npm - @graphty/graph-io - Versions diffs - 0.3.17 → 0.3.18 - Mend

@graphty/graph-io 0.3.17 → 0.3.18

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (91) hide show

package/LICENSE +1 -1
package/README.md +29 -3
package/dist/chunks/{escape-scjHxjpr.js → escape-D-gZWO26.js} +3 -2
package/dist/chunks/{escape-scjHxjpr.js.map → escape-D-gZWO26.js.map} +1 -1
package/dist/chunks/{importer-Xg07gk7p.js → importer-Br_QeAeE.js} +4 -3
package/dist/chunks/{importer-Xg07gk7p.js.map → importer-Br_QeAeE.js.map} +1 -1
package/dist/chunks/{importer-ruMWWvVs.js → importer-DHagxvDD.js} +4 -3
package/dist/chunks/{importer-ruMWWvVs.js.map → importer-DHagxvDD.js.map} +1 -1
package/dist/chunks/{importer-B6rKRxzv.js → importer-Du5crN9l.js} +509 -25
package/dist/chunks/importer-Du5crN9l.js.map +1 -0
package/dist/chunks/importer-aNJfe0qu.js +1614 -0
package/dist/chunks/importer-aNJfe0qu.js.map +1 -0
package/dist/chunks/{importer-BmOl9gLW.js → importer-d0uQxFp6.js} +4 -3
package/dist/chunks/{importer-BmOl9gLW.js.map → importer-d0uQxFp6.js.map} +1 -1
package/dist/chunks/ontology-BnrJ4I98.js +113 -0
package/dist/chunks/ontology-BnrJ4I98.js.map +1 -0
package/dist/chunks/{records-DSpbTE5s.js → records-Bk9jgodz.js} +2 -2
package/dist/chunks/{records-DSpbTE5s.js.map → records-Bk9jgodz.js.map} +1 -1
package/dist/chunks/{writer-DHHfHn11.js → report-BOk0p5y8.js} +97 -919
package/dist/chunks/report-BOk0p5y8.js.map +1 -0
package/dist/chunks/writer-GAdltGmC.js +827 -0
package/dist/chunks/writer-GAdltGmC.js.map +1 -0
package/dist/csv.js +4 -3
package/dist/csv.js.map +1 -1
package/dist/dot.js +1 -1
package/dist/gexf.js +3 -2
package/dist/gexf.js.map +1 -1
package/dist/gml.js +3 -2
package/dist/gml.js.map +1 -1
package/dist/graph-io.js +160 -141
package/dist/graph-io.js.map +1 -1
package/dist/graphml.js +1 -1
package/dist/json.js +1 -1
package/dist/neo4j.js +4 -3
package/dist/neo4j.js.map +1 -1
package/dist/obo.d.ts +1 -0
package/dist/obo.js +6 -0
package/dist/obo.js.map +1 -0
package/dist/pajek.js +1 -1
package/dist/src/common/ontology.d.ts +59 -0
package/dist/src/common/ontology.d.ts.map +1 -0
package/dist/src/common/ontology.js +147 -0
package/dist/src/common/ontology.js.map +1 -0
package/dist/src/formats/json/dialect.d.ts +8 -6
package/dist/src/formats/json/dialect.d.ts.map +1 -1
package/dist/src/formats/json/dialect.js +26 -3
package/dist/src/formats/json/dialect.js.map +1 -1
package/dist/src/formats/json/importer.d.ts +324 -7
package/dist/src/formats/json/importer.d.ts.map +1 -1
package/dist/src/formats/json/importer.js +153 -22
package/dist/src/formats/json/importer.js.map +1 -1
package/dist/src/formats/json/obographs.d.ts +21 -0
package/dist/src/formats/json/obographs.d.ts.map +1 -0
package/dist/src/formats/json/obographs.js +476 -0
package/dist/src/formats/json/obographs.js.map +1 -0
package/dist/src/formats/obo/importer.d.ts +90 -0
package/dist/src/formats/obo/importer.d.ts.map +1 -0
package/dist/src/formats/obo/importer.js +1248 -0
package/dist/src/formats/obo/importer.js.map +1 -0
package/dist/src/formats/obo/index.d.ts +7 -0
package/dist/src/formats/obo/index.d.ts.map +1 -0
package/dist/src/formats/obo/index.js +7 -0
package/dist/src/formats/obo/index.js.map +1 -0
package/dist/src/formats/obo/syntax.d.ts +121 -0
package/dist/src/formats/obo/syntax.d.ts.map +1 -0
package/dist/src/formats/obo/syntax.js +424 -0
package/dist/src/formats/obo/syntax.js.map +1 -0
package/dist/src/index.d.ts +1 -0
package/dist/src/index.d.ts.map +1 -1
package/dist/src/index.js +1 -0
package/dist/src/index.js.map +1 -1
package/dist/src/registry.d.ts.map +1 -1
package/dist/src/registry.js +3 -1
package/dist/src/registry.js.map +1 -1
package/dist/src/sniff.d.ts +1 -1
package/dist/src/sniff.d.ts.map +1 -1
package/dist/src/sniff.js +23 -3
package/dist/src/sniff.js.map +1 -1
package/package.json +6 -1
package/src/common/ontology.ts +169 -0
package/src/formats/json/dialect.ts +37 -7
package/src/formats/json/importer.ts +204 -27
package/src/formats/json/obographs.ts +563 -0
package/src/formats/obo/importer.ts +1695 -0
package/src/formats/obo/index.ts +7 -0
package/src/formats/obo/syntax.ts +466 -0
package/src/index.ts +1 -0
package/src/registry.ts +3 -1
package/src/sniff.ts +35 -5
package/dist/chunks/importer-B6rKRxzv.js.map +0 -1
package/dist/chunks/writer-DHHfHn11.js.map +0 -1

