From 523467404b15eb29429d16945bbcf55c2135a90f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrian=20Or=C5=82=C3=B3w?= <adrian.orlow@fishbrain.com>
Date: Thu, 29 Feb 2024 19:36:02 +0100
Subject: [PATCH] feat: add plugin data bio entities
---
docs/data/bioentities.md | 116 +++
docs/types/BioEntity.md | 623 +++++++++++++++
docs/types/Chemical.md | 744 ++++++++++++++++++
docs/types/Drug.md | 725 +++++++++++++++++
docs/types/Marker.md | 12 +
index.d.ts | 3 +
package-lock.json | 79 +-
package.json | 7 +-
.../OverlayData/OverlayData.types.ts | 2 +-
.../BioEntitiesAccordion.component.test.tsx | 4 +-
.../ResultsList/PinsList/PinsList.types.tsx | 2 +-
.../MapViewer/utils/config/getCanvasIcon.ts | 8 +-
...rseSurfaceMarkersToBioEntityRender.test.ts | 96 +++
.../parseSurfaceMarkersToBioEntityRender.ts | 24 +
.../overlaysLayer/useOverlayFeatures.test.ts | 20 +-
.../overlaysLayer/useOverlayFeatures.ts | 30 +-
.../pinsLayer/getMarkerSingleFeature.test.ts | 58 ++
.../pinsLayer/getMarkerSingleFeature.ts | 24 +
.../config/pinsLayer/getMarkersFeatures.ts | 19 +
.../config/pinsLayer/getPinFeature.test.ts | 15 +
.../utils/config/pinsLayer/getPinFeature.ts | 8 +-
.../utils/config/pinsLayer/getPinStyle.ts | 2 +-
.../config/pinsLayer/useOlMapPinsLayer.ts | 12 +-
src/models/bioEntitySchema.ts | 2 +-
src/redux/bioEntity/bioEntity.reducers.ts | 7 +-
src/redux/bioEntity/bioEntity.selectors.ts | 6 +
src/redux/bioEntity/bioEntity.slice.ts | 7 +-
src/redux/chemicals/chemicals.selectors.ts | 6 +
src/redux/contextMenu/contextMenu.types.ts | 2 +-
src/redux/drawer/drawer.types.ts | 4 +-
src/redux/drugs/drugs.selectors.ts | 6 +
src/redux/markers/markers.constants.ts | 5 +
src/redux/markers/markers.mock.ts | 5 +
src/redux/markers/markers.reducers.ts | 31 +
src/redux/markers/markers.selectors.ts | 33 +
src/redux/markers/markers.slice.ts | 23 +
src/redux/markers/markers.types.ts | 30 +
src/redux/markers/markers.utils.ts | 4 +
src/redux/models/marker.mock.ts | 25 +
src/redux/root/root.fixtures.ts | 8 +-
src/redux/store.ts | 6 +-
.../bioEntities/addSingleMarker.ts | 12 +
.../bioEntities/clearAllElements.ts | 27 +
.../bioEntities/getAllChemicals.ts | 10 +
.../bioEntities/getAllContent.ts | 10 +
.../pluginsManager/bioEntities/getAllDrugs.ts | 10 +
.../bioEntities/getAllMarkers.ts | 10 +
.../bioEntities/getShownElements.ts | 22 +
.../bioEntities/getShownElements.types.ts | 9 +
.../pluginsManager/bioEntities/index.ts | 23 +
.../bioEntities/removeAllMarkers.ts | 7 +
.../bioEntities/removeSingleMarker.ts | 7 +
src/services/pluginsManager/pluginsManager.ts | 4 +
src/types/OLrendering.ts | 3 +-
54 files changed, 2955 insertions(+), 42 deletions(-)
create mode 100644 docs/data/bioentities.md
create mode 100644 docs/types/BioEntity.md
create mode 100644 docs/types/Chemical.md
create mode 100644 docs/types/Drug.md
create mode 100644 docs/types/Marker.md
create mode 100644 src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.test.ts
create mode 100644 src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.ts
create mode 100644 src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.test.ts
create mode 100644 src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.ts
create mode 100644 src/components/Map/MapViewer/utils/config/pinsLayer/getMarkersFeatures.ts
create mode 100644 src/redux/markers/markers.constants.ts
create mode 100644 src/redux/markers/markers.mock.ts
create mode 100644 src/redux/markers/markers.reducers.ts
create mode 100644 src/redux/markers/markers.selectors.ts
create mode 100644 src/redux/markers/markers.slice.ts
create mode 100644 src/redux/markers/markers.types.ts
create mode 100644 src/redux/markers/markers.utils.ts
create mode 100644 src/redux/models/marker.mock.ts
create mode 100644 src/services/pluginsManager/bioEntities/addSingleMarker.ts
create mode 100644 src/services/pluginsManager/bioEntities/clearAllElements.ts
create mode 100644 src/services/pluginsManager/bioEntities/getAllChemicals.ts
create mode 100644 src/services/pluginsManager/bioEntities/getAllContent.ts
create mode 100644 src/services/pluginsManager/bioEntities/getAllDrugs.ts
create mode 100644 src/services/pluginsManager/bioEntities/getAllMarkers.ts
create mode 100644 src/services/pluginsManager/bioEntities/getShownElements.ts
create mode 100644 src/services/pluginsManager/bioEntities/getShownElements.types.ts
create mode 100644 src/services/pluginsManager/bioEntities/index.ts
create mode 100644 src/services/pluginsManager/bioEntities/removeAllMarkers.ts
create mode 100644 src/services/pluginsManager/bioEntities/removeSingleMarker.ts
diff --git a/docs/data/bioentities.md b/docs/data/bioentities.md
new file mode 100644
index 00000000..e17f46d1
--- /dev/null
+++ b/docs/data/bioentities.md
@@ -0,0 +1,116 @@
+### Data / BioEntities
+
+The methods contained within 'Data / BioEntities' are used to access/modify data on content/drugs/chemicals entities, as well as pin and surface markers.
+
+Below is a description of the methods, as well as the types they return. A description of the object types can be found in folder `/docs/types/`.
+
+**Available data access methods include:**
+
+- `getAllChemicals`
+ - gets list of searched chemicals
+ - returns array of `Chemical`
+- `getAllContent`
+ - gets list of searched content
+ - returns array of `BioEntity`
+- `getAllDrugs`
+ - gets list of searched drugs
+ - returns array of `Drug`
+- `getAllMarkers`
+ - gets list of added markers
+ - returns array of `Marker`
+- `getShownElements`
+ - gets list of all currently shown content/chemicals/drugs bioentities + markers
+ - returns object of
+ ```
+ {
+ content: BioEntity[]
+ drugs: BioEntity[]
+ chemicals: BioEntity[]
+ markers: Marker[]
+ }
+ ```
+
+**Available data modify methods include:**
+
+##### `clearAllElements`
+
+- accepts single argument
+ - array of `string` which includes one or more of: `'drugs'`, `'chemicals'`, `'content'`, `'marker'`
+- clears **all** elements of provided type(s)
+- returns nothing
+- example:
+ ```ts
+ window.minerva.data.bioEntities.clearAllElements(['drugs', 'chemicals']);
+ ```
+
+##### `addSingleMarker`
+
+- accepts single argument of object below
+ - **object:**
+ ```
+ {
+ type: 'pin' OR 'surface'
+ id: string [optional]
+ color: string
+ opacity: number
+ x: number
+ y: number
+ width: number [optional]
+ height: number [optional]
+ number: number [optional]
+ modelId: number [optional]
+ }
+ ```
+ - **id** - optional, if not provided uuidv4 is generated
+ - **color** - should be provided in hex format with hash (example: `#FF0000`)
+ - **opacity** - should be a float between `0` and `1` (example: `0.54`)
+ - **x** - x coord on the map
+ - **y** - y coord on the map
+ - **width** - width of surface [surface marker only]
+ - **height** - width of height [surface marker only]
+ - **number** - number presented on the pin [pin marker only]
+ - **modelId** - if marker should be visible only on single map, modelId should be provided
+- adds one marker to markers list
+- returns created `Marker`
+- examples:
+ ```ts
+ window.minerva.data.bioEntities.addSingleMarker({
+ type: 'surface',
+ color: '#106AD7',
+ opacity: 0.67,
+ x: 4438,
+ y: 1124,
+ width: 200,
+ height: 300,
+ modelId: 52,
+ });
+ ```
+ ```ts
+ window.minerva.data.bioEntities.addSingleMarker({
+ type: 'pin',
+ color: '#106AD7',
+ opacity: 1,
+ x: 8723,
+ y: 4322,
+ number: 43,
+ });
+ ```
+
+##### `removeSingleMarker`
+
+- accepts single argument of `string` which represents marker `id`
+- removes one marker from markers list
+- returns nothing
+- example:
+ ```ts
+ window.minerva.data.bioEntities.removeSingleMarker('f4c068d1-9695-4f1b-928c-d0cff92164b2');
+ ```
+
+##### `removeAllMarkers`
+
+- removes all markers from markers list
+- returns nothing
+- example:
+ ```ts
+ window.minerva.data.bioEntities.removeAllMarkers();
+ ```
diff --git a/docs/types/BioEntity.md b/docs/types/BioEntity.md
new file mode 100644
index 00000000..faba904a
--- /dev/null
+++ b/docs/types/BioEntity.md
@@ -0,0 +1,623 @@
+```json
+{
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "stringType": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "elementId": {
+ "type": "string"
+ },
+ "model": {
+ "type": "number"
+ },
+ "references": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "link": {
+ "anyOf": [
+ {
+ "type": "string",
+ "format": "uri"
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "article": {
+ "type": "object",
+ "properties": {
+ "title": {
+ "type": "string"
+ },
+ "authors": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "journal": {
+ "type": "string"
+ },
+ "year": {
+ "type": "number"
+ },
+ "link": {
+ "type": "string"
+ },
+ "pubmedId": {
+ "type": "string"
+ },
+ "citationCount": {
+ "type": "number"
+ }
+ },
+ "required": [
+ "title",
+ "authors",
+ "journal",
+ "year",
+ "link",
+ "pubmedId",
+ "citationCount"
+ ],
+ "additionalProperties": false
+ },
+ "type": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
+ },
+ "id": {
+ "type": "number"
+ },
+ "annotatorClassName": {
+ "type": "string"
+ }
+ },
+ "required": ["link", "type", "resource", "id", "annotatorClassName"],
+ "additionalProperties": false
+ }
+ },
+ "z": {
+ "type": "number"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "symbol": {
+ "type": ["string", "null"]
+ },
+ "homodimer": {
+ "type": "number"
+ },
+ "nameX": {
+ "type": "number"
+ },
+ "nameY": {
+ "type": "number"
+ },
+ "nameWidth": {
+ "type": "number"
+ },
+ "nameHeight": {
+ "type": "number"
+ },
+ "nameVerticalAlign": {
+ "type": "string"
+ },
+ "nameHorizontalAlign": {
+ "type": "string"
+ },
+ "width": {
+ "type": "number"
+ },
+ "height": {
+ "type": "number"
+ },
+ "visibilityLevel": {
+ "type": "string"
+ },
+ "transparencyLevel": {
+ "type": "string"
+ },
+ "synonyms": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "formerSymbols": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "fullName": {
+ "type": ["string", "null"]
+ },
+ "compartmentName": {
+ "type": ["string", "null"]
+ },
+ "abbreviation": {
+ "type": ["string", "null"]
+ },
+ "formula": {
+ "type": ["string", "null"]
+ },
+ "glyph": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "file": {
+ "type": "number"
+ }
+ },
+ "required": ["file"],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "activity": {
+ "type": "boolean"
+ },
+ "structuralState": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "value": {
+ "type": "string"
+ },
+ "position": {
+ "type": "object",
+ "properties": {
+ "x": {
+ "type": "number"
+ },
+ "y": {
+ "type": "number"
+ }
+ },
+ "required": ["x", "y"],
+ "additionalProperties": false
+ },
+ "z": {
+ "type": "number"
+ },
+ "width": {
+ "type": "number"
+ },
+ "height": {
+ "type": "number"
+ },
+ "fontSize": {
+ "type": "number"
+ },
+ "size": {
+ "type": "number"
+ },
+ "center": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/position"
+ },
+ "borderColor": {
+ "type": "object",
+ "properties": {
+ "alpha": {
+ "type": "number"
+ },
+ "rgb": {
+ "type": "number"
+ }
+ },
+ "required": ["alpha", "rgb"],
+ "additionalProperties": false
+ },
+ "elementId": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "value",
+ "position",
+ "z",
+ "width",
+ "height",
+ "fontSize",
+ "size",
+ "center",
+ "borderColor",
