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Protein", "lcsb.mapviewer.model.map.species.Rna", "lcsb.mapviewer.model.map.species.Gene" ],
"parameters" : [ {
"field" : null,
"annotation_type" : "ENSEMBL",
"order" : 0,
"type" : "INPUT"
}, {
"field" : null,
"annotation_type" : "ENTREZ",
"order" : 1,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "HGNC",
"order" : 2,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "HGNC_SYMBOL",
"order" : 3,
"type" : "OUTPUT"
}, {
"field" : "FULL_NAME",
"annotation_type" : null,
"order" : 4,
"type" : "OUTPUT"
}, {
"field" : "SYMBOL",
"annotation_type" : null,
"order" : 5,
"type" : "OUTPUT"
}, {
"field" : "SYNONYMS",
"annotation_type" : null,
"order" : 6,
"type" : "OUTPUT"
} ]
}, {
"className" : "lcsb.mapviewer.annotation.services.annotators.HgncAnnotator",
"name" : "HGNC",
"description" : "",
"url" : "http://www.genenames.org",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Protein", "lcsb.mapviewer.model.map.species.Rna", "lcsb.mapviewer.model.map.species.Gene" ],
"parameters" : [ {
"field" : null,
"annotation_type" : "HGNC_SYMBOL",
"order" : 0,
"type" : "INPUT"
}, {
"field" : null,
"annotation_type" : "HGNC",
"order" : 1,
"type" : "INPUT"
}, {
"field" : "NAME",
"annotation_type" : "HGNC_SYMBOL",
"order" : 2,
"type" : "INPUT"
}, {
"field" : null,
"annotation_type" : "ENSEMBL",
"order" : 3,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "ENTREZ",
"order" : 4,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "HGNC",
"order" : 5,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "HGNC_SYMBOL",
"order" : 6,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "REFSEQ",
"order" : 7,
"type" : "OUTPUT"
}, {
"field" : null,
"annotation_type" : "UNIPROT",
"order" : 8,
"type" : "OUTPUT"
}, {
"field" : "SYMBOL",
"annotation_type" : null,
"order" : 9,
"type" : "OUTPUT"
}, {
"field" : "SYNONYMS",
"annotation_type" : null,
"order" : 10,
"type" : "OUTPUT"
}, {
"field" : "NAME",
"annotation_type" : null,
"order" : 11,
"type" : "OUTPUT"
}, {
"field" : "FULL_NAME",
"annotation_type" : null,
"order" : 12,
"type" : "OUTPUT"
} ]
}, {
"className" : "lcsb.mapviewer.annotation.services.annotators.PdbAnnotator",
"name" : "Protein Data Bank",
"description" : "",
"url" : "http://www.pdbe.org/",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Protein", "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.CazyAnnotator",
"name" : "CAZy",
"description" : "",
"url" : "http://commonchemistry.org",
"elementClassNames" : [ "lcsb.mapviewer.model.map.species.Protein", "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" : "CAZY",
"order" : 2,
"type" : "OUTPUT"
} ]
} ],
"bioEntityFields" : [ {
"commonName" : "Abbreviation",
"name" : "ABBREVIATION"
}, {
"commonName" : "Charge",
"name" : "CHARGE"
}, {
"commonName" : "Description",
"name" : "DESCRIPTION"
}, {
"commonName" : "Formula",
"name" : "FORMULA"
}, {
"commonName" : "Full name",
"name" : "FULL_NAME"
}, {
"commonName" : "InChi",
"name" : "INCHI"
}, {
"commonName" : "InChi Key",
"name" : "INCHI_KEY"
}, {
"commonName" : "Name",
"name" : "NAME"
}, {
"commonName" : "Mechanical Confidence Score",
"name" : "MCS"
}, {
"commonName" : "Previous Symbols",
"name" : "PREVIOUS_SYMBOLS"
}, {
"commonName" : "Smile",
"name" : "SMILE"
}, {
"commonName" : "Symbol",
"name" : "SYMBOL"
}, {
"commonName" : "Synonyms",
"name" : "SYNONYMS"
}, {
"commonName" : "Subsystem",
"name" : "SUBSYSTEM"
} ]
}2. List configuration options
List configuration options.