package/dist/src/formats/obo/syntax.js.map ADDED Viewed

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package/dist/src/index.d.ts CHANGED Viewed

@@ -18,6 +18,7 @@ export { GML_ISSUE, GML_LOSS, gmlExporter, type GmlExportOptions, gmlImporter, t
 export { GRAPHML_ISSUE, GRAPHML_LOSS, graphmlExporter, type GraphmlExportOptions, graphmlImporter, type GraphmlImportOptions, } from "./formats/graphml/index.js";
 export { dialectCapabilities, JSON_DIALECTS, JSON_ISSUE, JSON_LOSS, jsonCapabilities, type JsonDialect, jsonExporter, type JsonExportOptions, type JsonImportDialect, jsonImporter, type JsonImportOptions, type JsonShapeMeta, } from "./formats/json/index.js";
 export { ID_SPACE_COLUMN, LABELS_COLUMN, NEO4J_CAPABILITIES, NEO4J_ISSUE, NEO4J_LOSS, neo4jExporter, type Neo4jExportOptions, neo4jImporter, type Neo4jImportOptions, ORIGINAL_ID_COLUMN, TYPE_COLUMN, } from "./formats/neo4j/index.js";
+export { OBO_ISSUE, oboImporter, type OboImportOptions } from "./formats/obo/index.js";
 export { PAJEK_ISSUE, PAJEK_LOSS, pajekExporter, type PajekExportOptions, pajekImporter, type PajekImportOptions, } from "./formats/pajek/index.js";
 export { BAD_DEFAULT_CODE, BAD_OPTIONS_CODE, declareCompanion, declareResolved, PRECISION_CODE, RENAMED_CODE, type ResolvedDeclaration, ROLE_TAKEN_CODE, UNKNOWN_TYPE_CODE, } from "./common/attributes.js";
 export * from "./common/codes.js";

package/dist/src/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/src/index.js CHANGED Viewed