+ "elementId"
+ ],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "hypothetical": {
+ "type": ["boolean", "null"]
+ },
+ "boundaryCondition": {
+ "type": "boolean"
+ },
+ "constant": {
+ "type": "boolean"
+ },
+ "initialAmount": {
+ "type": ["number", "null"]
+ },
+ "initialConcentration": {
+ "type": ["number", "null"]
+ },
+ "charge": {
+ "type": ["number", "null"]
+ },
+ "substanceUnits": {
+ "type": ["string", "null"]
+ },
+ "onlySubstanceUnits": {
+ "type": "boolean"
+ },
+ "modificationResidues": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "idModificationResidue": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "position": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/position"
+ },
+ "z": {
+ "type": "number"
+ },
+ "borderColor": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "state": {
+ "anyOf": [
+ {
+ "type": ["string", "number"]
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "size": {
+ "type": "number"
+ },
+ "elementId": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "id",
+ "idModificationResidue",
+ "name",
+ "z",
+ "borderColor",
+ "size",
+ "elementId"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "complex": {
+ "type": ["number", "null"]
+ },
+ "compartment": {
+ "type": ["number", "null"]
+ },
+ "submodel": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "mapId": {
+ "type": "number"
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["mapId", "type"],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "x": {
+ "type": "number"
+ },
+ "y": {
+ "type": "number"
+ },
+ "lineWidth": {
+ "type": "number"
+ },
+ "fontColor": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "fontSize": {
+ "type": "number"
+ },
+ "fillColor": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "borderColor": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "smiles": {
+ "anyOf": [
+ {
+ "anyOf": [
+ {
+ "not": {}
+ },
+ {
+ "type": "string"
+ }
+ ]
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "inChI": {
+ "type": ["string", "null"]
+ },
+ "inChIKey": {
+ "type": ["string", "null"]
+ },
+ "thickness": {
+ "type": "number"
+ },
+ "outerWidth": {
+ "type": "number"
+ },
+ "innerWidth": {
+ "type": "number"
+ },
+ "idReaction": {
+ "type": "string"
+ },
+ "reversible": {
+ "type": "boolean"
+ },
+ "mechanicalConfidenceScore": {
+ "type": "boolean"
+ },
+ "lowerBound": {
+ "type": "boolean"
+ },
+ "upperBound": {
+ "type": "boolean"
+ },
+ "subsystem": {
+ "type": "string"
+ },
+ "geneProteinReaction": {
+ "type": "string"
+ },
+ "kinetics": {
+ "type": "null"
+ },
+ "products": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "aliasId": {
+ "type": "number"
+ },
+ "stoichiometry": {
+ "type": ["number", "null"]
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["aliasId", "stoichiometry"],
+ "additionalProperties": false
+ }
+ },
+ "reactants": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/products/items"
+ }
+ },
+ "modifiers": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/products/items"
+ }
+ },
+ "processCoordinates": {
+ "type": "null"
+ },
+ "line": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "width": {
+ "type": "number"
+ },
+ "color": {
+ "$ref": "#/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "z": {
+ "type": "number"
+ },
+ "segments": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "x1": {
+ "type": "number"
+ },
+ "y1": {
+ "type": "number"
+ },
+ "x2": {
+ "type": "number"
+ },
+ "y2": {
+ "type": "number"
+ }
+ },
+ "required": ["x1", "y1", "x2", "y2"],
+ "additionalProperties": false
+ }
+ },
+ "startArrow": {
+ "type": "object",
+ "properties": {
+ "arrowType": {
+ "type": "string"
+ },
+ "angle": {
+ "type": "number"
+ },
+ "lineType": {
+ "type": "string"
+ },
+ "length": {
+ "type": "number"
+ }
+ },
+ "required": ["arrowType", "angle", "lineType", "length"],
+ "additionalProperties": false
+ },
+ "endArrow": {
+ "$ref": "#/properties/line/properties/startArrow"
+ },
+ "lineType": {
+ "type": "string"
+ }
+ },
+ "required": ["id", "width", "color", "z", "segments", "startArrow", "endArrow", "lineType"],
+ "additionalProperties": false
+ },
+ "operators": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "line": {
+ "$ref": "#/properties/line"
+ },
+ "inputs": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ }
+ },
+ "required": ["id"],
+ "additionalProperties": false
+ }
+ },
+ "outputs": {
+ "not": {}
+ },
+ "operatorText": {
+ "type": "string"
+ },
+ "reactantOperator": {
+ "type": "boolean"
+ },
+ "productOperator": {
+ "type": "boolean"
+ },
+ "modifierOperator": {
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "id",
+ "line",
+ "inputs",
+ "operatorText",
+ "reactantOperator",
+ "productOperator",
+ "modifierOperator"
+ ],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": [
+ "id",
+ "stringType",
+ "name",
+ "elementId",
+ "model",
+ "references",
+ "z",
+ "notes",
+ "symbol",
+ "nameX",
+ "nameY",
+ "nameWidth",
+ "nameHeight",
+ "nameVerticalAlign",
+ "nameHorizontalAlign",
+ "width",
+ "height",
+ "visibilityLevel",
+ "transparencyLevel",
+ "synonyms",
+ "formerSymbols",
+ "fullName",
+ "abbreviation",
+ "formula",
+ "glyph",
+ "compartment",
+ "submodel",
+ "x",
+ "y",
+ "fontColor",
+ "fontSize",
+ "fillColor",
+ "borderColor"
+ ],
+ "additionalProperties": false,
+ "$schema": "http://json-schema.org/draft-07/schema#"
+}
+```
diff --git a/docs/types/Chemical.md b/docs/types/Chemical.md
new file mode 100644
index 00000000..61add593
--- /dev/null
+++ b/docs/types/Chemical.md
@@ -0,0 +1,744 @@
+```json
+{
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "object",
+ "properties": {
+ "annotatorClassName": {
+ "type": "string"
+ },
+ "id": {
+ "type": "number"
+ },
+ "link": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["annotatorClassName", "id", "link", "resource", "type"],
+ "additionalProperties": false
+ },
+ "name": {
+ "type": "string"
+ },
+ "description": {
+ "type": "string"
+ },
+ "directEvidence": {
+ "type": ["string", "null"]
+ },
+ "directEvidenceReferences": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "link": {
+ "anyOf": [
+ {
+ "type": "string",
+ "format": "uri"
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "article": {
+ "type": "object",
+ "properties": {
+ "title": {
+ "type": "string"
+ },
+ "authors": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "journal": {
+ "type": "string"
+ },
+ "year": {
+ "type": "number"
+ },
+ "link": {
+ "type": "string"
+ },
+ "pubmedId": {
+ "type": "string"
+ },
+ "citationCount": {
+ "type": "number"
+ }
+ },
+ "required": [
+ "title",
+ "authors",
+ "journal",
+ "year",
+ "link",
+ "pubmedId",
+ "citationCount"
+ ],
+ "additionalProperties": false
+ },
+ "type": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
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+ }
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+ "synonyms": {
+ "type": "array",
+ "items": {
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+ "references": {
+ "type": "array",
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+ }
+ },
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+ "items": {
+ "type": "object",
+ "properties": {
+ "name": {
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+ "references": {
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+ "items": {
+ "$ref": "#/properties/directEvidenceReferences/items"
+ }
+ },
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+ "height": {
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+ "visibilityLevel": {
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+ "type": "string"
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+ "synonyms": {
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+ "items": {
+ "type": "string"
+ }
+ },
+ "formerSymbols": {
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+ }
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+ "fullName": {
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+ "compartmentName": {
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+ "formula": {
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+ "glyph": {
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+ "properties": {
+ "file": {
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+ }
+ },
+ "required": ["file"],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
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+ },
+ "activity": {
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+ {
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+ "properties": {
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+ "type": "string"
+ },
+ "position": {
+ "type": "object",
+ "properties": {
+ "x": {
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+ },
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+ "required": ["x", "y"],
+ "additionalProperties": false
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+ "fontSize": {
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+ "size": {
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+ "center": {
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+ },
+ "borderColor": {
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+ "properties": {
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+ "width",
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+ "size",
+ "center",
+ "borderColor",
+ "elementId"
+ ],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "hypothetical": {
+ "type": ["boolean", "null"]
+ },
+ "boundaryCondition": {
+ "type": "boolean"
+ },
+ "constant": {
+ "type": "boolean"
+ },
+ "initialAmount": {
+ "type": ["number", "null"]
+ },
+ "initialConcentration": {
+ "type": ["number", "null"]
+ },
+ "charge": {
+ "type": ["number", "null"]
+ },
+ "substanceUnits": {
+ "type": ["string", "null"]
+ },
+ "onlySubstanceUnits": {
+ "type": "boolean"
+ },
+ "modificationResidues": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "idModificationResidue": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "position": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/position"
+ },
+ "z": {
+ "type": "number"
+ },
+ "borderColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "state": {
+ "anyOf": [
+ {
+ "type": ["string", "number"]
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "size": {
+ "type": "number"
+ },
+ "elementId": {
+ "type": "string"
+ }
+ },
+ "required": [
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+ "name",
+ "z",
+ "borderColor",
+ "size",
+ "elementId"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "complex": {
+ "type": ["number", "null"]
+ },
+ "compartment": {
+ "type": ["number", "null"]
+ },
+ "submodel": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "mapId": {
+ "type": "number"
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["mapId", "type"],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "x": {
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+ },
+ "y": {
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+ },
+ "lineWidth": {
+ "type": "number"
+ },
+ "fontColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "fontSize": {
+ "type": "number"
+ },