2.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/options/' -X GET2.2. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of options |
|
|
human readable name of configuration option |
|
|
group of options where this configuration option belongs to |
|
|
TRUE/FALSE - is the option responsible for server side processing or frontend |
|
|
option type |
|
|
value of the configuration option |
|
|
type of the configuration option. Available options: BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, CUSTOM_CSS, DAPI_LOGIN, DAPI_PASSWORD, DEFAULT_CAN_CREATE_OVERLAYS, DEFAULT_MAP, DEFAULT_READ_PROJECT, DEFAULT_WRITE_PROJECT, EMAIL_ADDRESS, EMAIL_IMAP_SERVER, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, GOOGLE_ANALYTICS_IDENTIFIER, GOOGLE_MAPS_API_KEY, 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, MAX_COLOR_VAL, MAX_NUMBER_OF_MAP_LEVELS, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SEARCH_DISTANCE, SEARCH_RESULT_NUMBER, SESSION_LENGTH, SHOW_ELEMENT_ABBREVIATION, SHOW_ELEMENT_ANNOTATIONS, SHOW_ELEMENT_CHARGE, SHOW_ELEMENT_COMPARTMENT, SHOW_ELEMENT_DESCRIPTION, SHOW_ELEMENT_FORMER_SYMBOLS, SHOW_ELEMENT_FORMULA, SHOW_ELEMENT_FULL_NAME, SHOW_ELEMENT_GROUP_SIZE, SHOW_ELEMENT_ID, SHOW_ELEMENT_LINKED_SUBMAP, SHOW_ELEMENT_MODIFICATIONS, SHOW_ELEMENT_SYMBOL, SHOW_ELEMENT_SYNONYMS, SHOW_ELEMENT_TITLE, SHOW_ELEMENT_TYPE, SHOW_REACTION_ABBREVIATION, SHOW_REACTION_ANNOTATIONS, SHOW_REACTION_DESCRIPTION, SHOW_REACTION_FORMULA, SHOW_REACTION_GENE_PROTEIN_REACTION, SHOW_REACTION_LINKED_SUBMAP, SHOW_REACTION_LOWER_BOUND, SHOW_REACTION_MECHANICAL_CONFIDENCE_SCORE, SHOW_REACTION_NAME, SHOW_REACTION_SUBSYSTEM, SHOW_REACTION_SYMBOL, SHOW_REACTION_SYNONYMS, SHOW_REACTION_TITLE, SHOW_REACTION_TYPE, SHOW_REACTION_UPPER_BOUND, SIMPLE_COLOR_VAL, TERMS_OF_USE, USER_MANUAL_FILE, X_FRAME_DOMAIN |
2.3. Sample Response
[ {
"idObject" : 7,
"type" : "DEFAULT_MAP",
"valueType" : "STRING",
"commonName" : "Default Project Id",
"isServerSide" : false,
"value" : "empty",
"group" : "Server configuration"
}, {
"idObject" : 19,
"type" : "LEFT_LOGO_IMG",
"valueType" : "URL",
"commonName" : "Left logo icon",
"isServerSide" : false,
"value" : "resources/images/udl.png",
"group" : "Legend and logo"
}, {
"idObject" : 20,
"type" : "LEFT_LOGO_LINK",
"valueType" : "URL",
"commonName" : "Left logo link (after click)",
"isServerSide" : false,
"value" : "http://wwwen.uni.lu/",
"group" : "Legend and logo"
}, {
"idObject" : 21,
"type" : "LEFT_LOGO_TEXT",
"valueType" : "STRING",
"commonName" : "Left logo description",
"isServerSide" : false,
"value" : "University of Luxembourg",
"group" : "Legend and logo"
}, {
"idObject" : 22,
"type" : "RIGHT_LOGO_IMG",
"valueType" : "URL",
"commonName" : "Right logo icon",
"isServerSide" : false,
"value" : "resources/images/lcsb.png",
"group" : "Legend and logo"
}, {
"idObject" : 23,
"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" : 24,
"type" : "RIGHT_LOGO_TEXT",
"valueType" : "STRING",
"commonName" : "Right logo description",
"isServerSide" : false,
"value" : "LCSB - Luxembourg Centre for Systems Biomedicine",
"group" : "Legend and logo"
}, {
"idObject" : 25,
"type" : "SEARCH_DISTANCE",
"valueType" : "DOUBLE",
"commonName" : "Max distance for clicking on element (px)",
"isServerSide" : false,
"value" : "10",
"group" : "Point and click"
}, {
"idObject" : 26,
"type" : "REQUEST_ACCOUNT_EMAIL",
"valueType" : "EMAIL",
"commonName" : "Email used for requesting an account",
"isServerSide" : false,
"value" : "",
"group" : "Email notification details"
}, {
"idObject" : 27,
"type" : "SEARCH_RESULT_NUMBER",
"valueType" : "INTEGER",