@@ -21,6 +21,7 @@ export { GML_ISSUE, GML_LOSS, gmlExporter, gmlImporter, } from "./formats/gml/in
 export { GRAPHML_ISSUE, GRAPHML_LOSS, graphmlExporter, graphmlImporter, } from "./formats/graphml/index.js";
 export { dialectCapabilities, JSON_DIALECTS, JSON_ISSUE, JSON_LOSS, jsonCapabilities, jsonExporter, jsonImporter, } from "./formats/json/index.js";
 export { ID_SPACE_COLUMN, LABELS_COLUMN, NEO4J_CAPABILITIES, NEO4J_ISSUE, NEO4J_LOSS, neo4jExporter, neo4jImporter, ORIGINAL_ID_COLUMN, TYPE_COLUMN, } from "./formats/neo4j/index.js";
+export { OBO_ISSUE, oboImporter } from "./formats/obo/index.js";
 export { PAJEK_ISSUE, PAJEK_LOSS, pajekExporter, pajekImporter, } from "./formats/pajek/index.js";
 // ============================================================ shared helpers for plugin authors (8.4, 8.5, 8.6)
 export { BAD_DEFAULT_CODE, BAD_OPTIONS_CODE, declareCompanion, declareResolved, PRECISION_CODE, RENAMED_CODE, ROLE_TAKEN_CODE, UNKNOWN_TYPE_CODE, } from "./common/attributes.js";

package/dist/src/index.js.map CHANGED Viewed

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package/dist/src/registry.js CHANGED Viewed

@@ -16,6 +16,7 @@ import { gmlExporter, gmlImporter } from "./formats/gml/index.js";
 import { graphmlExporter, graphmlImporter } from "./formats/graphml/index.js";
 import { jsonExporter, jsonImporter } from "./formats/json/index.js";
 import { neo4jExporter, neo4jImporter } from "./formats/neo4j/index.js";
+import { oboImporter } from "./formats/obo/index.js";
 import { pajekExporter, pajekImporter } from "./formats/pajek/index.js";
 import { rankFormats, SNIFF_HEAD_BYTES } from "./sniff.js";
 /** The issue code of an input whose format no registered importer recognises. */
@@ -278,7 +279,8 @@ export function createRegistry() {
         .registerImporter(pajekImporter)
         .registerExporter(pajekExporter)
         .registerImporter(neo4jImporter)
-        .registerExporter(neo4jExporter);
+        .registerExporter(neo4jExporter)
+        .registerImporter(oboImporter);
 }
 /** The default registry: every built-in format. */
 export const registry = createRegistry();

package/dist/src/registry.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/src/sniff.d.ts CHANGED Viewed

@@ -23,7 +23,7 @@
 import { type JsonImportDialect } from "./formats/json/dialect.js";
 import { type GraphImporter } from "./types.js";
 /** The format names of the eight built-in importers and exporters. */
-export type GraphFormatName = "gexf" | "graphml" | "gml" | "dot" | "pajek" | "csv" | "json" | "neo4j";
+export type GraphFormatName = "gexf" | "graphml" | "gml" | "dot" | "pajek" | "csv" | "json" | "neo4j" | "obo";
 /**
  * The built-in format names in the default registry's order, which is also the tie-break order of
  * sniffing: the more common format wins an extension two formats claim (`.xml` GraphML before GEXF,