+ "fillColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "borderColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "smiles": {
+ "anyOf": [
+ {
+ "anyOf": [
+ {
+ "not": {}
+ },
+ {
+ "type": "string"
+ }
+ ]
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+ {
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+ }
+ ]
+ },
+ "inChI": {
+ "type": ["string", "null"]
+ },
+ "inChIKey": {
+ "type": ["string", "null"]
+ },
+ "thickness": {
+ "type": "number"
+ },
+ "outerWidth": {
+ "type": "number"
+ },
+ "innerWidth": {
+ "type": "number"
+ },
+ "idReaction": {
+ "type": "string"
+ },
+ "reversible": {
+ "type": "boolean"
+ },
+ "mechanicalConfidenceScore": {
+ "type": "boolean"
+ },
+ "lowerBound": {
+ "type": "boolean"
+ },
+ "upperBound": {
+ "type": "boolean"
+ },
+ "subsystem": {
+ "type": "string"
+ },
+ "geneProteinReaction": {
+ "type": "string"
+ },
+ "kinetics": {
+ "type": "null"
+ },
+ "products": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "aliasId": {
+ "type": "number"
+ },
+ "stoichiometry": {
+ "type": ["number", "null"]
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["aliasId", "stoichiometry"],
+ "additionalProperties": false
+ }
+ },
+ "reactants": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/products/items"
+ }
+ },
+ "modifiers": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/products/items"
+ }
+ },
+ "processCoordinates": {
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+ },
+ "line": {
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+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "width": {
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+ },
+ "color": {
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+ },
+ "z": {
+ "type": "number"
+ },
+ "segments": {
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+ "items": {
+ "type": "object",
+ "properties": {
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+ "y1": {
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+ },
+ "x2": {
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+ },
+ "y2": {
+ "type": "number"
+ }
+ },
+ "required": ["x1", "y1", "x2", "y2"],
+ "additionalProperties": false
+ }
+ },
+ "startArrow": {
+ "type": "object",
+ "properties": {
+ "arrowType": {
+ "type": "string"
+ },
+ "angle": {
+ "type": "number"
+ },
+ "lineType": {
+ "type": "string"
+ },
+ "length": {
+ "type": "number"
+ }
+ },
+ "required": ["arrowType", "angle", "lineType", "length"],
+ "additionalProperties": false
+ },
+ "endArrow": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/line/properties/startArrow"
+ },
+ "lineType": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "id",
+ "width",
+ "color",
+ "z",
+ "segments",
+ "startArrow",
+ "endArrow",
+ "lineType"
+ ],
+ "additionalProperties": false
+ },
+ "operators": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "line": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/line"
+ },
+ "inputs": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ }
+ },
+ "required": ["id"],
+ "additionalProperties": false
+ }
+ },
+ "outputs": {
+ "not": {}
+ },
+ "operatorText": {
+ "type": "string"
+ },
+ "reactantOperator": {
+ "type": "boolean"
+ },
+ "productOperator": {
+ "type": "boolean"
+ },
+ "modifierOperator": {
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "id",
+ "line",
+ "inputs",
+ "operatorText",
+ "reactantOperator",
+ "productOperator",
+ "modifierOperator"
+ ],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": [
+ "id",
+ "stringType",
+ "name",
+ "elementId",
+ "model",
+ "references",
+ "z",
+ "notes",
+ "symbol",
+ "nameX",
+ "nameY",
+ "nameWidth",
+ "nameHeight",
+ "nameVerticalAlign",
+ "nameHorizontalAlign",
+ "width",
+ "height",
+ "visibilityLevel",
+ "transparencyLevel",
+ "synonyms",
+ "formerSymbols",
+ "fullName",
+ "abbreviation",
+ "formula",
+ "glyph",
+ "compartment",
+ "submodel",
+ "x",
+ "y",
+ "fontColor",
+ "fontSize",
+ "fillColor",
+ "borderColor"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "targetParticipants": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "link": {
+ "type": "string"
+ },
+ "type": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
+ },
+ "id": {
+ "type": "number"
+ },
+ "annotatorClassName": {
+ "type": "string"
+ }
+ },
+ "required": ["link", "type", "resource", "id", "annotatorClassName"],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": ["name", "references", "targetElements", "targetParticipants"],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": [
+ "id",
+ "name",
+ "description",
+ "directEvidence",
+ "directEvidenceReferences",
+ "synonyms",
+ "references",
+ "targets"
+ ],
+ "additionalProperties": false,
+ "$schema": "http://json-schema.org/draft-07/schema#"
+}
+```
diff --git a/docs/types/Drug.md b/docs/types/Drug.md
new file mode 100644
index 00000000..f7b21990
--- /dev/null
+++ b/docs/types/Drug.md
@@ -0,0 +1,725 @@
+```json
+{
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "description": {
+ "type": ["string", "null"]
+ },
+ "synonyms": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "brandNames": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "bloodBrainBarrier": {
+ "type": "string"
+ },
+ "references": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "link": {
+ "anyOf": [
+ {
+ "type": "string",
+ "format": "uri"
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "article": {
+ "type": "object",
+ "properties": {
+ "title": {
+ "type": "string"
+ },
+ "authors": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "journal": {
+ "type": "string"
+ },
+ "year": {
+ "type": "number"
+ },
+ "link": {
+ "type": "string"
+ },
+ "pubmedId": {
+ "type": "string"
+ },
+ "citationCount": {
+ "type": "number"
+ }
+ },
+ "required": [
+ "title",
+ "authors",
+ "journal",
+ "year",
+ "link",
+ "pubmedId",
+ "citationCount"
+ ],
+ "additionalProperties": false
+ },
+ "type": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
+ },
+ "id": {
+ "type": "number"
+ },
+ "annotatorClassName": {
+ "type": "string"
+ }
+ },
+ "required": ["link", "type", "resource", "id", "annotatorClassName"],
+ "additionalProperties": false
+ }
+ },
+ "targets": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "name": {
+ "type": "string"
+ },
+ "references": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/references/items"
+ }
+ },
+ "targetElements": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "stringType": {
+ "type": "string"
+ },
+ "name": {
+ "type": "string"
+ },
+ "elementId": {
+ "type": "string"
+ },
+ "model": {
+ "type": "number"
+ },
+ "references": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/references/items"
+ }
+ },
+ "z": {
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+ },
+ "notes": {
+ "type": "string"
+ },
+ "symbol": {
+ "type": ["string", "null"]
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+ "type": "number"
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+ "nameX": {
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+ },
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+ },
+ "nameWidth": {
+ "type": "number"
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+ "nameHeight": {
+ "type": "number"
+ },
+ "nameVerticalAlign": {
+ "type": "string"
+ },
+ "nameHorizontalAlign": {
+ "type": "string"
+ },
+ "width": {
+ "type": "number"
+ },
+ "height": {
+ "type": "number"
+ },
+ "visibilityLevel": {
+ "type": "string"
+ },
+ "transparencyLevel": {
+ "type": "string"
+ },
+ "synonyms": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "formerSymbols": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "fullName": {
+ "type": ["string", "null"]
+ },
+ "compartmentName": {
+ "type": ["string", "null"]
+ },
+ "abbreviation": {
+ "type": ["string", "null"]
+ },
+ "formula": {
+ "type": ["string", "null"]
+ },
+ "glyph": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "file": {
+ "type": "number"
+ }
+ },
+ "required": ["file"],
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+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "activity": {
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+ },
+ "structuralState": {
+ "anyOf": [
+ {
+ "type": "object",
+ "properties": {
+ "value": {
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+ },
+ "position": {
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+ "properties": {
+ "x": {
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+ },
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+ }
+ },
+ "required": ["x", "y"],
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+ "z": {
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+ "width": {
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+ "height": {
+ "type": "number"
+ },
+ "fontSize": {
+ "type": "number"
+ },
+ "size": {
+ "type": "number"
+ },
+ "center": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/position"
+ },
+ "borderColor": {
+ "type": "object",
+ "properties": {
+ "alpha": {
+ "type": "number"
+ },
+ "rgb": {
+ "type": "number"
+ }
+ },
+ "required": ["alpha", "rgb"],
+ "additionalProperties": false
+ },
+ "elementId": {
+ "type": "string"
+ }
+ },
+ "required": [
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+ "position",
+ "z",
+ "width",
+ "height",
+ "fontSize",
+ "size",
+ "center",
+ "borderColor",
+ "elementId"
+ ],
+ "additionalProperties": false
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "hypothetical": {
+ "type": ["boolean", "null"]
+ },
+ "boundaryCondition": {
+ "type": "boolean"
+ },
+ "constant": {
+ "type": "boolean"
+ },
+ "initialAmount": {
+ "type": ["number", "null"]
+ },
+ "initialConcentration": {
+ "type": ["number", "null"]
+ },
+ "charge": {
+ "type": ["number", "null"]
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+ },
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+ "name": {
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+ },
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+ },
+ "z": {
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+ "borderColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "state": {
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+ }
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+ "additionalProperties": false
+ }
+ },
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+ "compartment": {
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+ "submodel": {
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+ "type": {
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+ }
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+ "x": {
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+ "y": {
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+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "fontSize": {
+ "type": "number"
+ },
+ "fillColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "borderColor": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "smiles": {
+ "anyOf": [
+ {
+ "anyOf": [
+ {
+ "not": {}
+ },
+ {
+ "type": "string"
+ }
+ ]
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "inChI": {
+ "type": ["string", "null"]
+ },
+ "inChIKey": {
+ "type": ["string", "null"]
+ },
+ "thickness": {
+ "type": "number"
+ },
+ "outerWidth": {
+ "type": "number"
+ },
+ "innerWidth": {
+ "type": "number"
+ },