"commonName" : "Max number of results (this value indicates the max number of elements that will be returned from search - not the number of aggregated elements in the search box).",
"isServerSide" : false,
"value" : "100",
"group" : "Point and click"
}, {
"idObject" : 28,
"type" : "GOOGLE_ANALYTICS_IDENTIFIER",
"valueType" : "STRING",
"commonName" : "Google Analytics tracking ID used for statistics",
"isServerSide" : false,
"value" : "",
"group" : "Server configuration"
}, {
"idObject" : 1,
"type" : "X_FRAME_DOMAIN",
"valueType" : "URL",
"commonName" : "Domain allowed to connect via x-frame technology",
"isServerSide" : false,
"value" : "https://minerva.uni.lu",
"group" : "Server configuration"
}, {
"idObject" : 2,
"type" : "CORS_DOMAIN",
"valueType" : "BOOLEAN",
"commonName" : "Disable CORS (when disabled 'ORIGIN' http header is required)",
"isServerSide" : false,
"value" : "false",
"group" : "Server configuration"
}, {
"idObject" : 29,
"type" : "BIG_FILE_STORAGE_DIR",
"valueType" : "STRING",
"commonName" : "Path to store big files",
"isServerSide" : false,
"value" : "minerva-big/",
"group" : "Server configuration"
}, {
"idObject" : 30,
"type" : "LEGEND_FILE_1",
"valueType" : "URL",
"commonName" : "Legend 1 image file",
"isServerSide" : false,
"value" : "resources/images/legend_a.png",
"group" : "Legend and logo"
}, {
"idObject" : 31,
"type" : "LEGEND_FILE_2",
"valueType" : "URL",
"commonName" : "Legend 2 image file",
"isServerSide" : false,
"value" : "resources/images/legend_b.png",
"group" : "Legend and logo"
}, {
"idObject" : 32,
"type" : "LEGEND_FILE_3",
"valueType" : "URL",
"commonName" : "Legend 3 image file",
"isServerSide" : false,
"value" : "resources/images/legend_c.png",
"group" : "Legend and logo"
}, {
"idObject" : 33,
"type" : "LEGEND_FILE_4",
"valueType" : "URL",
"commonName" : "Legend 4 image file",
"isServerSide" : false,
"value" : "resources/images/legend_d.png",
"group" : "Legend and logo"
}, {
"idObject" : 34,
"type" : "USER_MANUAL_FILE",
"valueType" : "URL",
"commonName" : "User manual file",
"isServerSide" : false,
"value" : "resources/other/user_guide.pdf",
"group" : "Legend and logo"
}, {
"idObject" : 10,
"type" : "MIN_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for negative values",
"isServerSide" : false,
"value" : "FF0000",
"group" : "Overlays"
}, {
"idObject" : 11,
"type" : "MAX_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for postive values",
"isServerSide" : false,
"value" : "0000FF",
"group" : "Overlays"
}, {
"idObject" : 12,
"type" : "SIMPLE_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color when no values are defined",
"isServerSide" : false,
"value" : "00FF00",
"group" : "Overlays"
}, {
"idObject" : 13,
"type" : "NEUTRAL_COLOR_VAL",
"valueType" : "COLOR",
"commonName" : "Overlay color for value=0",
"isServerSide" : false,
"value" : "FFFFFF",
"group" : "Overlays"
}, {
"idObject" : 35,
"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" : 36,
"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" : 37,
"type" : "DEFAULT_READ_PROJECT",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: View project",
"isServerSide" : false,
"value" : "true",
"group" : "Default user privileges"
}, {
"idObject" : 38,
"type" : "DEFAULT_WRITE_PROJECT",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: Modify project",
"isServerSide" : false,
"value" : "false",
"group" : "Default user privileges"
}, {
"idObject" : 39,
"type" : "DEFAULT_CAN_CREATE_OVERLAYS",
"valueType" : "BOOLEAN",
"commonName" : "Default user privilege for: Can create data overlays",
"isServerSide" : false,
"value" : "true",