package/dist/src/sniff.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"sniff.d.ts","sourceRoot":"","sources":["../../src/sniff.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,KAAK,iBAAiB,EAAoB,MAAM,2BAA2B,CAAC;AACrF,OAAO,EAAE,KAAK,aAAa,EAAE,MAAM,YAAY,CAAC;AAEhD,sEAAsE;AACtE,MAAM,MAAM,eAAe,GAAG,MAAM,GAAG,SAAS,GAAG,KAAK,GAAG,KAAK,GAAG,OAAO,GAAG,KAAK,GAAG,MAAM,GAAG,OAAO,CAAC;~~AAEtG~~;;;;GAIG;AACH,eAAO,MAAM,aAAa,EAAE,SAAS,eAAe,~~EASlD~~,CAAC;AAEH,8GAA8G;AAC9G,eAAO,MAAM,gBAAgB,OAAO,CAAC;AAErC,sDAAsD;AACtD,MAAM,WAAW,UAAU;IACvB,uDAAuD;IACvD,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C,2EAA2E;IAC3E,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C,sDAAsD;IACtD,QAAQ,CAAC,IAAI,CAAC,EAAE,UAAU,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;CAC1D;AAED,uCAAuC;AACvC,MAAM,WAAW,WAAW;IACxB,kCAAkC;IAClC,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,sFAAsF;IACtF,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,+FAA+F;IAC/F,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,mEAAmE;IACnE,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC;IAC5B,wDAAwD;IACxD,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,+GAA+G;IAC/G,QAAQ,CAAC,OAAO,EAAE,iBAAiB,GAAG,IAAI,CAAC;CAC9C;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAO3D;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAG1D;AAED;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,UAAU,GAAG,MAAM,GAAG,UAAU,CAU/D;AAED;;;;;;;GAOG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,aAAa,CAAC,GAAG,SAAS,WAAW,EAAE,CAkCzG;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,aAAa,CAAC,GAAG,WAAW,GAAG,IAAI,CAGrG;AAED;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,UAAU,GAAG,MAAM,GAAG,iBAAiB,GAAG,IAAI,CAcxF"}
1	+ {"version":3,"file":"sniff.d.ts","sourceRoot":"","sources":["../../src/sniff.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,KAAK,iBAAiB,EAAoB,MAAM,2BAA2B,CAAC;AACrF,OAAO,EAAE,KAAK,aAAa,EAAE,MAAM,YAAY,CAAC;AAEhD,sEAAsE;AACtE,MAAM,MAAM,eAAe,GAAG,MAAM,GAAG,SAAS,GAAG,KAAK,GAAG,KAAK,GAAG,OAAO,GAAG,KAAK,GAAG,MAAM,GAAG,OAAO,GAAG,KAAK,CAAC;AAE9G;;;;GAIG;AACH,eAAO,MAAM,aAAa,EAAE,SAAS,eAAe,EAUlD,CAAC;AAEH,8GAA8G;AAC9G,eAAO,MAAM,gBAAgB,OAAO,CAAC;AAErC,sDAAsD;AACtD,MAAM,WAAW,UAAU;IACvB,uDAAuD;IACvD,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C,2EAA2E;IAC3E,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C,sDAAsD;IACtD,QAAQ,CAAC,IAAI,CAAC,EAAE,UAAU,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;CAC1D;AAED,uCAAuC;AACvC,MAAM,WAAW,WAAW;IACxB,kCAAkC;IAClC,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,sFAAsF;IACtF,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,+FAA+F;IAC/F,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,mEAAmE;IACnE,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC;IAC5B,wDAAwD;IACxD,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;IAC3B,+GAA+G;IAC/G,QAAQ,CAAC,OAAO,EAAE,iBAAiB,GAAG,IAAI,CAAC;CAC9C;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAO3D;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAG1D;AAED;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,UAAU,GAAG,MAAM,GAAG,UAAU,CAU/D;AAED;;;;;;;GAOG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,aAAa,CAAC,GAAG,SAAS,WAAW,EAAE,CAkCzG;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,aAAa,CAAC,GAAG,WAAW,GAAG,IAAI,CAGrG;AAED;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,UAAU,GAAG,MAAM,GAAG,iBAAiB,GAAG,IAAI,CAcxF"}