+ "idReaction": {
+ "type": "string"
+ },
+ "reversible": {
+ "type": "boolean"
+ },
+ "mechanicalConfidenceScore": {
+ "type": "boolean"
+ },
+ "lowerBound": {
+ "type": "boolean"
+ },
+ "upperBound": {
+ "type": "boolean"
+ },
+ "subsystem": {
+ "type": "string"
+ },
+ "geneProteinReaction": {
+ "type": "string"
+ },
+ "kinetics": {
+ "type": "null"
+ },
+ "products": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "aliasId": {
+ "type": "number"
+ },
+ "stoichiometry": {
+ "type": ["number", "null"]
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["aliasId", "stoichiometry"],
+ "additionalProperties": false
+ }
+ },
+ "reactants": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/products/items"
+ }
+ },
+ "modifiers": {
+ "type": "array",
+ "items": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/products/items"
+ }
+ },
+ "processCoordinates": {
+ "type": "null"
+ },
+ "line": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "width": {
+ "type": "number"
+ },
+ "color": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/structuralState/anyOf/0/properties/borderColor"
+ },
+ "z": {
+ "type": "number"
+ },
+ "segments": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "x1": {
+ "type": "number"
+ },
+ "y1": {
+ "type": "number"
+ },
+ "x2": {
+ "type": "number"
+ },
+ "y2": {
+ "type": "number"
+ }
+ },
+ "required": ["x1", "y1", "x2", "y2"],
+ "additionalProperties": false
+ }
+ },
+ "startArrow": {
+ "type": "object",
+ "properties": {
+ "arrowType": {
+ "type": "string"
+ },
+ "angle": {
+ "type": "number"
+ },
+ "lineType": {
+ "type": "string"
+ },
+ "length": {
+ "type": "number"
+ }
+ },
+ "required": ["arrowType", "angle", "lineType", "length"],
+ "additionalProperties": false
+ },
+ "endArrow": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/line/properties/startArrow"
+ },
+ "lineType": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "id",
+ "width",
+ "color",
+ "z",
+ "segments",
+ "startArrow",
+ "endArrow",
+ "lineType"
+ ],
+ "additionalProperties": false
+ },
+ "operators": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ },
+ "line": {
+ "$ref": "#/properties/targets/items/properties/targetElements/items/properties/line"
+ },
+ "inputs": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "number"
+ }
+ },
+ "required": ["id"],
+ "additionalProperties": false
+ }
+ },
+ "outputs": {
+ "not": {}
+ },
+ "operatorText": {
+ "type": "string"
+ },
+ "reactantOperator": {
+ "type": "boolean"
+ },
+ "productOperator": {
+ "type": "boolean"
+ },
+ "modifierOperator": {
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "id",
+ "line",
+ "inputs",
+ "operatorText",
+ "reactantOperator",
+ "productOperator",
+ "modifierOperator"
+ ],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": [
+ "id",
+ "stringType",
+ "name",
+ "elementId",
+ "model",
+ "references",
+ "z",
+ "notes",
+ "symbol",
+ "nameX",
+ "nameY",
+ "nameWidth",
+ "nameHeight",
+ "nameVerticalAlign",
+ "nameHorizontalAlign",
+ "width",
+ "height",
+ "visibilityLevel",
+ "transparencyLevel",
+ "synonyms",
+ "formerSymbols",
+ "fullName",
+ "abbreviation",
+ "formula",
+ "glyph",
+ "compartment",
+ "submodel",
+ "x",
+ "y",
+ "fontColor",
+ "fontSize",
+ "fillColor",
+ "borderColor"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "targetParticipants": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "link": {
+ "type": "string"
+ },
+ "type": {
+ "type": "string"
+ },
+ "resource": {
+ "type": "string"
+ },
+ "id": {
+ "type": "number"
+ },
+ "annotatorClassName": {
+ "type": "string"
+ }
+ },
+ "required": ["link", "type", "resource", "id", "annotatorClassName"],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": ["name", "references", "targetElements", "targetParticipants"],
+ "additionalProperties": false
+ }
+ }
+ },
+ "required": [
+ "id",
+ "name",
+ "description",
+ "synonyms",
+ "brandNames",
+ "bloodBrainBarrier",
+ "references",
+ "targets"
+ ],
+ "additionalProperties": false,
+ "$schema": "http://json-schema.org/draft-07/schema#"
+}
+```
diff --git a/docs/types/Marker.md b/docs/types/Marker.md
new file mode 100644
index 00000000..c9aa40ed
--- /dev/null
+++ b/docs/types/Marker.md
@@ -0,0 +1,12 @@
+```ts
+interface MarkerBase {
+ type: 'pin' | 'surface';
+ id: string;
+ color: string;
+ opacity: number;
+ x: number;
+ y: number;
+ number?: number;
+ modelId?: number;
+}
+```
diff --git a/index.d.ts b/index.d.ts
index 248f6f8e..dcca7b12 100644
--- a/index.d.ts
+++ b/index.d.ts
@@ -22,6 +22,9 @@ declare global {
plugins: {
registerPlugin: RegisterPlugin;
};
+ data: {
+ bioEntities: BioEntitiesMethods;
+ };
};
}
}
diff --git a/package-lock.json b/package-lock.json
index f03034da..016ad699 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -38,7 +38,9 @@
"tailwindcss": "3.3.3",
"ts-deepmerge": "^6.2.0",
"use-debounce": "^9.0.4",
- "zod": "^3.22.2"
+ "uuid": "^9.0.1",
+ "zod": "^3.22.2",
+ "zod-to-json-schema": "^3.22.4"
},
"devDependencies": {
"@commitlint/cli": "^17.7.1",
@@ -50,6 +52,7 @@
"@types/jest": "^29.5.5",
"@types/react-redux": "^7.1.26",
"@types/redux-mock-store": "^1.0.6",
+ "@types/uuid": "^9.0.8",
"@typescript-eslint/eslint-plugin": "^6.7.0",
"@typescript-eslint/parser": "^6.7.0",
"axios-mock-adapter": "^1.22.0",
@@ -1180,6 +1183,15 @@
"node": ">= 0.12"
}
},
+ "node_modules/@cypress/request/node_modules/uuid": {
+ "version": "8.3.2",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
+ "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
+ "dev": true,
+ "bin": {
+ "uuid": "dist/bin/uuid"
+ }
+ },
"node_modules/@cypress/xvfb": {
"version": "1.2.4",
"resolved": "https://registry.npmjs.org/@cypress/xvfb/-/xvfb-1.2.4.tgz",
@@ -2495,6 +2507,12 @@
"resolved": "https://registry.npmjs.org/@types/use-sync-external-store/-/use-sync-external-store-0.0.3.tgz",
"integrity": "sha512-EwmlvuaxPNej9+T4v5AuBPJa2x2UOJVdjCtDHgcDqitUeOtjnJKJ+apYjVcAoBEMjKW1VVFGZLUb5+qqa09XFA=="
},
+ "node_modules/@types/uuid": {
+ "version": "9.0.8",
+ "resolved": "https://registry.npmjs.org/@types/uuid/-/uuid-9.0.8.tgz",
+ "integrity": "sha512-jg+97EGIcY9AGHJJRaaPVgetKDsrTgbRjQ5Msgjh/DQKEFl0DtyRr/VCOyD1T2R1MNeWPK/u7JoGhlDZnKBAfA==",
+ "dev": true
+ },
"node_modules/@types/yargs": {
"version": "17.0.32",
"resolved": "https://registry.npmjs.org/@types/yargs/-/yargs-17.0.32.tgz",
@@ -8532,6 +8550,15 @@
"node": ">=8"
}
},
+ "node_modules/jest-junit/node_modules/uuid": {
+ "version": "8.3.2",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
+ "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
+ "dev": true,
+ "bin": {
+ "uuid": "dist/bin/uuid"
+ }
+ },
"node_modules/jest-leak-detector": {
"version": "29.7.0",
"resolved": "https://registry.npmjs.org/jest-leak-detector/-/jest-leak-detector-29.7.0.tgz",
@@ -13457,10 +13484,13 @@
"integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw=="
},
"node_modules/uuid": {
- "version": "8.3.2",
- "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
- "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
- "dev": true,
+ "version": "9.0.1",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.1.tgz",
+ "integrity": "sha512-b+1eJOlsR9K8HJpow9Ok3fiWOWSIcIzXodvv0rQjVoOVNpWMpxf1wZNpt4y9h10odCNrqnYp1OBzRktckBe3sA==",
+ "funding": [
+ "https://github.com/sponsors/broofa",
+ "https://github.com/sponsors/ctavan"
+ ],
"bin": {
"uuid": "dist/bin/uuid"
}
@@ -14004,6 +14034,14 @@
"zod": ">=3.0.0"
}
},
+ "node_modules/zod-to-json-schema": {
+ "version": "3.22.4",
+ "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.22.4.tgz",
+ "integrity": "sha512-2Ed5dJ+n/O3cU383xSY28cuVi0BCQhF8nYqWU5paEpl7fVdqdAmiLdqLyfblbNdfOFwFfi/mqU4O1pwc60iBhQ==",
+ "peerDependencies": {
+ "zod": "^3.22.4"
+ }
+ },
"node_modules/zstddec": {
"version": "0.1.0",
"resolved": "https://registry.npmjs.org/zstddec/-/zstddec-0.1.0.tgz",
@@ -14850,6 +14888,12 @@
"combined-stream": "^1.0.6",
"mime-types": "^2.1.12"
}
+ },
+ "uuid": {
+ "version": "8.3.2",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
+ "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
+ "dev": true
}
}
},
@@ -15861,6 +15905,12 @@
"resolved": "https://registry.npmjs.org/@types/use-sync-external-store/-/use-sync-external-store-0.0.3.tgz",
"integrity": "sha512-EwmlvuaxPNej9+T4v5AuBPJa2x2UOJVdjCtDHgcDqitUeOtjnJKJ+apYjVcAoBEMjKW1VVFGZLUb5+qqa09XFA=="
},
+ "@types/uuid": {
+ "version": "9.0.8",
+ "resolved": "https://registry.npmjs.org/@types/uuid/-/uuid-9.0.8.tgz",
+ "integrity": "sha512-jg+97EGIcY9AGHJJRaaPVgetKDsrTgbRjQ5Msgjh/DQKEFl0DtyRr/VCOyD1T2R1MNeWPK/u7JoGhlDZnKBAfA==",
+ "dev": true
+ },
"@types/yargs": {
"version": "17.0.32",
"resolved": "https://registry.npmjs.org/@types/yargs/-/yargs-17.0.32.tgz",
@@ -20183,6 +20233,12 @@
"requires": {
"ansi-regex": "^5.0.1"
}
+ },
+ "uuid": {
+ "version": "8.3.2",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
+ "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
+ "dev": true
}
}
},
@@ -23678,10 +23734,9 @@
"integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw=="
},
"uuid": {
- "version": "8.3.2",
- "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
- "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
- "dev": true
+ "version": "9.0.1",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.1.tgz",
+ "integrity": "sha512-b+1eJOlsR9K8HJpow9Ok3fiWOWSIcIzXodvv0rQjVoOVNpWMpxf1wZNpt4y9h10odCNrqnYp1OBzRktckBe3sA=="
},
"v8-compile-cache-lib": {
"version": "3.0.1",
@@ -24095,6 +24150,12 @@
"randexp": "^0.5.3"
}
},
+ "zod-to-json-schema": {
+ "version": "3.22.4",
+ "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.22.4.tgz",
+ "integrity": "sha512-2Ed5dJ+n/O3cU383xSY28cuVi0BCQhF8nYqWU5paEpl7fVdqdAmiLdqLyfblbNdfOFwFfi/mqU4O1pwc60iBhQ==",
+ "requires": {}
+ },
"zstddec": {
"version": "0.1.0",
"resolved": "https://registry.npmjs.org/zstddec/-/zstddec-0.1.0.tgz",
diff --git a/package.json b/package.json
index 730be9f5..f3a8ec09 100644
--- a/package.json
+++ b/package.json
@@ -52,18 +52,21 @@
"tailwindcss": "3.3.3",
"ts-deepmerge": "^6.2.0",
"use-debounce": "^9.0.4",
- "zod": "^3.22.2"
+ "uuid": "^9.0.1",
+ "zod": "^3.22.2",
+ "zod-to-json-schema": "^3.22.4"
},
"devDependencies": {
"@commitlint/cli": "^17.7.1",
"@commitlint/config-conventional": "^17.7.0",
"@testing-library/jest-dom": "^6.1.3",
"@testing-library/react": "^14.0.0",
- "@types/crypto-js": "^4.2.2",
"@testing-library/user-event": "^14.5.2",
+ "@types/crypto-js": "^4.2.2",
"@types/jest": "^29.5.5",
"@types/react-redux": "^7.1.26",
"@types/redux-mock-store": "^1.0.6",
+ "@types/uuid": "^9.0.8",
"@typescript-eslint/eslint-plugin": "^6.7.0",
"@typescript-eslint/parser": "^6.7.0",
"axios-mock-adapter": "^1.22.0",
diff --git a/src/components/Map/Drawer/BioEntityDrawer/OverlayData/OverlayData.types.ts b/src/components/Map/Drawer/BioEntityDrawer/OverlayData/OverlayData.types.ts
index 4f78ef61..3d43db8f 100644
--- a/src/components/Map/Drawer/BioEntityDrawer/OverlayData/OverlayData.types.ts
+++ b/src/components/Map/Drawer/BioEntityDrawer/OverlayData/OverlayData.types.ts
@@ -1,7 +1,7 @@
import { GeneVariant } from '@/types/models';
export interface OverlayDataAxis {
- id: number;
+ id: number | string;
title: string;
value?: number;
color: string;