"group" : "Default user privileges"
}, {
"idObject" : 40,
"type" : "SHOW_REACTION_TYPE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction type",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 41,
"type" : "GOOGLE_MAPS_API_KEY",
"valueType" : "STRING",
"commonName" : "By providing this Google Maps Platform API key I declare that I am aware that I am a Customer of the Google Maps Platform and I agree to the terms of the <a href=\"https://cloud.google.com/maps-platform/terms/\" target='_blank'>license of Google Maps Platform</a>.In particular, I warrant that neither any of the maps nor publicly available data overlays (\"General overlays\") on this MINERVA server contain Protected Health Information (as defined in and subject to HIPAA).",
"isServerSide" : false,
"value" : "",
"group" : "Server configuration"
}, {
"idObject" : 42,
"type" : "TERMS_OF_USE",
"valueType" : "URL",
"commonName" : "URL of platform's Terms of Service",
"isServerSide" : false,
"value" : "",
"group" : "Legend and logo"
}, {
"idObject" : 43,
"type" : "COOKIE_POLICY_URL",
"valueType" : "URL",
"commonName" : "Privacy policy (url)",
"isServerSide" : false,
"value" : "default-cookie-policy.xhtml",
"group" : "Server configuration"
}, {
"idObject" : 55,
"type" : "SHOW_REACTION_TITLE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction title",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 56,
"type" : "SHOW_REACTION_NAME",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction name",
"isServerSide" : false,
"value" : "false",
"group" : "Search panel options"
}, {
"idObject" : 57,
"type" : "SHOW_REACTION_LINKED_SUBMAP",
"valueType" : "BOOLEAN",
"commonName" : "Show linked submap for reaction",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 58,
"type" : "SHOW_REACTION_SYMBOL",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 59,
"type" : "SHOW_REACTION_ABBREVIATION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction abbreviation",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 60,
"type" : "SHOW_REACTION_FORMULA",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction formula",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 61,
"type" : "SHOW_REACTION_MECHANICAL_CONFIDENCE_SCORE",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction mechanical confidence score",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 62,
"type" : "SHOW_REACTION_LOWER_BOUND",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction lower bound",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 63,
"type" : "SHOW_REACTION_UPPER_BOUND",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction upper bound",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 64,
"type" : "SHOW_REACTION_GENE_PROTEIN_REACTION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction gene protein reaction",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 65,
"type" : "SHOW_REACTION_SUBSYSTEM",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction subsystem",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 66,
"type" : "SHOW_REACTION_SYNONYMS",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction synonyms",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 67,
"type" : "SHOW_REACTION_DESCRIPTION",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction description",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 68,
"type" : "SHOW_REACTION_ANNOTATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show reaction annotations",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 69,
"type" : "SHOW_ELEMENT_TYPE",
"valueType" : "BOOLEAN",