package/dist/src/sniff.js CHANGED Viewed

@@ -35,6 +35,7 @@ export const GRAPH_FORMATS = Object.freeze([
     "dot",
     "pajek",
     "neo4j",
+    "obo",
 ]);
 /** How many bytes of the input the sniffers look at; the registry reads no more than this before deciding. */
 export const SNIFF_HEAD_BYTES = 8192;
@@ -183,9 +184,20 @@ function skeletonOf(text) {
             case "options":
                 root[key] = objectOf(keys.get(key));
                 break;
-            case "graphs":
-                root[key] = [];
+            case "graphs": {
+                // the keys of any node or edge of the first graph: OBO Graphs or JGF (design 1.6)
+                const nodes = keys.get("graphs[0].nodes[]");
+                const edges = keys.get("graphs[0].edges[]");
+                const graph = {};
+                if (nodes !== undefined) {
+                    graph.nodes = [objectOf(nodes)];
+                }
+                if (edges !== undefined) {
+                    graph.edges = [objectOf(edges)];
+                }
+                root[key] = nodes === undefined && edges === undefined ? [] : [graph];
                 break;
+            }
             case "nodes":
             case "edges":
             case "links": {
@@ -220,7 +232,8 @@ function objectOf(names) {
  * scanner tracks a container stack (the key each object sits under, the index of each array
  * element) and records a key when it is at one of the watched paths; a head cut inside a string
  * or a number simply ends the scan. For a top-level array the first element's keys are recorded
- * under `nodes[0]`.
+ * under `nodes[0]`; the keys of every node and edge of `graphs[0]` under `graphs[0].nodes[]` and
+ * `graphs[0].edges[]`.
  * @param text - the head, starting with `{` or `[`
  * @returns key sets by path
  */
@@ -243,6 +256,13 @@ function scanKeys(text) {
         if (depth === 2 && kinds[0] === "object" && kinds[1] === "object") {
             return labels[1] === "graph" || labels[1] === "options" ? labels[1] : null;
         }
+        if (depth === 5 &&
+            kinds.join() === "object,array,object,array,object" &&
+            labels[1] === "graphs" &&
+            labels[2] === "0" &&
+            (labels[3] === "nodes" || labels[3] === "edges")) {
+            return labels[3] === "nodes" ? "graphs[0].nodes[]" : "graphs[0].edges[]";
+        }
         if (depth === 3 && kinds[0] === "object" && kinds[1] === "array" && kinds[2] === "object") {
             const section = labels[1];
             if ((section === "nodes" || section === "edges" || section === "links") && labels[2] === "0") {

package/dist/src/sniff.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@graphty/graph-io",
-  "version": "0.3.17",
+  "version": "0.3.18",
   "description": "Importers and exporters (GEXF, GraphML, GML, DOT, Pajek, CSV, JSON, Neo4j) for the @graphty/graph-format snapshot",
   "author": "Adam Powers <apowers@ato.ms>",
   "type": "module",
@@ -51,6 +51,11 @@
       "types": "./dist/neo4j.d.ts",
       "import": "./dist/neo4j.js",
       "default": "./dist/neo4j.js"
+    },
+    "./obo": {
+      "types": "./dist/obo.d.ts",
+      "import": "./dist/obo.js",
+      "default": "./dist/obo.js"
     }
   },
   "sideEffects": false,