diff --git a/src/components/Map/Drawer/SearchDrawerWrapper/GroupedSearchResults/BioEntitiesAccordion/BioEntitiesAccordion.component.test.tsx b/src/components/Map/Drawer/SearchDrawerWrapper/GroupedSearchResults/BioEntitiesAccordion/BioEntitiesAccordion.component.test.tsx
index d65d2915..33d06350 100644
--- a/src/components/Map/Drawer/SearchDrawerWrapper/GroupedSearchResults/BioEntitiesAccordion/BioEntitiesAccordion.component.test.tsx
+++ b/src/components/Map/Drawer/SearchDrawerWrapper/GroupedSearchResults/BioEntitiesAccordion/BioEntitiesAccordion.component.test.tsx
@@ -74,7 +74,7 @@ describe('BioEntitiesAccordion - component', () => {
expect(screen.getByText('Content (10)')).toBeInTheDocument();
expect(screen.getByText('Core PD map (5)')).toBeInTheDocument();
- expect(screen.getByText('Histamine signaling (2)')).toBeInTheDocument();
- expect(screen.getByText('PRKN substrates (3)')).toBeInTheDocument();
+ expect(screen.getByText('Histamine signaling (3)')).toBeInTheDocument();
+ expect(screen.getByText('PRKN substrates (2)')).toBeInTheDocument();
});
});
diff --git a/src/components/Map/Drawer/SearchDrawerWrapper/ResultsList/PinsList/PinsList.types.tsx b/src/components/Map/Drawer/SearchDrawerWrapper/ResultsList/PinsList/PinsList.types.tsx
index 74d6fe34..e0bdafa3 100644
--- a/src/components/Map/Drawer/SearchDrawerWrapper/ResultsList/PinsList/PinsList.types.tsx
+++ b/src/components/Map/Drawer/SearchDrawerWrapper/ResultsList/PinsList/PinsList.types.tsx
@@ -10,7 +10,7 @@ export type PinItem = {
export type PinTypeWithNone = PinType | 'none';
export type AvailableSubmaps = {
- id: number;
+ id: number | string;
modelId: number;
name: string;
};
diff --git a/src/components/Map/MapViewer/utils/config/getCanvasIcon.ts b/src/components/Map/MapViewer/utils/config/getCanvasIcon.ts
index c377b0ef..7d3e6925 100644
--- a/src/components/Map/MapViewer/utils/config/getCanvasIcon.ts
+++ b/src/components/Map/MapViewer/utils/config/getCanvasIcon.ts
@@ -59,7 +59,9 @@ export const drawNumberOnCanvas = (
ctx.fillText(text, x, y);
};
-export const getCanvasIcon = (args: Args): HTMLCanvasElement => {
+export const getCanvasIcon = (
+ args: Omit<Args, 'value'> & { value?: number },
+): HTMLCanvasElement => {
const canvas = createCanvas(PIN_SIZE);
const ctx = canvas.getContext('2d');
if (!ctx) {
@@ -67,7 +69,9 @@ export const getCanvasIcon = (args: Args): HTMLCanvasElement => {
}
drawPinOnCanvas(args, ctx);
- drawNumberOnCanvas(args, ctx);
+ if (args?.value !== undefined) {
+ drawNumberOnCanvas({ value: args.value }, ctx);
+ }
return canvas;
};
diff --git a/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.test.ts b/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.test.ts
new file mode 100644
index 00000000..0510f572
--- /dev/null
+++ b/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.test.ts
@@ -0,0 +1,96 @@
+import { MarkerSurface } from '@/redux/markers/markers.types';
+import { OverlayBioEntityRender } from '@/types/OLrendering';
+import { parseSurfaceMarkersToBioEntityRender } from './parseSurfaceMarkersToBioEntityRender';
+
+const MARKERS: MarkerSurface[] = [
+ {
+ type: 'surface',
+ id: '1',
+ color: '#000000',
+ opacity: 0.1,
+ x: 1200,
+ y: 500,
+ width: 100,
+ height: 50,
+ number: 0,
+ modelId: 0,
+ },
+ {
+ type: 'surface',
+ id: '2',
+ color: '#FF0000',
+ opacity: 0.67,
+ x: 432,
+ y: 2343,
+ width: 100,
+ height: 50,
+ number: 23,
+ modelId: 33,
+ },
+ {
+ type: 'surface',
+ id: '3',
+ color: '#FFFFFF',
+ opacity: 0,
+ x: 1,
+ y: 1,
+ width: 2,
+ height: 2,
+ number: 1,
+ modelId: 1,
+ },
+];
+
+const EXPECTED_RETURN: OverlayBioEntityRender[] = [
+ {
+ color: null,
+ height: 50,
+ hexColor: '#0000001a',
+ id: '1',
+ modelId: 0,
+ overlayId: 0,
+ type: 'rectangle',
+ value: 0.1,
+ width: 100,
+ x1: 1200,
+ x2: 1300,
+ y1: 550,
+ y2: 500,
+ },
+ {
+ color: null,
+ height: 50,
+ hexColor: '#FF0000ab',
+ id: '2',
+ modelId: 33,
+ overlayId: 0,
+ type: 'rectangle',
+ value: 0.67,
+ width: 100,
+ x1: 432,
+ x2: 532,
+ y1: 2393,
+ y2: 2343,
+ },
+ {
+ color: null,
+ height: 2,
+ hexColor: '#FFFFFF00',
+ id: '3',
+ modelId: 1,
+ overlayId: 0,
+ type: 'rectangle',
+ value: 0,
+ width: 2,
+ x1: 1,
+ x2: 3,
+ y1: 3,
+ y2: 1,
+ },
+];
+
+describe('parseSurfaceMarkersToBioEntityRender - util', () => {
+ it('returns correctly parsed markers for every element', () => {
+ expect(parseSurfaceMarkersToBioEntityRender(MARKERS)).toStrictEqual(EXPECTED_RETURN);
+ });
+});
diff --git a/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.ts b/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.ts
new file mode 100644
index 00000000..bd6461e9
--- /dev/null
+++ b/src/components/Map/MapViewer/utils/config/overlaysLayer/parseSurfaceMarkersToBioEntityRender.ts
@@ -0,0 +1,24 @@
+import { ZERO } from '@/constants/common';
+import { MarkerSurface } from '@/redux/markers/markers.types';
+import { OverlayBioEntityRender } from '@/types/OLrendering';
+import { addAlphaToHexString } from '@/utils/convert/addAlphaToHexString';
+
+export const parseSurfaceMarkersToBioEntityRender = (
+ markers: MarkerSurface[],
+): OverlayBioEntityRender[] => {
+ return markers.map(({ id, modelId, x, y, width, height, color, opacity }) => ({
+ type: 'rectangle',
+ id,
+ x1: x,
+ y1: y + height,
+ x2: x + width,
+ y2: y,
+ width,
+ height,
+ value: opacity,
+ modelId: modelId || ZERO, // ignored in next steps
+ overlayId: ZERO, // ignored in next steps
+ color: null, // replaced by hexColor in next steps
+ hexColor: addAlphaToHexString(color, opacity),
+ }));
+};
diff --git a/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.test.ts b/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.test.ts
index 15c9cf3e..3c4dbcfd 100644
--- a/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.test.ts
+++ b/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.test.ts
@@ -1,6 +1,7 @@
/* eslint-disable no-magic-numbers */
import { CONFIGURATION_INITIAL_STORE_MOCKS } from '@/redux/configuration/configuration.mock';
import { mapStateWithCurrentlySelectedMainMapFixture } from '@/redux/map/map.fixtures';
+import { SURFACE_MARKER } from '@/redux/models/marker.mock';
import { MODELS_DATA_MOCK_WITH_MAIN_MAP } from '@/redux/models/models.mock';
import { MOCKED_OVERLAY_BIO_ENTITY_RENDER } from '@/redux/overlayBioEntity/overlayBioEntity.mock';
import { OVERLAYS_PUBLIC_FETCHED_STATE_MOCK } from '@/redux/overlays/overlays.mock';
@@ -43,6 +44,9 @@ describe('useOverlayFeatures', () => {
models: {
...MODELS_DATA_MOCK_WITH_MAIN_MAP,
},
+ markers: {
+ data: [SURFACE_MARKER],
+ },
});
it('should return an array of features', () => {
@@ -52,7 +56,7 @@ describe('useOverlayFeatures', () => {
wrapper: Wrapper,
});
- expect(features).toHaveLength(10);
+ expect(features).toHaveLength(11);
// type: rectangle
expect(features[0].getGeometry()?.getCoordinates()).toEqual([
@@ -81,5 +85,19 @@ describe('useOverlayFeatures', () => {
// eslint-disable-next-line @typescript-eslint/ban-ts-comment
// @ts-ignore
expect(features[7].getStyle().getFill().getColor()).toBe('#ff0000cc');
+
+ // type: rectangle (marker)
+ expect(features[10].getGeometry()?.getCoordinates()).toEqual([
+ [
+ [-19588560, 19831740],
+ [-19588560, 19850446],
+ [-19551147, 19850446],
+ [-19551147, 19831740],
+ [-19588560, 19831740],
+ ],
+ ]);
+ // eslint-disable-next-line @typescript-eslint/ban-ts-comment
+ // @ts-ignore
+ expect(features[10].getStyle().getFill().getColor()).toBe('#0000001a');
});
});
diff --git a/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.ts b/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.ts
index 98e528f3..93e24ec8 100644
--- a/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.ts
+++ b/src/components/Map/MapViewer/utils/config/overlaysLayer/useOverlayFeatures.ts
@@ -1,5 +1,6 @@
import { ZERO } from '@/constants/common';
import { useAppSelector } from '@/redux/hooks/useAppSelector';
+import { markersSufraceOfCurrentMapDataSelector } from '@/redux/markers/markers.selectors';
import { getOverlayOrderSelector } from '@/redux/overlayBioEntity/overlayBioEntity.selector';
import { LinePoint } from '@/types/reactions';
import { usePointToProjection } from '@/utils/map/usePointToProjection';
@@ -9,17 +10,36 @@ import type Polygon from 'ol/geom/Polygon';
import { useMemo } from 'react';
import { createOverlayGeometryFeature } from './createOverlayGeometryFeature';
import { createOverlayLineFeature } from './createOverlayLineFeature';
+import { createOverlaySubmapLinkRectangleFeature } from './createOverlaySubmapLinkRectangleFeature';
import { getPolygonLatitudeCoordinates } from './getPolygonLatitudeCoordinates';
-import { useGetOverlayColor } from './useGetOverlayColor';
+import { parseSurfaceMarkersToBioEntityRender } from './parseSurfaceMarkersToBioEntityRender';
import { useBioEntitiesWithSubmapsLinks } from './useBioEntitiesWithSubmapLinks';
-import { createOverlaySubmapLinkRectangleFeature } from './createOverlaySubmapLinkRectangleFeature';
+import { useGetOverlayColor } from './useGetOverlayColor';
export const useOverlayFeatures = (): Feature<Polygon>[] | Feature<SimpleGeometry>[] => {
const pointToProjection = usePointToProjection();
const { getOverlayBioEntityColorByAvailableProperties } = useGetOverlayColor();
const overlaysOrder = useAppSelector(getOverlayOrderSelector);
+ const currentMarkers = useAppSelector(markersSufraceOfCurrentMapDataSelector);
+ const markersRender = parseSurfaceMarkersToBioEntityRender(currentMarkers);
const bioEntities = useBioEntitiesWithSubmapsLinks();
+ const markersFeatures = useMemo(
+ () =>
+ markersRender.map(entity => {
+ const color = getOverlayBioEntityColorByAvailableProperties(entity);
+
+ return createOverlayGeometryFeature(
+ [
+ ...pointToProjection({ x: entity.x1, y: entity.y1 }),
+ ...pointToProjection({ x: entity.x2, y: entity.y2 }),
+ ],
+ entity?.hexColor || color,
+ );
+ }),
+ [getOverlayBioEntityColorByAvailableProperties, markersRender, pointToProjection],
+ );
+
const features = useMemo(
() =>
bioEntities.map(entity => {
@@ -36,7 +56,9 @@ export const useOverlayFeatures = (): Feature<Polygon>[] | Feature<SimpleGeometr
overlaysOrder.find(({ id }) => id === entity.overlayId)?.index || ZERO,
});
- const color = getOverlayBioEntityColorByAvailableProperties(entity);
+ const calculatedColor = getOverlayBioEntityColorByAvailableProperties(entity);
+ const hexColor = entity?.hexColor;
+ const color = hexColor || calculatedColor;
if (entity.type === 'submap-link') {
return createOverlaySubmapLinkRectangleFeature(
@@ -72,5 +94,5 @@ export const useOverlayFeatures = (): Feature<Polygon>[] | Feature<SimpleGeometr
[overlaysOrder, pointToProjection, getOverlayBioEntityColorByAvailableProperties, bioEntities],
);
- return features;
+ return [...features, ...markersFeatures];
};
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.test.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.test.ts
new file mode 100644
index 00000000..b83827e5
--- /dev/null
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.test.ts
@@ -0,0 +1,58 @@
+import { initialMapStateFixture } from '@/redux/map/map.fixtures';
+import { PIN_MARKER } from '@/redux/models/marker.mock';
+import { UsePointToProjectionResult, usePointToProjection } from '@/utils/map/usePointToProjection';
+import {
+ GetReduxWrapperUsingSliceReducer,