"commonName" : "Show element type",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 70,
"type" : "SHOW_ELEMENT_TITLE",
"valueType" : "BOOLEAN",
"commonName" : "Show element title",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 71,
"type" : "SHOW_ELEMENT_LINKED_SUBMAP",
"valueType" : "BOOLEAN",
"commonName" : "Show linked submap for element",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 72,
"type" : "SHOW_ELEMENT_GROUP_SIZE",
"valueType" : "BOOLEAN",
"commonName" : "Show element group size",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 73,
"type" : "SHOW_ELEMENT_COMPARTMENT",
"valueType" : "BOOLEAN",
"commonName" : "Show element compartment",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 74,
"type" : "SHOW_ELEMENT_FULL_NAME",
"valueType" : "BOOLEAN",
"commonName" : "Show element full name",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 75,
"type" : "SHOW_ELEMENT_SYMBOL",
"valueType" : "BOOLEAN",
"commonName" : "Show element symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 76,
"type" : "SHOW_ELEMENT_ABBREVIATION",
"valueType" : "BOOLEAN",
"commonName" : "Show element abbreviation",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 77,
"type" : "SHOW_ELEMENT_FORMULA",
"valueType" : "BOOLEAN",
"commonName" : "Show element formula",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 78,
"type" : "SHOW_ELEMENT_FORMER_SYMBOLS",
"valueType" : "BOOLEAN",
"commonName" : "Show element former symbol",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 79,
"type" : "SHOW_ELEMENT_MODIFICATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show element modifications",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 80,
"type" : "SHOW_ELEMENT_CHARGE",
"valueType" : "BOOLEAN",
"commonName" : "Show element charge",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 81,
"type" : "SHOW_ELEMENT_SYNONYMS",
"valueType" : "BOOLEAN",
"commonName" : "Show element synonyms",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 82,
"type" : "SHOW_ELEMENT_DESCRIPTION",
"valueType" : "BOOLEAN",
"commonName" : "Show element description",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 83,
"type" : "SHOW_ELEMENT_ANNOTATIONS",
"valueType" : "BOOLEAN",
"commonName" : "Show element annotations",
"isServerSide" : false,
"value" : "true",
"group" : "Search panel options"
}, {
"idObject" : 84,
"type" : "SHOW_ELEMENT_ID",
"valueType" : "BOOLEAN",
"commonName" : "Show element id",
"isServerSide" : false,
"value" : "false",
"group" : "Search panel options"
}, {
"idObject" : 3,
"type" : "SESSION_LENGTH",
"valueType" : "INTEGER",
"commonName" : "Max session inactivity time (in seconds)",
"isServerSide" : false,
"value" : "7200",
"group" : "Server configuration"
}, {
"idObject" : 85,
"type" : "MAX_NUMBER_OF_MAP_LEVELS",
"valueType" : "INTEGER",
"commonName" : "Max number of map zoom levels",
"isServerSide" : false,
"value" : "10",
"group" : "Point and click"
}, {
"idObject" : 86,
"type" : "DAPI_LOGIN",
"valueType" : "STRING",
"commonName" : "Login to Data-API system",
"isServerSide" : false,
"value" : "",
"group" : "Data-API configuration"
}, {
"idObject" : 87,
"type" : "DAPI_PASSWORD",
"valueType" : "PASSWORD",
"commonName" : "Password to Data-API system",
"isServerSide" : false,
"group" : "Data-API configuration"
}, {
"idObject" : 4,
"type" : "MINERVA_ROOT",
"valueType" : "URL",
"commonName" : "Minerva root url",
"isServerSide" : false,
"value" : "https://minerva-dev.lcsb.uni.lu/minerva/",
"group" : "Server configuration"
}, {
"idObject" : 88,
"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" : 89,
"type" : "CUSTOM_CSS",