package/src/common/ontology.ts ADDED Viewed

@@ -0,0 +1,169 @@
+/**
+ * What the OBO importer and the JSON importer's `obographs` dialect share (design section 1.0, the
+ * `ontology.ts` building block): the OBO column vocabulary (names, dtypes, roles), so the `.obo` and
+ * the `.json` of one ontology give the same columns, and the OBO 1.4 rule for turning the IRIs
+ * OBO Graphs writes back into the identifiers the `.obo` file writes (section 4.6).
+ */
+import { type ColumnDecl } from "@graphty/graph-format";
+/** The dtypes the OBO vocabulary uses. */
+type OboDtype = "string" | "dict" | "bool" | "list" | "json";
+/** One column of the OBO vocabulary. */
+interface OboColumnSpec {
+    /** The dtype. */
+    readonly dtype: OboDtype;
+    /** The role, when the column carries one. */
+    readonly role?: "label" | "kind" | undefined;
+}
+/**
+ * The node columns of the OBO vocabulary, keyed by column name (design section 4.2). The names are
+ * the OBO tag names, so a Gene Ontology user finds `namespace`, `def` and `is_obsolete` under the
+ * names the GO documentation uses.
+ */
+export const OBO_NODE_COLUMNS: Readonly<Record<string, OboColumnSpec>> = Object.freeze({
+    type: { dtype: "dict" },
+    name: { dtype: "string", role: "label" },
+    namespace: { dtype: "dict" },
+    def: { dtype: "string" },
+    "def.xrefs": { dtype: "list" },
+    comment: { dtype: "string" },
+    synonym: { dtype: "json" },
+    xref: { dtype: "list" },
+    "xref.descriptions": { dtype: "json" },
+    alt_id: { dtype: "list" },
+    subset: { dtype: "list" },
+    replaced_by: { dtype: "list" },
+    consider: { dtype: "list" },
+    is_obsolete: { dtype: "bool" },
+    is_anonymous: { dtype: "bool" },
+    builtin: { dtype: "bool" },
+    created_by: { dtype: "string" },
+    creation_date: { dtype: "string" },
+    intersection_of: { dtype: "json" },
+    union_of: { dtype: "list" },
+    equivalent_to: { dtype: "list" },
+    disjoint_from: { dtype: "list" },
+    property_value: { dtype: "json" },
+    // Typedef frames, under typedefs: "nodes"
+    domain: { dtype: "string" },
+    range: { dtype: "string" },
+    inverse_of: { dtype: "string" },
+    transitive_over: { dtype: "list" },
+    disjoint_over: { dtype: "list" },
+    holds_over_chain: { dtype: "json" },
+    equivalent_to_chain: { dtype: "json" },
+    expand_assertion_to: { dtype: "json" },
+    expand_expression_to: { dtype: "json" },
+    is_cyclic: { dtype: "bool" },
+    is_reflexive: { dtype: "bool" },
+    is_symmetric: { dtype: "bool" },
+    is_anti_symmetric: { dtype: "bool" },
+    is_asymmetric: { dtype: "bool" },
+    is_transitive: { dtype: "bool" },
+    is_functional: { dtype: "bool" },
+    is_inverse_functional: { dtype: "bool" },
+    is_metadata_tag: { dtype: "bool" },
+    is_class_level: { dtype: "bool" },
+    // OBO Graphs only
+    propertyType: { dtype: "dict" },
+    // what has no column of its own
+    "obo.qualifiers": { dtype: "json" },
+    "obo.unrecognized": { dtype: "json" },
+});
+/** The edge columns of the OBO vocabulary. */
+const OBO_EDGE_COLUMNS: Readonly<Record<string, OboColumnSpec>> = Object.freeze({
+    relation: { dtype: "dict", role: "kind" },
+    qualifiers: { dtype: "json" },
+    meta: { dtype: "json" },
+});
+/** The node column that marks a node made for an undeclared reference (design section 4.2). */
+export const PLACEHOLDER_COLUMN = "graphty.placeholder";
+/**
+ * The declaration of an OBO vocabulary column.
+ * @param domain - node or edge
+ * @param name - the column name (a key of OBO_NODE_COLUMNS / OBO_EDGE_COLUMNS, or the placeholder column)
