@graphty/graph-io 0.3.16 → 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-B8lsjFWx.js";
+import { P, a, p, b } from "./chunks/importer-d0uQxFp6.js";
 export {
   P as PAJEK_ISSUE,
   a as PAJEK_LOSS,

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

@@ -74,6 +74,49 @@ export declare const BAD_DEFAULT_CODE = "W_BAD_DEFAULT";
 export declare const BAD_OPTIONS_CODE = "W_BAD_OPTIONS";
 /** A repeated edge id in a format whose edge ids are unique; the second edge is skipped. */
 export declare const DUPLICATE_EDGE_ID_CODE = "E_DUPLICATE_EDGE_ID";
+/** A value does not parse as its declared type; the cell is left unset. */
+export declare const BAD_VALUE_CODE = "E_BAD_VALUE";
+/**
+ * A column's dtype was widened (design section 5.1) because a later value did not fit: an i32
+ * column meeting a value above 2^31, two declared types for one attribute.
+ */
+export declare const WIDENED_CODE = "W_WIDENED";
+/**
+ * A reference that is not a containment link (an attribute's element id, a layout or bypass
+ * entry, a subnetwork member, a view's network, an undeclared target) names nothing; reported
+ * once per kind with the count.
+ */
+export declare const DANGLING_REFERENCE_CODE = "W_DANGLING_REFERENCE";
+/** The same attribute twice on one element; one value is kept (the later, unless the format's specification says the first). */
+export declare const DUPLICATE_ATTRIBUTE_CODE = "W_DUPLICATE_ATTRIBUTE";
+/** A containment link would close a parent cycle; that one link is dropped. */
+export declare const PARENT_CYCLE_CODE = "E_PARENT_CYCLE";
+/** A formula (Cytoscape's `=ABS($x)`) is kept as its text; it is never evaluated. */
+export declare const EQUATION_AS_TEXT_CODE = "W_EQUATION_AS_TEXT";
+/**
+ * The file's style rules (defaults, mappings, dependencies, visual property aspects) are not
+ * applied to the snapshot; recorded once per import, the message names what was not applied.
+ */
+export declare const STYLES_NOT_IMPORTED_CODE = "W_STYLES_NOT_IMPORTED";
+/** A CX array member that is not a one-key object holding an array or an object; the block is skipped. */
+export declare const BAD_ASPECT_BLOCK_CODE = "E_BAD_ASPECT_BLOCK";
+/** A CX aspect out of its place (after the post-metadata, a status that is not last, a block buffered for what it depends on). */
+export declare const ASPECT_ORDER_CODE = "W_ASPECT_ORDER";
+/** A declared element count disagrees with what was read. */
+export declare const COUNT_MISMATCH_CODE = "W_COUNT_MISMATCH";
+/** The producer marked the document as failed (CX `status.success: false`): it is incomplete (fatal). */
+export declare const STATUS_FAILED_CODE = "E_STATUS_FAILED";
+/** The producer marked the document as successful but attached an error text. */
+export declare const STATUS_WARNING_CODE = "W_STATUS_WARNING";
+/**
+ * The input is beyond a size limit (a zip's uncompressed total or ratio, a document longer than
+ * one string); the same string as graph-format's E_TOO_LARGE, recorded with category "unsupported".
+ */
+export declare const TOO_LARGE_CODE = "E_TOO_LARGE";
+/** `graphIndex` is beyond the graphs of the input, or `graphName` names none of them (fatal). */
+export declare const GRAPH_NOT_FOUND_CODE = "E_GRAPH_NOT_FOUND";
+/** `graphName` names more than one graph of the input; the message lists their indexes (fatal). */
+export declare const AMBIGUOUS_GRAPH_NAME_CODE = "E_AMBIGUOUS_GRAPH_NAME";
 /** A role column the format has no slot for is written as a plain attribute (the role is lost). */
 export declare const ROLE_DROPPED_CODE = "W_ROLE_DROPPED";
 /** A parents (multi-parent) column in a format with single containment only. */