"valueType" : "TEXT",
"commonName" : "Custom CSS",
"isServerSide" : false,
"value" : "",
"group" : "Legend and logo"
} ]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
| Parameter | Description |
|---|---|
|
option type |
3.3. Request Fields
| Path | Type | Description |
|---|---|---|
|
|
new option value |
3.4. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
human readable name of configuration option |
|
|
group of options where this configuration option belongs to |
|
|
TRUE/FALSE - is the option responsible for server side processing or frontend |
|
|
option type |
|
|
value of the configuration option |
|
|
type of the configuration option. Available options: BIG_FILE_STORAGE_DIR, COOKIE_POLICY_URL, CORS_DOMAIN, CUSTOM_CSS, DAPI_LOGIN, DAPI_PASSWORD, DEFAULT_CAN_CREATE_OVERLAYS, DEFAULT_MAP, DEFAULT_READ_PROJECT, DEFAULT_WRITE_PROJECT, EMAIL_ADDRESS, EMAIL_IMAP_SERVER, EMAIL_LOGIN, EMAIL_PASSWORD, EMAIL_SMTP_PORT, EMAIL_SMTP_SERVER, GOOGLE_ANALYTICS_IDENTIFIER, GOOGLE_MAPS_API_KEY, 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, MAX_COLOR_VAL, MAX_NUMBER_OF_MAP_LEVELS, MINERVANET_AUTH_TOKEN, MINERVANET_URL, MINERVA_ROOT, MIN_COLOR_VAL, NEUTRAL_COLOR_VAL, OVERLAY_OPACITY, REQUEST_ACCOUNT_DEFAULT_CONTENT, REQUEST_ACCOUNT_DEFAULT_TITLE, REQUEST_ACCOUNT_EMAIL, RIGHT_LOGO_IMG, RIGHT_LOGO_LINK, RIGHT_LOGO_TEXT, SEARCH_DISTANCE, SEARCH_RESULT_NUMBER, SESSION_LENGTH, SHOW_ELEMENT_ABBREVIATION, SHOW_ELEMENT_ANNOTATIONS, SHOW_ELEMENT_CHARGE, SHOW_ELEMENT_COMPARTMENT, SHOW_ELEMENT_DESCRIPTION, SHOW_ELEMENT_FORMER_SYMBOLS, SHOW_ELEMENT_FORMULA, SHOW_ELEMENT_FULL_NAME, SHOW_ELEMENT_GROUP_SIZE, SHOW_ELEMENT_ID, SHOW_ELEMENT_LINKED_SUBMAP, SHOW_ELEMENT_MODIFICATIONS, SHOW_ELEMENT_SYMBOL, SHOW_ELEMENT_SYNONYMS, SHOW_ELEMENT_TITLE, SHOW_ELEMENT_TYPE, SHOW_REACTION_ABBREVIATION, SHOW_REACTION_ANNOTATIONS, SHOW_REACTION_DESCRIPTION, SHOW_REACTION_FORMULA, SHOW_REACTION_GENE_PROTEIN_REACTION, SHOW_REACTION_LINKED_SUBMAP, SHOW_REACTION_LOWER_BOUND, SHOW_REACTION_MECHANICAL_CONFIDENCE_SCORE, SHOW_REACTION_NAME, SHOW_REACTION_SUBSYSTEM, SHOW_REACTION_SYMBOL, SHOW_REACTION_SYNONYMS, SHOW_REACTION_TITLE, SHOW_REACTION_TYPE, SHOW_REACTION_UPPER_BOUND, SIMPLE_COLOR_VAL, TERMS_OF_USE, USER_MANUAL_FILE, X_FRAME_DOMAIN |
3.5. Sample Response
{
"idObject" : 18,
"type" : "EMAIL_SMTP_PORT",
"valueType" : "INTEGER",
"commonName" : "SMTP port",
"isServerSide" : true,
"value" : "25",
"group" : "Email notification details"
}4. DAPI configuration details
Provide information about DAPI connection.
4.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/dapi/' -X GET4.2. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
is the DAPI connection configured properly |
4.3. Sample Response
{
"validConnection" : true
}5. Register new DAPI user
Creates new DAPI user in the https://dapi.lcsb.uni.lu/ system.
5.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/dapi:registerUser' -X POST \
-d '{"login":"admin","password":"admin","email":"piotr.gawron@uni.lu"}' \
--cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" \
-H 'Content-Type: application/json'5.2. Request Fields
| Path | Type | Description |
|---|---|---|
|
|
user login |
|
|
user password |
|
|
email address |
6. List available DAPI databases
List available DAPI databases.
6.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/dapi/database/' -X GET6.2. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of available databases |
|
|
name of the database |
6.3. Sample Response
[ {
"name" : "DrugBank"
}, {
"name" : "CTD"
} ]7. List available DAPI database releases
List available DAPI databases.