+ * @returns the declaration, nullable, with origin `{ format: "obo", id: name }`
+ */
+export function oboColumnDecl(domain: "node" | "edge", name: string): ColumnDecl {
+    if (name === PLACEHOLDER_COLUMN) {
+        return { name, dtype: "bool", nullable: true, origin: { format: "graphty", id: "placeholder" } };
+    }
+    const spec = (domain === "node" ? OBO_NODE_COLUMNS : OBO_EDGE_COLUMNS)[name];
+    const decl: ColumnDecl = { name, dtype: spec.dtype, nullable: true, origin: { format: "obo", id: name } };
+    if (spec.dtype === "list") {
+        decl.itemDtype = "string";
+    }
+    if (spec.role !== undefined) {
+        decl.role = spec.role;
+    }
+    return decl;
+}
+/** The OBO PURL base every OBO Foundry IRI starts with. */
+const OBO_PURL = "http://purl.obolibrary.org/obo/";
+/** The oboInOwl namespace of the OBO-to-OWL mapping's annotation properties. */
+const OBO_IN_OWL = "http://www.geneontology.org/formats/oboInOwl#";
+/**
+ * An IRI as the identifier the `.obo` file writes (the OBO 1.4 mapping, section 5.9, read
+ * backwards): `http://purl.obolibrary.org/obo/GO_0008150` is `GO:0008150` (the prefix is the text
+ * before the first underscore), and `http://purl.obolibrary.org/obo/go#regulates` (how the OWL
+ * translation writes an unprefixed OBO id: subsets, relations, synonym types) is `regulates`.
+ * Every other IRI, and an OBO PURL that fits neither form (`.../obo/T/Female`), is kept.
+ * @param iri - the IRI
+ * @returns the CURIE or local id, or the IRI unchanged
+ */
+export function compactOboIri(iri: string): string {
+    if (!iri.startsWith(OBO_PURL)) {
+        return iri;
+    }
+    const rest = iri.slice(OBO_PURL.length);
+    const hash = rest.indexOf("#");
+    if (hash > 0) {
+        const local = rest.slice(hash + 1);
+        return local.length > 0 && !rest.slice(0, hash).includes("/") ? local : iri;
+    }
+    const underscore = rest.indexOf("_");
+    if (underscore <= 0 || rest.includes("/") || underscore === rest.length - 1) {
+        return iri;
+    }
+    return `${rest.slice(0, underscore)}:${rest.slice(underscore + 1)}`;
+}
+/** The OBO synonym scopes. */
+export const SYNONYM_SCOPES: ReadonlySet<string> = new Set(["EXACT", "BROAD", "NARROW", "RELATED"]);
+/**
+ * The OBO synonym scope of an OBO Graphs synonym predicate (`hasExactSynonym`, with or without the
+ * oboInOwl namespace).
+ * @param pred - the predicate
+ * @returns the scope, or null for a predicate that is not one of the four
+ */
+export function synonymScopeOf(pred: string): string | null {
+    const local = pred.startsWith(OBO_IN_OWL) ? pred.slice(OBO_IN_OWL.length) : pred;
+    const match = /^has(Exact|Broad|Narrow|Related)Synonym$/.exec(local);
+    return match === null ? null : match[1].toUpperCase();
+}
+/**
+ * The OBO tag a `basicPropertyValues` predicate of OBO Graphs came from (the OBO-to-OWL mapping of
+ * the tags that are annotations), so the `.json` of an ontology fills the same columns as its
+ * `.obo`. `shorthand` is the relation's short name; every predicate not listed is a
+ * `property_value`.
+ */
+export const OBOGRAPHS_PREDICATE_TAGS: ReadonlyMap<string, string> = new Map([
+    [`${OBO_IN_OWL}hasOBONamespace`, "namespace"],
+    [`${OBO_IN_OWL}hasAlternativeId`, "alt_id"],
+    [`${OBO_IN_OWL}created_by`, "created_by"],
+    [`${OBO_IN_OWL}creation_date`, "creation_date"],
+    [`${OBO_PURL}IAO_0100001`, "replaced_by"],
+    [`${OBO_IN_OWL}consider`, "consider"],
+    [`${OBO_IN_OWL}shorthand`, "shorthand"],
+]);