+ getReduxWrapperWithStore,
+} from '@/utils/testing/getReduxWrapperWithStore';
+import { renderHook } from '@testing-library/react';
+import { Feature } from 'ol';
+import Style from 'ol/style/Style';
+import { getMarkerSingleFeature } from './getMarkerSingleFeature';
+import * as getPinStyle from './getPinStyle';
+
+jest.mock('./getPinStyle', () => ({
+ __esModule: true,
+ ...jest.requireActual('./getPinStyle'),
+}));
+
+const getPinStyleSpy = jest.spyOn(getPinStyle, 'getPinStyle');
+
+const getPointToProjection = (
+ wrapper: ReturnType<GetReduxWrapperUsingSliceReducer>['Wrapper'],
+): UsePointToProjectionResult => {
+ const { result: usePointToProjectionHook } = renderHook(() => usePointToProjection(), {
+ wrapper,
+ });
+
+ return usePointToProjectionHook.current;
+};
+
+describe('getMarkerSingleFeature - subUtil', () => {
+ const { Wrapper } = getReduxWrapperWithStore({
+ map: initialMapStateFixture,
+ });
+ const pointToProjection = getPointToProjection(Wrapper);
+
+ it('should return instance of Feature with Style type=%s', () => {
+ const result = getMarkerSingleFeature(PIN_MARKER, {
+ pointToProjection,
+ });
+
+ const style = result.getStyle() as Style;
+
+ expect(result).toBeInstanceOf(Feature);
+ expect(style).toBeInstanceOf(Style);
+ });
+
+ it('should run getPinStyle with valid args for type=%s', () => {
+ getMarkerSingleFeature(PIN_MARKER, {
+ pointToProjection,
+ });
+
+ expect(getPinStyleSpy).toHaveBeenCalledWith({
+ color: '#0000001a',
+ value: PIN_MARKER.number,
+ });
+ });
+});
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.ts
new file mode 100644
index 00000000..705debb6
--- /dev/null
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkerSingleFeature.ts
@@ -0,0 +1,24 @@
+import { Marker } from '@/redux/markers/markers.types';
+import { addAlphaToHexString } from '@/utils/convert/addAlphaToHexString';
+import { UsePointToProjectionResult } from '@/utils/map/usePointToProjection';
+import { Feature } from 'ol';
+import { getPinFeature } from './getPinFeature';
+import { getPinStyle } from './getPinStyle';
+
+export const getMarkerSingleFeature = (
+ marker: Marker,
+ {
+ pointToProjection,
+ }: {
+ pointToProjection: UsePointToProjectionResult;
+ },
+): Feature => {
+ const feature = getPinFeature(marker, pointToProjection);
+ const style = getPinStyle({
+ color: addAlphaToHexString(marker.color, marker.opacity),
+ value: marker.number,
+ });
+
+ feature.setStyle(style);
+ return feature;
+};
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkersFeatures.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkersFeatures.ts
new file mode 100644
index 00000000..fa12fb5e
--- /dev/null
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getMarkersFeatures.ts
@@ -0,0 +1,19 @@
+import { Marker } from '@/redux/markers/markers.types';
+import { UsePointToProjectionResult } from '@/utils/map/usePointToProjection';
+import { Feature } from 'ol';
+import { getMarkerSingleFeature } from './getMarkerSingleFeature';
+
+export const getMarkersFeatures = (
+ markers: Marker[],
+ {
+ pointToProjection,
+ }: {
+ pointToProjection: UsePointToProjectionResult;
+ },
+): Feature[] => {
+ return markers.map(marker =>
+ getMarkerSingleFeature(marker, {
+ pointToProjection,
+ }),
+ );
+};
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.test.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.test.ts
index 64f3decc..28610fd8 100644
--- a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.test.ts
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.test.ts
@@ -1,6 +1,7 @@
import { HALF } from '@/constants/dividers';
import { bioEntityContentFixture } from '@/models/fixtures/bioEntityContentsFixture';
import { initialMapStateFixture } from '@/redux/map/map.fixtures';
+import { PIN_MARKER } from '@/redux/models/marker.mock';
import { usePointToProjection } from '@/utils/map/usePointToProjection';
import { getReduxWrapperWithStore } from '@/utils/testing/getReduxWrapperWithStore';
import { renderHook } from '@testing-library/react';
@@ -35,4 +36,18 @@ describe('getPinFeature - subUtil', () => {
expect([x, y]).toStrictEqual(geometryPoint);
});
+
+ describe('when is Marker Pin', () => {
+ const pinMarkerResult = getPinFeature(PIN_MARKER, pointToProjection);
+
+ it('should return point parsed with point to projection', () => {
+ const [x, y] = pinMarkerResult.getGeometry()?.getExtent() || [];
+ const geometryPoint = pointToProjection({
+ x: PIN_MARKER.x,
+ y: PIN_MARKER.y,
+ });
+
+ expect([x, y]).toStrictEqual(geometryPoint);
+ });
+ });
});
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.ts
index ec09a90d..ff7bfb00 100644
--- a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.ts
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinFeature.ts
@@ -1,16 +1,18 @@
+import { ZERO } from '@/constants/common';
import { HALF } from '@/constants/dividers';
+import { Marker } from '@/redux/markers/markers.types';
import { BioEntity } from '@/types/models';
import { UsePointToProjectionResult } from '@/utils/map/usePointToProjection';
import { Feature } from 'ol';
import { Point } from 'ol/geom';
export const getPinFeature = (
- { x, y, width, height, id }: BioEntity,
+ { x, y, width, height, id }: Pick<BioEntity, 'id' | 'width' | 'height' | 'x' | 'y'> | Marker,
pointToProjection: UsePointToProjectionResult,
): Feature => {
const point = {
- x: x + width / HALF,
- y: y + height / HALF,
+ x: x + (width || ZERO) / HALF,
+ y: y + (height || ZERO) / HALF,
};
return new Feature({
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinStyle.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinStyle.ts
index 3e91dfc0..77ee5c7f 100644
--- a/src/components/Map/MapViewer/utils/config/pinsLayer/getPinStyle.ts
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/getPinStyle.ts
@@ -4,7 +4,7 @@ import Icon from 'ol/style/Icon';
import Style from 'ol/style/Style';
import { getCanvasIcon } from '../getCanvasIcon';
-export const getPinStyle = ({ value, color }: { value: number; color: string }): Style =>
+export const getPinStyle = ({ value, color }: { value?: number; color: string }): Style =>
new Style({
image: new Icon({
displacement: [ZERO, PIN_SIZE.height],
diff --git a/src/components/Map/MapViewer/utils/config/pinsLayer/useOlMapPinsLayer.ts b/src/components/Map/MapViewer/utils/config/pinsLayer/useOlMapPinsLayer.ts
index ceecf01f..2e986604 100644
--- a/src/components/Map/MapViewer/utils/config/pinsLayer/useOlMapPinsLayer.ts
+++ b/src/components/Map/MapViewer/utils/config/pinsLayer/useOlMapPinsLayer.ts
@@ -2,6 +2,7 @@
import { searchedBioEntitesSelectorOfCurrentMap } from '@/redux/bioEntity/bioEntity.selectors';
import { searchedChemicalsBioEntitesOfCurrentMapSelector } from '@/redux/chemicals/chemicals.selectors';
import { searchedDrugsBioEntitesOfCurrentMapSelector } from '@/redux/drugs/drugs.selectors';
+import { markersPinsOfCurrentMapDataSelector } from '@/redux/markers/markers.selectors';
import { usePointToProjection } from '@/utils/map/usePointToProjection';
import Feature from 'ol/Feature';
import { Geometry } from 'ol/geom';
@@ -10,28 +11,31 @@ import VectorSource from 'ol/source/Vector';
import { useMemo } from 'react';
import { useSelector } from 'react-redux';
import { getBioEntitiesFeatures } from './getBioEntitiesFeatures';
+import { getMarkersFeatures } from './getMarkersFeatures';
export const useOlMapPinsLayer = (): VectorLayer<VectorSource<Feature<Geometry>>> => {
const pointToProjection = usePointToProjection();
const contentBioEntites = useSelector(searchedBioEntitesSelectorOfCurrentMap);
const chemicalsBioEntities = useSelector(searchedChemicalsBioEntitesOfCurrentMapSelector);
const drugsBioEntities = useSelector(searchedDrugsBioEntitesOfCurrentMapSelector);
+ const markersEntities = useSelector(markersPinsOfCurrentMapDataSelector);
- const bioEntityFeatures = useMemo(
+ const elementsFeatures = useMemo(
() =>
[
getBioEntitiesFeatures(contentBioEntites, { pointToProjection, type: 'bioEntity' }),
getBioEntitiesFeatures(chemicalsBioEntities, { pointToProjection, type: 'chemicals' }),
getBioEntitiesFeatures(drugsBioEntities, { pointToProjection, type: 'drugs' }),
+ getMarkersFeatures(markersEntities, { pointToProjection }),
].flat(),
- [contentBioEntites, drugsBioEntities, chemicalsBioEntities, pointToProjection],
+ [contentBioEntites, drugsBioEntities, chemicalsBioEntities, pointToProjection, markersEntities],
);
const vectorSource = useMemo(() => {
return new VectorSource({
- features: [...bioEntityFeatures],
+ features: [...elementsFeatures],
});
- }, [bioEntityFeatures]);
+ }, [elementsFeatures]);
const pinsLayer = useMemo(
() =>
diff --git a/src/models/bioEntitySchema.ts b/src/models/bioEntitySchema.ts
index a747e0cd..6f786cc8 100644
--- a/src/models/bioEntitySchema.ts
+++ b/src/models/bioEntitySchema.ts
@@ -10,7 +10,7 @@ import { structuralStateSchema } from './structuralStateSchema';
import { submodelSchema } from './submodelSchema';
export const bioEntitySchema = z.object({
- id: z.number(),
+ id: z.union([z.number(), z.string()]),
stringType: z.string(),
name: z.string(),
elementId: z.string(),
diff --git a/src/redux/bioEntity/bioEntity.reducers.ts b/src/redux/bioEntity/bioEntity.reducers.ts
index 53ad51de..7eb3b66c 100644
--- a/src/redux/bioEntity/bioEntity.reducers.ts
+++ b/src/redux/bioEntity/bioEntity.reducers.ts
@@ -1,5 +1,5 @@
-import { ActionReducerMapBuilder } from '@reduxjs/toolkit';
import { DEFAULT_ERROR } from '@/constants/errors';
+import { ActionReducerMapBuilder } from '@reduxjs/toolkit';
import { getBioEntity, getMultiBioEntity } from './bioEntity.thunks';
import { BioEntityContentsState } from './bioEntity.types';
@@ -49,3 +49,8 @@ export const getMultiBioEntityContentsReducer = (
// TODO: error management to be discussed in the team
});
};
+
+export const clearBioEntitiesDataReducer = (state: BioEntityContentsState): void => {
+ state.data = [];
+ state.loading = 'idle';
+};
diff --git a/src/redux/bioEntity/bioEntity.selectors.ts b/src/redux/bioEntity/bioEntity.selectors.ts
index 8b39954f..b9566eb7 100644
--- a/src/redux/bioEntity/bioEntity.selectors.ts
+++ b/src/redux/bioEntity/bioEntity.selectors.ts
@@ -14,6 +14,12 @@ import { currentModelIdSelector, modelsDataSelector } from '../models/models.sel
export const bioEntitySelector = createSelector(rootSelector, state => state.bioEntity);
+export const bioEntityDataSelector = createSelector(bioEntitySelector, bioEntity => bioEntity.data);
+
+export const bioEntityDataListSelector = createSelector(bioEntityDataSelector, bioEntityData =>
+ bioEntityData.map(b => b.data || []).flat(),
+);
+
export const bioEntitiesForSelectedSearchElement = createSelector(
bioEntitySelector,
currentSelectedSearchElement,
diff --git a/src/redux/bioEntity/bioEntity.slice.ts b/src/redux/bioEntity/bioEntity.slice.ts
index 14821569..428e00ce 100644
--- a/src/redux/bioEntity/bioEntity.slice.ts
+++ b/src/redux/bioEntity/bioEntity.slice.ts
@@ -1,6 +1,7 @@
import { BioEntityContentsState } from '@/redux/bioEntity/bioEntity.types';
import { createSlice } from '@reduxjs/toolkit';
import {
+ clearBioEntitiesDataReducer,
getBioEntityContentsReducer,
getMultiBioEntityContentsReducer,
} from './bioEntity.reducers';
@@ -14,11 +15,15 @@ const initialState: BioEntityContentsState = {
