@graphty/graph-io 0.3.17 → 0.3.18

package/dist/obo.d.ts

@@ -0,0 +1 @@
+export * from "./src/formats/obo/index.js";

package/dist/obo.js

@@ -0,0 +1,6 @@
+import { O, o } from "./chunks/importer-aNJfe0qu.js";
+export {
+  O as OBO_ISSUE,
+  o as oboImporter
+};
+//# sourceMappingURL=obo.js.map

package/dist/obo.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"obo.js","sources":[],"sourcesContent":[],"names":[],"mappings":";"}

package/dist/pajek.js

@@ -1,4 +1,4 @@
-import { P, a, p, b } from "./chunks/importer-BmOl9gLW.js";
+import { P, a, p, b } from "./chunks/importer-d0uQxFp6.js";
 export {
   P as PAJEK_ISSUE,
   a as PAJEK_LOSS,

package/dist/src/common/ontology.d.ts

@@ -0,0 +1,59 @@
+/**
+ * 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 declare const OBO_NODE_COLUMNS: Readonly<Record<string, OboColumnSpec>>;
+/** The node column that marks a node made for an undeclared reference (design section 4.2). */
+export declare 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 declare function oboColumnDecl(domain: "node" | "edge", name: string): ColumnDecl;
+/**
+ * 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 declare function compactOboIri(iri: string): string;
+/** The OBO synonym scopes. */
+export declare const SYNONYM_SCOPES: ReadonlySet<string>;
+/**
+ * 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 declare function synonymScopeOf(pred: string): string | null;
+/**
+ * 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 declare const OBOGRAPHS_PREDICATE_TAGS: ReadonlyMap<string, string>;
+export {};
+//# sourceMappingURL=ontology.d.ts.map

package/dist/src/common/ontology.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ontology.d.ts","sourceRoot":"","sources":["../../../src/common/ontology.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,KAAK,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,0CAA0C;AAC1C,KAAK,QAAQ,GAAG,QAAQ,GAAG,MAAM,GAAG,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;AAE7D,wCAAwC;AACxC,UAAU,aAAa;IACnB,iBAAiB;IACjB,QAAQ,CAAC,KAAK,EAAE,QAAQ,CAAC;IACzB,6CAA6C;IAC7C,QAAQ,CAAC,IAAI,CAAC,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC;CAChD;AAED;;;;GAIG;AACH,eAAO,MAAM,gBAAgB,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,aAAa,CAAC,CAiDnE,CAAC;AASH,+FAA+F;AAC/F,eAAO,MAAM,kBAAkB,wBAAwB,CAAC;AAExD;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,UAAU,CAa/E;AAQD;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAejD;AAED,8BAA8B;AAC9B,eAAO,MAAM,cAAc,EAAE,WAAW,CAAC,MAAM,CAAoD,CAAC;AAEpG;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAI1D;AAED;;;;;GAKG;AACH,eAAO,MAAM,wBAAwB,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAQ/D,CAAC"}

package/dist/src/common/ontology.js

@@ -0,0 +1,147 @@
+/**
+ * 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).
+ */
+/**
+ * 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 = 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 = 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, name) {
+    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 = { 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) {
+    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 = 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) {
+    const local = pred.startsWith(OBO_IN_OWL) ? pred.slice(OBO_IN_OWL.length) : pred;
+    const match = /^has(Exact|Broad|Narrow|Related)Synonym$/.exec(local);
+    return match === null ? null : match[1].toUpperCase();
+}
+/**
+ * The OBO tag a `basicPropertyValues` predicate of OBO Graphs came from (the OBO-to-OWL mapping of
+ * the tags that are annotations), so the `.json` of an ontology fills the same columns as its
+ * `.obo`. `shorthand` is the relation's short name; every predicate not listed is a
+ * `property_value`.
+ */
+export const OBOGRAPHS_PREDICATE_TAGS = new Map([
+    [`${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"],
+]);
+//# sourceMappingURL=ontology.js.map

package/dist/src/common/ontology.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/json/dialect.d.ts

@@ -19,11 +19,12 @@ export type JsonDialect = "node-link" | "d3" | "jgf" | "cytoscape" | "graphology
 /** Every dialect name, for option checking and messages. */
 export declare const JSON_DIALECTS: readonly JsonDialect[];
 /**
- * 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 declare const JSON_IMPORT_DIALECTS: readonly JsonImportDialect[];
 /** The key under `meta.extra` that holds the shape record (design section 8.5). */
@@ -83,8 +84,9 @@ export declare function isJsonDialect(value: unknown): value is JsonDialect;
 export declare 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

package/dist/src/formats/json/dialect.d.ts.map

@@ -1 +1 @@
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package/dist/src/formats/json/dialect.js

@@ -27,6 +27,7 @@ export const JSON_IMPORT_DIALECTS = Object.freeze([
     ...JSON_DIALECTS,
     "adjacency",
     "tree",
+    "obographs",
 ]);
 /** The key under `meta.extra` that holds the shape record (design section 8.5). */
 export const META_KEY = "json";
@@ -66,8 +67,9 @@ export function isJsonImportDialect(value) {
 }
 /**
  * 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
@@ -91,7 +93,7 @@ export function sniffJsonDialect(root) {
         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")) {
@@ -120,6 +122,25 @@ export function sniffJsonDialect(root) {
     const bare = !hasKey(root, "directed") && !hasKey(root, "multigraph") && !hasKey(root, "graph");
     return bare && hasKey(root, "links") ? "d3" : "node-link";
 }
+/** The node types of OBO Graphs (the OWL entity kinds). */
+const OBOGRAPHS_NODE_TYPES = 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) {
+    if (graph === null) {
+        return false;
+    }
+    const isEdge = (e) => isJsonObject(e) && ((hasKey(e, "obj") && (hasKey(e, "sub") || hasKey(e, "subj"))) || hasKey(e, "pred"));
+    const isNode = (n) => 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
@@ -170,6 +191,8 @@ export const DIALECT_DEFAULT_DIRECTED = Object.freeze({
     // 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,
 });
 /**
  * The dtypes a JSON dialect keeps as declared: JSON declares no types, so a value reads back as

package/dist/src/formats/json/dialect.js.map

@@ -1 +1 @@
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