package/src/formats/json/dialect.ts CHANGED Viewed

@@ -32,17 +32,19 @@ export const JSON_DIALECTS: readonly JsonDialect[] = Object.freeze([
 ]);
 /**
- * The dialects the importer reads: every JsonDialect plus two it only reads, NetworkX
- * adjacency_data (`nodes` plus one neighbour list per node under `adjacency`) and tree_data (a
- * nested `id` / `children` record). The exporter writes neither; write node-link instead.
+ * The dialects the importer reads: every JsonDialect plus three it only reads, NetworkX
+ * adjacency_data (`nodes` plus one neighbour list per node under `adjacency`), tree_data (a
+ * nested `id` / `children` record) and OBO Graphs (`graphs[]` of `sub` / `pred` / `obj` edges, the
+ * JSON form of the Gene Ontology and the OBO Foundry ontologies). The exporter writes none of them.
  */
-export type JsonImportDialect = JsonDialect | "adjacency" | "tree";
+export type JsonImportDialect = JsonDialect | "adjacency" | "tree" | "obographs";
 /** Every dialect the importer reads, for option checking and messages. */
 export const JSON_IMPORT_DIALECTS: readonly JsonImportDialect[] = Object.freeze([
     ...JSON_DIALECTS,
     "adjacency",
     "tree",
+    "obographs",
 ]);
 /** The key under `meta.extra` that holds the shape record (design section 8.5). */
@@ -116,8 +118,9 @@ export function isJsonImportDialect(value: unknown): value is JsonImportDialect
 /**
  * The dialect of a parsed JSON document, by the shape rules of design section 8.2 (Cytoscape:
- * `elements` or a top-level array of `{ data }` elements; JGF: `graph.nodes` / `graph.edges` or
- * `graphs[]`; graphology: `options.type` / `options.multi`, `key` nodes without `id`, edges with
+ * `elements` or a top-level array of `{ data }` elements; OBO Graphs: `graphs[]` whose first graph
+ * has an edge with `sub` (or `subj`) and `obj` or a `pred`, or a node with `lbl`, `meta` or an OWL
+ * `type`; JGF: `graph.nodes` / `graph.edges` or any other `graphs[]`; graphology: `options.type` / `options.multi`, `key` nodes without `id`, edges with
  * `undirected` or an `attributes` record; vis: edges with `from` / `to`; d3: `links` without
  * `directed` / `multigraph` / `graph`; NetworkX adjacency_data: `nodes` and `adjacency` without
  * `links` / `edges`; NetworkX tree_data: `children` without `nodes` / `links` / `edges`; else
@@ -141,7 +144,7 @@ export function sniffJsonDialect(root: unknown): JsonImportDialect | null {
         return "jgf";
     }
     if (Array.isArray(root.graphs)) {
-        return "jgf";
+        return isOboGraph(firstJsonObject(root.graphs)) ? "obographs" : "jgf";
     }
     if (!hasKey(root, "edges") && !hasKey(root, "links")) {
         if (hasKey(root, "nodes") && hasKey(root, "adjacency")) {
@@ -171,6 +174,31 @@ export function sniffJsonDialect(root: unknown): JsonImportDialect | null {
     return bare && hasKey(root, "links") ? "d3" : "node-link";
 }
+/** The node types of OBO Graphs (the OWL entity kinds). */
+const OBOGRAPHS_NODE_TYPES: ReadonlySet<unknown> = new Set(["CLASS", "INDIVIDUAL", "PROPERTY"]);
+/**
+ * Whether a graph of a `graphs[]` document is an OBO Graphs graph rather than JGF: anywhere in its
+ * nodes or edges, an edge with `sub` (or the outdated `subj`) and `obj`, or a `pred`, or a node
+ * with `lbl`, `meta` or a `type` of CLASS / INDIVIDUAL / PROPERTY (design 1.6: looking only at the
+ * first node and edge misses graphs with no edges and graphs whose first node has no `lbl`).
+ * @param graph - the first graph, or null
+ * @returns true for OBO Graphs
+ */
+function isOboGraph(graph: Record<string, unknown> | null): boolean {
+    if (graph === null) {
+        return false;
+    }
+    const isEdge = (e: unknown): boolean =>
+        isJsonObject(e) && ((hasKey(e, "obj") && (hasKey(e, "sub") || hasKey(e, "subj"))) || hasKey(e, "pred"));
+    const isNode = (n: unknown): boolean =>
+        isJsonObject(n) && (hasKey(n, "lbl") || hasKey(n, "meta") || OBOGRAPHS_NODE_TYPES.has(n.type));
+    return (
+        (Array.isArray(graph.edges) && graph.edges.some(isEdge)) ||
+        (Array.isArray(graph.nodes) && graph.nodes.some(isNode))
+    );
+}
 /**
  * The first object of an array, or null.
  * @param value - maybe an array
@@ -223,6 +251,8 @@ export const DIALECT_DEFAULT_DIRECTED: Readonly<Record<JsonImportDialect, boolea
     // networkx adjacency_data declares `directed`; tree_graph always builds a DiGraph
     adjacency: false,
     tree: true,
+    // OBO Graphs edges point from the subject (child) to the object (parent)
+    obographs: true,
 });
 /**