export const bioEntityContentsSlice = createSlice({
name: 'bioEntityContents',
initialState,
- reducers: {},
+ reducers: {
+ clearBioEntitiesData: clearBioEntitiesDataReducer,
+ },
extraReducers: builder => {
getBioEntityContentsReducer(builder);
getMultiBioEntityContentsReducer(builder);
},
});
+export const { clearBioEntitiesData } = bioEntityContentsSlice.actions;
+
export default bioEntityContentsSlice.reducer;
diff --git a/src/redux/chemicals/chemicals.selectors.ts b/src/redux/chemicals/chemicals.selectors.ts
index f2d10808..03f829f8 100644
--- a/src/redux/chemicals/chemicals.selectors.ts
+++ b/src/redux/chemicals/chemicals.selectors.ts
@@ -8,6 +8,12 @@ import { currentModelIdSelector } from '../models/models.selectors';
export const chemicalsSelector = createSelector(rootSelector, state => state.chemicals);
+export const chemicalsDataSelector = createSelector(chemicalsSelector, chemicals => chemicals.data);
+
+export const chemicalsDataListSelector = createSelector(chemicalsDataSelector, chemicalsData =>
+ chemicalsData.map(c => c.data || []).flat(),
+);
+
export const chemicalsForSelectedSearchElementSelector = createSelector(
chemicalsSelector,
currentSelectedSearchElement,
diff --git a/src/redux/contextMenu/contextMenu.types.ts b/src/redux/contextMenu/contextMenu.types.ts
index d95c38c9..7ab84923 100644
--- a/src/redux/contextMenu/contextMenu.types.ts
+++ b/src/redux/contextMenu/contextMenu.types.ts
@@ -4,5 +4,5 @@ export interface ContextMenuState {
isOpen: boolean;
coordinates: Pixel;
uniprot: string;
- currentSelectedBioEntityId: number;
+ currentSelectedBioEntityId: number | string;
}
diff --git a/src/redux/drawer/drawer.types.ts b/src/redux/drawer/drawer.types.ts
index f4104f25..a348517b 100644
--- a/src/redux/drawer/drawer.types.ts
+++ b/src/redux/drawer/drawer.types.ts
@@ -20,7 +20,7 @@ export type ReactionDrawerState = {
};
export type BioEntityDrawerState = {
- bioentityId?: number;
+ bioentityId?: number | string;
drugs: KeyedFetchDataState<Drug[], []>;
chemicals: KeyedFetchDataState<Chemical[], []>;
};
@@ -41,5 +41,5 @@ export type OpenSearchDrawerWithSelectedTabReducerAction =
export type OpenReactionDrawerByIdPayload = number;
export type OpenReactionDrawerByIdAction = PayloadAction<OpenReactionDrawerByIdPayload>;
-export type OpenBioEntityDrawerByIdPayload = number;
+export type OpenBioEntityDrawerByIdPayload = number | string;
export type OpenBioEntityDrawerByIdAction = PayloadAction<OpenBioEntityDrawerByIdPayload>;
diff --git a/src/redux/drugs/drugs.selectors.ts b/src/redux/drugs/drugs.selectors.ts
index 6790c081..45e9c16c 100644
--- a/src/redux/drugs/drugs.selectors.ts
+++ b/src/redux/drugs/drugs.selectors.ts
@@ -8,6 +8,12 @@ import { currentModelIdSelector } from '../models/models.selectors';
export const drugsSelector = createSelector(rootSelector, state => state.drugs);
+export const drugsDataSelector = createSelector(drugsSelector, drugs => drugs.data);
+
+export const drugsDataListSelector = createSelector(drugsDataSelector, drugsData =>
+ drugsData.map(d => d.data || []).flat(),
+);
+
export const drugsForSelectedSearchElementSelector = createSelector(
drugsSelector,
currentSelectedSearchElement,
diff --git a/src/redux/markers/markers.constants.ts b/src/redux/markers/markers.constants.ts
new file mode 100644
index 00000000..576e0557
--- /dev/null
+++ b/src/redux/markers/markers.constants.ts
@@ -0,0 +1,5 @@
+import { MarkersState } from './markers.types';
+
+export const MARKERS_INITIAL_STATE: MarkersState = {
+ data: [],
+};
diff --git a/src/redux/markers/markers.mock.ts b/src/redux/markers/markers.mock.ts
new file mode 100644
index 00000000..3f7df875
--- /dev/null
+++ b/src/redux/markers/markers.mock.ts
@@ -0,0 +1,5 @@
+import { MarkersState } from './markers.types';
+
+export const MARKERS_INITIAL_STATE_MOCK: MarkersState = {
+ data: [],
+};
diff --git a/src/redux/markers/markers.reducers.ts b/src/redux/markers/markers.reducers.ts
new file mode 100644
index 00000000..d0cad10d
--- /dev/null
+++ b/src/redux/markers/markers.reducers.ts
@@ -0,0 +1,31 @@
+import { PayloadAction } from '@reduxjs/toolkit';
+import { Marker, MarkersState } from './markers.types';
+
+export const setMarkersDataReducer = (
+ state: MarkersState,
+ action: PayloadAction<Marker[]>,
+): void => {
+ const { payload } = action;
+
+ state.data = payload;
+};
+
+export const addMarkerToMarkersDataReducer = (
+ state: MarkersState,
+ action: PayloadAction<Marker>,
+): void => {
+ const { payload } = action;
+
+ state.data.push(payload);
+};
+
+export const removeMarkerFromMarkersDataReducer = (
+ state: MarkersState,
+ action: PayloadAction<string>,
+): void => {
+ const currentMarkers = state.data;
+ const { payload: markerId } = action;
+ const newMarkers = currentMarkers.filter(m => m.id !== markerId);
+
+ state.data = newMarkers;
+};
diff --git a/src/redux/markers/markers.selectors.ts b/src/redux/markers/markers.selectors.ts
new file mode 100644
index 00000000..da6987b3
--- /dev/null
+++ b/src/redux/markers/markers.selectors.ts
@@ -0,0 +1,33 @@
+import { createSelector } from '@reduxjs/toolkit';
+import { currentModelIdSelector } from '../models/models.selectors';
+import { rootSelector } from '../root/root.selectors';
+import { MarkerSurface } from './markers.types';
+import { isMarkerSurface } from './markers.utils';
+
+export const markersSelector = createSelector(rootSelector, state => state.markers);
+
+export const markersDataSelector = createSelector(markersSelector, markers => markers.data);
+
+export const markersDataOfCurrentMapSelector = createSelector(
+ markersDataSelector,
+ currentModelIdSelector,
+ (markers, modelId) => markers.filter(p => (p.modelId ? p.modelId === modelId : true)),
+);
+
+export const markersPinsDataSelector = createSelector(markersDataSelector, markersData =>
+ markersData.filter(m => m.type === 'pin'),
+);
+
+export const markersPinsOfCurrentMapDataSelector = createSelector(
+ markersDataOfCurrentMapSelector,
+ markersData => markersData.filter(m => m.type === 'pin'),
+);
+
+export const markersSufraceSelector = createSelector(markersDataSelector, markersData =>
+ markersData.filter(m => m.type === 'surface'),
+);
+
+export const markersSufraceOfCurrentMapDataSelector = createSelector(
+ markersDataOfCurrentMapSelector,
+ (markers): MarkerSurface[] => markers.filter(isMarkerSurface),
+);
diff --git a/src/redux/markers/markers.slice.ts b/src/redux/markers/markers.slice.ts
new file mode 100644
index 00000000..d37bd497
--- /dev/null
+++ b/src/redux/markers/markers.slice.ts
@@ -0,0 +1,23 @@
+import { createSlice } from '@reduxjs/toolkit';
+import { MARKERS_INITIAL_STATE } from './markers.constants';
+import {
+ addMarkerToMarkersDataReducer,
+ removeMarkerFromMarkersDataReducer,
+ setMarkersDataReducer,
+} from './markers.reducers';
+
+const markersSlice = createSlice({
+ name: 'markers',
+ initialState: MARKERS_INITIAL_STATE,
+ reducers: {
+ setMarkersData: setMarkersDataReducer,
+ addMarkerToMarkersData: addMarkerToMarkersDataReducer,
+ removeMarkerFromMarkersData: removeMarkerFromMarkersDataReducer,
+ },
+ extraReducers: () => {},
+});
+
+export const { setMarkersData, addMarkerToMarkersData, removeMarkerFromMarkersData } =
+ markersSlice.actions;
+
+export default markersSlice.reducer;
diff --git a/src/redux/markers/markers.types.ts b/src/redux/markers/markers.types.ts
new file mode 100644
index 00000000..4ea83078
--- /dev/null
+++ b/src/redux/markers/markers.types.ts
@@ -0,0 +1,30 @@
+export type MarkerType = 'pin' | 'surface';
+
+interface MarkerBase {
+ type: MarkerType;
+ id: string;
+ color: string;
+ opacity: number;
+ x: number;
+ y: number;
+ number?: number;
+ modelId?: number;
+}
+
+export interface MarkerPin extends MarkerBase {
+ width?: number;
+ height?: number;
+}
+
+export interface MarkerSurface extends MarkerBase {
+ width: number;
+ height: number;
+}
+
+export type Marker = MarkerPin | MarkerSurface;
+
+export type MarkerWithoutId = Omit<Marker, 'id'>;
+
+export interface MarkersState {
+ data: Marker[];
+}
diff --git a/src/redux/markers/markers.utils.ts b/src/redux/markers/markers.utils.ts
new file mode 100644
index 00000000..08b862e3
--- /dev/null
+++ b/src/redux/markers/markers.utils.ts
@@ -0,0 +1,4 @@
+import { Marker, MarkerSurface } from './markers.types';
+
+export const isMarkerSurface = (marker: Marker): marker is MarkerSurface =>
+ Boolean(marker?.width && marker?.height && marker.type === 'surface');
diff --git a/src/redux/models/marker.mock.ts b/src/redux/models/marker.mock.ts
new file mode 100644
index 00000000..951b5d62
--- /dev/null
+++ b/src/redux/models/marker.mock.ts
@@ -0,0 +1,25 @@
+import { MarkerPin, MarkerSurface } from '../markers/markers.types';
+
+export const SURFACE_MARKER: MarkerSurface = {
+ type: 'surface',
+ id: '1',
+ color: '#000000',
+ opacity: 0.1,
+ x: 1200,
+ y: 500,
+ width: 100,
+ height: 50,
+ number: 0,
+ modelId: 0,
+};
+
+export const PIN_MARKER: MarkerPin = {
+ type: 'pin',
+ id: '1',
+ color: '#000000',
+ opacity: 0.1,
+ x: 1200,
+ y: 500,
+ number: 0,
+ modelId: 0,
+};
diff --git a/src/redux/root/root.fixtures.ts b/src/redux/root/root.fixtures.ts
index b27b88cc..66b6151c 100644
--- a/src/redux/root/root.fixtures.ts
+++ b/src/redux/root/root.fixtures.ts
@@ -1,6 +1,7 @@
import { BACKGROUND_INITIAL_STATE_MOCK } from '../backgrounds/background.mock';
import { BIOENTITY_INITIAL_STATE_MOCK } from '../bioEntity/bioEntity.mock';
import { CHEMICALS_INITIAL_STATE_MOCK } from '../chemicals/chemicals.mock';
+import { COMPARTMENT_PATHWAYS_INITIAL_STATE_MOCK } from '../compartmentPathways/compartmentPathways.mock';
import { CONFIGURATION_INITIAL_STATE } from '../configuration/configuration.adapter';
import { CONTEXT_MENU_INITIAL_STATE } from '../contextMenu/contextMenu.constants';
import { COOKIE_BANNER_INITIAL_STATE_MOCK } from '../cookieBanner/cookieBanner.mock';
@@ -9,19 +10,19 @@ import { DRUGS_INITIAL_STATE_MOCK } from '../drugs/drugs.mock';
import { EXPORT_INITIAL_STATE_MOCK } from '../export/export.mock';
import { LEGEND_INITIAL_STATE_MOCK } from '../legend/legend.mock';
import { initialMapStateFixture } from '../map/map.fixtures';
+import { MARKERS_INITIAL_STATE_MOCK } from '../markers/markers.mock';
import { MODAL_INITIAL_STATE_MOCK } from '../modal/modal.mock';
import { MODELS_INITIAL_STATE_MOCK } from '../models/models.mock';
import { OVERLAY_BIO_ENTITY_INITIAL_STATE_MOCK } from '../overlayBioEntity/overlayBioEntity.mock';
import { OVERLAYS_INITIAL_STATE_MOCK } from '../overlays/overlays.mock';
import { PLUGINS_INITIAL_STATE_MOCK } from '../plugins/plugins.mock';
import { PROJECT_STATE_INITIAL_MOCK } from '../project/project.mock';
+import { PUBLICATIONS_INITIAL_STATE_MOCK } from '../publications/publications.mock';
import { REACTIONS_STATE_INITIAL_MOCK } from '../reactions/reactions.mock';
import { SEARCH_STATE_INITIAL_MOCK } from '../search/search.mock';
+import { STATISTICS_STATE_INITIAL_MOCK } from '../statistics/statistics.mock';
import { RootState } from '../store';
import { USER_INITIAL_STATE_MOCK } from '../user/user.mock';
-import { STATISTICS_STATE_INITIAL_MOCK } from '../statistics/statistics.mock';
-import { COMPARTMENT_PATHWAYS_INITIAL_STATE_MOCK } from '../compartmentPathways/compartmentPathways.mock';