7.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/dapi/database/DrugBank/release/' -X GET7.2. Path Parameters
| Parameter | Description |
|---|---|
|
database name |
7.3. Response Fields
| Path | Type | Description |
|---|---|---|
|
|
list of available releases |
|
|
url with the content of license used for this release |
|
|
text content of license used for this release |
|
|
version of the database release |
|
|
was this release accepted by currently logged in DAPI user |
7.4. Sample Response
[ {
"licenseUrl" : "https://creativecommons.org/licenses/by-nc/4.0/legalcode",
"licenseContent" : "By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NonCommercial 4.0 International Public License (\"Public License\"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.\r\n\r\nSection 1 – Definitions.\r\n\r\nAdapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.\r\nAdapter`s License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.\r\nCopyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.\r\nEffective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.\r\nExceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.\r\nLicensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.\r\nLicensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.\r\nLicensor means the individual(s) or entity(ies) granting rights under this Public License.\r\nNonCommercial means not primarily intended for or directed towards commercial advantage or monetary compensation. For purposes of this Public License, the exchange of the Licensed Material for other material subject to Copyright and Similar Rights by digital file-sharing or similar means is NonCommercial provided there is no payment of monetary compensation in connection with the exchange.\r\nShare means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.\r\nSui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.\r\nYou means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.\r\nSection 2 – Scope.\r\n\r\nLicense grant.\r\nSubject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:\r\nreproduce and Share the Licensed Material, in whole or in part, for NonCommercial purposes only; and\r\nproduce, reproduce, and Share Adapted Material for NonCommercial purposes only.\r\nExceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.\r\nTerm. The term of this Public License is specified in Section 6(a).\r\nMedia and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material.\r\nDownstream recipients.\r\nOffer from the Licensor – Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.\r\nNo downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.\r\nNo endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).\r\nOther rights.\r\n\r\nMoral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.\r\nPatent and trademark rights are not licensed under this Public License.\r\nTo the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties, including when the Licensed Material is used other than for NonCommercial purposes.\r\nSection 3 – License Conditions.\r\n\r\nYour exercise of the Licensed Rights is expressly made subject to the following conditions.\r\n\r\nAttribution.\r\n\r\nIf You Share the Licensed Material (including in modified form), You must:\r\n\r\nretain the following if it is supplied by the Licensor with the Licensed Material:\r\nidentification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated);\r\na copyright notice;\r\na notice that refers to this Public License;\r\na notice that refers to the disclaimer of warranties;\r\na URI or hyperlink to the Licensed Material to the extent reasonably practicable;\r\nindicate if You modified the Licensed Material and retain an indication of any previous modifications; and\r\nindicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License.\r\nYou may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information.\r\nIf requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable.\r\nIf You Share Adapted Material You produce, the Adapter`s License You apply must not prevent recipients of the Adapted Material from complying with this Public License.\r\nSection 4 – Sui Generis Database Rights.\r\n\r\nWhere the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:\r\n\r\nfor the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database for NonCommercial purposes only;\r\nif You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and\r\nYou must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.\r\nFor the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.\r\nSection 5 – Disclaimer of Warranties and Limitation of Liability.\r\n\r\nUnless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.\r\nTo the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.\r\nThe disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.\r\nSection 6 – Term and Termination.\r\n\r\nThis Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.\r\nWhere Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:\r\n\r\nautomatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or\r\nupon express reinstatement by the Licensor.\r\nFor the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.\r\nFor the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.\r\nSections 1, 5, 6, 7, and 8 survive termination of this Public License.\r\nSection 7 – Other Terms and Conditions.\r\n\r\nThe Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.\r\nAny arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.\r\nSection 8 – Interpretation.\r\n\r\nFor the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.\r\nTo the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.\r\nNo term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.\r\nNothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.\r\n",
"name" : "5.1",
"accepted" : true
} ]8. Accept DAPI database release license
Accept DAPI database release license.
8.1. CURL sample
$ curl 'https://minerva-service.lcsb.uni.lu/minerva/api/configuration/dapi/database/DrugBank/release/5.1:acceptLicense' -X POST \
--cookie "MINERVA_AUTH_TOKEN=xxxxxxxx"8.2. Path Parameters
| Parameter | Description |
|---|---|
|
database name |
|
version of the database |