-import { PUBLICATIONS_INITIAL_STATE_MOCK } from '../publications/publications.mock';
export const INITIAL_STORE_STATE_MOCK: RootState = {
search: SEARCH_STATE_INITIAL_MOCK,
@@ -47,4 +48,5 @@ export const INITIAL_STORE_STATE_MOCK: RootState = {
publications: PUBLICATIONS_INITIAL_STATE_MOCK,
export: EXPORT_INITIAL_STATE_MOCK,
plugins: PLUGINS_INITIAL_STATE_MOCK,
+ markers: MARKERS_INITIAL_STATE_MOCK,
};
diff --git a/src/redux/store.ts b/src/redux/store.ts
index 6aa4c445..2391ea22 100644
--- a/src/redux/store.ts
+++ b/src/redux/store.ts
@@ -22,13 +22,14 @@ import {
TypedStartListening,
configureStore,
} from '@reduxjs/toolkit';
+import compartmentPathwaysReducer from './compartmentPathways/compartmentPathways.slice';
import exportReducer from './export/export.slice';
import legendReducer from './legend/legend.slice';
import { mapListenerMiddleware } from './map/middleware/map.middleware';
+import markersReducer from './markers/markers.slice';
import pluginsReducer from './plugins/plugins.slice';
-import statisticsReducer from './statistics/statistics.slice';
-import compartmentPathwaysReducer from './compartmentPathways/compartmentPathways.slice';
import publicationsReducer from './publications/publications.slice';
+import statisticsReducer from './statistics/statistics.slice';
export const reducers = {
search: searchReducer,
@@ -54,6 +55,7 @@ export const reducers = {
publications: publicationsReducer,
export: exportReducer,
plugins: pluginsReducer,
+ markers: markersReducer,
};
export const middlewares = [mapListenerMiddleware.middleware];
diff --git a/src/services/pluginsManager/bioEntities/addSingleMarker.ts b/src/services/pluginsManager/bioEntities/addSingleMarker.ts
new file mode 100644
index 00000000..0b496795
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/addSingleMarker.ts
@@ -0,0 +1,12 @@
+import { addMarkerToMarkersData } from '@/redux/markers/markers.slice';
+import { Marker, MarkerWithoutId } from '@/redux/markers/markers.types';
+import { store } from '@/redux/store';
+import { v4 as uuidv4 } from 'uuid';
+
+export const addSingleMarker = (markerWithoutId: MarkerWithoutId): Marker => {
+ const { dispatch } = store;
+ const marker = { id: uuidv4(), ...markerWithoutId };
+ dispatch(addMarkerToMarkersData(marker));
+
+ return marker;
+};
diff --git a/src/services/pluginsManager/bioEntities/clearAllElements.ts b/src/services/pluginsManager/bioEntities/clearAllElements.ts
new file mode 100644
index 00000000..9177d501
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/clearAllElements.ts
@@ -0,0 +1,27 @@
+import { clearBioEntitiesData } from '@/redux/bioEntity/bioEntity.slice';
+import { clearChemicalsData } from '@/redux/chemicals/chemicals.slice';
+import { clearDrugsData } from '@/redux/drugs/drugs.slice';
+import { setMarkersData } from '@/redux/markers/markers.slice';
+import { store } from '@/redux/store';
+
+type ElementName = 'drugs' | 'chemicals' | 'content' | 'marker';
+
+export const clearAllElements = (elements: ElementName[]): void => {
+ const { dispatch } = store;
+
+ if (elements.includes('content')) {
+ dispatch(clearBioEntitiesData());
+ }
+
+ if (elements.includes('chemicals')) {
+ dispatch(clearChemicalsData());
+ }
+
+ if (elements.includes('drugs')) {
+ dispatch(clearDrugsData());
+ }
+
+ if (elements.includes('marker')) {
+ dispatch(setMarkersData([]));
+ }
+};
diff --git a/src/services/pluginsManager/bioEntities/getAllChemicals.ts b/src/services/pluginsManager/bioEntities/getAllChemicals.ts
new file mode 100644
index 00000000..92cf1727
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getAllChemicals.ts
@@ -0,0 +1,10 @@
+import { chemicalsDataListSelector } from '@/redux/chemicals/chemicals.selectors';
+import { store } from '@/redux/store';
+import { Chemical } from '@/types/models';
+
+export const getAllChemicals = (): Chemical[] => {
+ const { getState } = store;
+ const chemicals = chemicalsDataListSelector(getState());
+
+ return chemicals || [];
+};
diff --git a/src/services/pluginsManager/bioEntities/getAllContent.ts b/src/services/pluginsManager/bioEntities/getAllContent.ts
new file mode 100644
index 00000000..af8f6d11
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getAllContent.ts
@@ -0,0 +1,10 @@
+import { bioEntityDataListSelector } from '@/redux/bioEntity/bioEntity.selectors';
+import { store } from '@/redux/store';
+import { BioEntityContent } from '@/types/models';
+
+export const getAllBioEntities = (): BioEntityContent[] => {
+ const { getState } = store;
+ const bioEntities = bioEntityDataListSelector(getState());
+
+ return bioEntities || [];
+};
diff --git a/src/services/pluginsManager/bioEntities/getAllDrugs.ts b/src/services/pluginsManager/bioEntities/getAllDrugs.ts
new file mode 100644
index 00000000..3cd7b8c8
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getAllDrugs.ts
@@ -0,0 +1,10 @@
+import { drugsDataListSelector } from '@/redux/drugs/drugs.selectors';
+import { store } from '@/redux/store';
+import { Drug } from '@/types/models';
+
+export const getAllDrugs = (): Drug[] => {
+ const { getState } = store;
+ const drugs = drugsDataListSelector(getState());
+
+ return drugs || [];
+};
diff --git a/src/services/pluginsManager/bioEntities/getAllMarkers.ts b/src/services/pluginsManager/bioEntities/getAllMarkers.ts
new file mode 100644
index 00000000..1ed70af6
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getAllMarkers.ts
@@ -0,0 +1,10 @@
+import { markersDataSelector } from '@/redux/markers/markers.selectors';
+import { Marker } from '@/redux/markers/markers.types';
+import { store } from '@/redux/store';
+
+export const getAllMarkers = (): Marker[] => {
+ const { getState } = store;
+ const markers = markersDataSelector(getState());
+
+ return markers;
+};
diff --git a/src/services/pluginsManager/bioEntities/getShownElements.ts b/src/services/pluginsManager/bioEntities/getShownElements.ts
new file mode 100644
index 00000000..89cf67bd
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getShownElements.ts
@@ -0,0 +1,22 @@
+import { searchedBioEntitesSelectorOfCurrentMap } from '@/redux/bioEntity/bioEntity.selectors';
+import { searchedChemicalsBioEntitesOfCurrentMapSelector } from '@/redux/chemicals/chemicals.selectors';
+import { searchedDrugsBioEntitesOfCurrentMapSelector } from '@/redux/drugs/drugs.selectors';
+import { markersPinsOfCurrentMapDataSelector } from '@/redux/markers/markers.selectors';
+import { store } from '@/redux/store';
+import { GetShownElementsPluginMethodResult } from './getShownElements.types';
+
+export const getShownElements = (): GetShownElementsPluginMethodResult => {
+ const { getState } = store;
+
+ const content = searchedBioEntitesSelectorOfCurrentMap(getState());
+ const chemicals = searchedChemicalsBioEntitesOfCurrentMapSelector(getState());
+ const drugs = searchedDrugsBioEntitesOfCurrentMapSelector(getState());
+ const markers = markersPinsOfCurrentMapDataSelector(getState());
+
+ return {
+ content,
+ chemicals,
+ drugs,
+ markers,
+ };
+};
diff --git a/src/services/pluginsManager/bioEntities/getShownElements.types.ts b/src/services/pluginsManager/bioEntities/getShownElements.types.ts
new file mode 100644
index 00000000..dcbacd29
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/getShownElements.types.ts
@@ -0,0 +1,9 @@
+import { Marker } from '@/redux/markers/markers.types';
+import { BioEntity } from '@/types/models';
+
+export interface GetShownElementsPluginMethodResult {
+ content: BioEntity[];
+ drugs: BioEntity[];
+ chemicals: BioEntity[];
+ markers: Marker[];
+}
diff --git a/src/services/pluginsManager/bioEntities/index.ts b/src/services/pluginsManager/bioEntities/index.ts
new file mode 100644
index 00000000..0e77668c
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/index.ts
@@ -0,0 +1,23 @@
+import { addSingleMarker } from './addSingleMarker';
+import { clearAllElements } from './clearAllElements';
+import { getAllChemicals } from './getAllChemicals';
+import { getAllBioEntities } from './getAllContent';
+import { getAllDrugs } from './getAllDrugs';
+import { getAllMarkers } from './getAllMarkers';
+import { getShownElements } from './getShownElements';
+import { removeAllMarkers } from './removeAllMarkers';
+import { removeSingleMarker } from './removeSingleMarker';
+
+export const bioEntitiesMethods = {
+ getAllBioEntities,
+ getAllChemicals,
+ getAllDrugs,
+ getAllMarkers,
+ getShownElements,
+ addSingleMarker,
+ removeSingleMarker,
+ removeAllMarkers,
+ clearAllElements,
+};
+
+export type BioEntitiesMethods = typeof bioEntitiesMethods;
diff --git a/src/services/pluginsManager/bioEntities/removeAllMarkers.ts b/src/services/pluginsManager/bioEntities/removeAllMarkers.ts
new file mode 100644
index 00000000..3224d83b
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/removeAllMarkers.ts
@@ -0,0 +1,7 @@
+import { setMarkersData } from '@/redux/markers/markers.slice';
+import { store } from '@/redux/store';
+
+export const removeAllMarkers = (): void => {
+ const { dispatch } = store;
+ dispatch(setMarkersData([]));
+};
diff --git a/src/services/pluginsManager/bioEntities/removeSingleMarker.ts b/src/services/pluginsManager/bioEntities/removeSingleMarker.ts
new file mode 100644
index 00000000..d8254453
--- /dev/null
+++ b/src/services/pluginsManager/bioEntities/removeSingleMarker.ts
@@ -0,0 +1,7 @@
+import { removeMarkerFromMarkersData } from '@/redux/markers/markers.slice';
+import { store } from '@/redux/store';
+
+export const removeSingleMarker = (id: string): void => {
+ const { dispatch } = store;
+ dispatch(removeMarkerFromMarkersData(id));
+};
diff --git a/src/services/pluginsManager/pluginsManager.ts b/src/services/pluginsManager/pluginsManager.ts
index 66ad3b93..fce57569 100644
--- a/src/services/pluginsManager/pluginsManager.ts
+++ b/src/services/pluginsManager/pluginsManager.ts
@@ -2,6 +2,7 @@ import { PLUGINS_CONTENT_ELEMENT_ATTR_NAME, PLUGINS_CONTENT_ELEMENT_ID } from '@
import { registerPlugin } from '@/redux/plugins/plugins.thunks';
import { store } from '@/redux/store';
import md5 from 'crypto-js/md5';
+import { bioEntitiesMethods } from './bioEntities';
import type { PluginsManagerType } from './pluginsManager.types';
import { configurationMapper } from './pluginsManager.utils';
@@ -19,6 +20,9 @@ export const PluginsManager: PluginsManagerType = {
plugins: {
registerPlugin: PluginsManager.registerPlugin,
},
+ data: {
+ bioEntities: bioEntitiesMethods,
+ },
};
const unsubscribe = store.subscribe(() => {
diff --git a/src/types/OLrendering.ts b/src/types/OLrendering.ts
index 9769064d..54f0c7ab 100644
--- a/src/types/OLrendering.ts
+++ b/src/types/OLrendering.ts
@@ -3,7 +3,7 @@ import { Color, GeneVariant } from './models';
export type OverlayBioEntityRenderType = 'line' | 'rectangle' | 'submap-link';
export type OverlayBioEntityRender = {
- id: number;
+ id: number | string;
modelId: number;
/** bottom left corner of whole element, Xmin */
x1: number;
@@ -18,6 +18,7 @@ export type OverlayBioEntityRender = {
value: number | null;
overlayId: number;
color: Color | null;
+ hexColor?: string;
type: OverlayBioEntityRenderType;
geneVariants?: GeneVariant[] | null;
};
--
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