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

@@ -1 +1 @@
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+{"version":3,"file":"codes.d.ts","sourceRoot":"","sources":["../../../src/common/codes.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAIH,uFAAuF;AACvF,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,0CAA0C;AAC1C,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,8EAA8E;AAC9E,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD,qDAAqD;AACrD,eAAO,MAAM,aAAa,eAAe,CAAC;AAE1C,+DAA+D;AAC/D,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,kCAAkC;AAClC,eAAO,MAAM,gBAAgB,kBAAkB,CAAC;AAEhD,0FAA0F;AAC1F,eAAO,MAAM,WAAW,aAAa,CAAC;AAEtC,uFAAuF;AACvF,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,uEAAuE;AACvE,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,8DAA8D;AAC9D,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,2EAA2E;AAC3E,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD,kEAAkE;AAClE,eAAO,MAAM,cAAc,gBAAgB,CAAC;AAE5C,4DAA4D;AAC5D,eAAO,MAAM,kBAAkB,oBAAoB,CAAC;AAEpD;;;GAGG;AACH,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD,6GAA6G;AAC7G,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,mFAAmF;AACnF,eAAO,MAAM,cAAc,gBAAgB,CAAC;AAE5C,uFAAuF;AACvF,eAAO,MAAM,cAAc,gBAAgB,CAAC;AAE5C,uGAAuG;AACvG,eAAO,MAAM,gBAAgB,kBAAkB,CAAC;AAEhD,uHAAuH;AACvH,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD,sDAAsD;AACtD,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,4GAA4G;AAC5G,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,gGAAgG;AAChG,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,0GAA0G;AAC1G,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,mGAAmG;AACnG,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,0EAA0E;AAC1E,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,wHAAwH;AACxH,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,wEAAwE;AACxE,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,qFAAqF;AACrF,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,2FAA2F;AAC3F,eAAO,MAAM,gBAAgB,kBAAkB,CAAC;AAEhD,sFAAsF;AACtF,eAAO,MAAM,gBAAgB,kBAAkB,CAAC;AAEhD,4FAA4F;AAC5F,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,2EAA2E;AAC3E,eAAO,MAAM,cAAc,gBAAgB,CAAC;AAE5C;;;GAGG;AACH,eAAO,MAAM,YAAY,cAAc,CAAC;AAExC;;;;GAIG;AACH,eAAO,MAAM,uBAAuB,yBAAyB,CAAC;AAE9D,gIAAgI;AAChI,eAAO,MAAM,wBAAwB,0BAA0B,CAAC;AAEhE,+EAA+E;AAC/E,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,qFAAqF;AACrF,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D;;;GAGG;AACH,eAAO,MAAM,wBAAwB,0BAA0B,CAAC;AAEhE,0GAA0G;AAC1G,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,kIAAkI;AAClI,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,6DAA6D;AAC7D,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD,yGAAyG;AACzG,eAAO,MAAM,kBAAkB,oBAAoB,CAAC;AAEpD,iFAAiF;AACjF,eAAO,MAAM,mBAAmB,qBAAqB,CAAC;AAEtD;;;GAGG;AACH,eAAO,MAAM,cAAc,gBAAgB,CAAC;AAE5C,iGAAiG;AACjG,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,mGAAmG;AACnG,eAAO,MAAM,yBAAyB,2BAA2B,CAAC;AAIlE,mGAAmG;AACnG,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,gFAAgF;AAChF,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,6EAA6E;AAC7E,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,8EAA8E;AAC9E,eAAO,MAAM,oBAAoB,sBAAsB,CAAC;AAExD,yGAAyG;AACzG,eAAO,MAAM,yBAAyB,2BAA2B,CAAC;AAElE,6FAA6F;AAC7F,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,yEAAyE;AACzE,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,gFAAgF;AAChF,eAAO,MAAM,0BAA0B,4BAA4B,CAAC;AAEpE,oFAAoF;AACpF,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,yEAAyE;AACzE,eAAO,MAAM,iBAAiB,mBAAmB,CAAC;AAElD,+FAA+F;AAC/F,eAAO,MAAM,wBAAwB,0BAA0B,CAAC;AAEhE,kGAAkG;AAClG,eAAO,MAAM,yBAAyB,2BAA2B,CAAC;AAElE,2GAA2G;AAC3G,eAAO,MAAM,kBAAkB,4BAA4B,CAAC;AAE5D,mGAAmG;AACnG,eAAO,MAAM,iBAAiB,0BAA0B,CAAC;AAEzD,8GAA8G;AAC9G,eAAO,MAAM,kBAAkB,oBAAoB,CAAC;AAEpD,wFAAwF;AACxF,eAAO,MAAM,qBAAqB,uBAAuB,CAAC;AAE1D,yFAAyF;AACzF,eAAO,MAAM,mBAAmB,qBAAqB,CAAC"}

package/dist/src/common/codes.js

@@ -75,6 +75,49 @@ export const BAD_DEFAULT_CODE = "W_BAD_DEFAULT";
 export const BAD_OPTIONS_CODE = "W_BAD_OPTIONS";
 /** A repeated edge id in a format whose edge ids are unique; the second edge is skipped. */
 export const DUPLICATE_EDGE_ID_CODE = "E_DUPLICATE_EDGE_ID";
+/** A value does not parse as its declared type; the cell is left unset. */
+export const BAD_VALUE_CODE = "E_BAD_VALUE";
+/**
+ * A column's dtype was widened (design section 5.1) because a later value did not fit: an i32
+ * column meeting a value above 2^31, two declared types for one attribute.
+ */
+export const WIDENED_CODE = "W_WIDENED";
+/**
+ * A reference that is not a containment link (an attribute's element id, a layout or bypass
+ * entry, a subnetwork member, a view's network, an undeclared target) names nothing; reported
+ * once per kind with the count.
+ */
+export const DANGLING_REFERENCE_CODE = "W_DANGLING_REFERENCE";
+/** The same attribute twice on one element; one value is kept (the later, unless the format's specification says the first). */
+export const DUPLICATE_ATTRIBUTE_CODE = "W_DUPLICATE_ATTRIBUTE";
+/** A containment link would close a parent cycle; that one link is dropped. */
+export const PARENT_CYCLE_CODE = "E_PARENT_CYCLE";
+/** A formula (Cytoscape's `=ABS($x)`) is kept as its text; it is never evaluated. */
+export const EQUATION_AS_TEXT_CODE = "W_EQUATION_AS_TEXT";
+/**
+ * The file's style rules (defaults, mappings, dependencies, visual property aspects) are not
+ * applied to the snapshot; recorded once per import, the message names what was not applied.
+ */
+export const STYLES_NOT_IMPORTED_CODE = "W_STYLES_NOT_IMPORTED";
+/** A CX array member that is not a one-key object holding an array or an object; the block is skipped. */
+export const BAD_ASPECT_BLOCK_CODE = "E_BAD_ASPECT_BLOCK";
+/** A CX aspect out of its place (after the post-metadata, a status that is not last, a block buffered for what it depends on). */
+export const ASPECT_ORDER_CODE = "W_ASPECT_ORDER";
+/** A declared element count disagrees with what was read. */
+export const COUNT_MISMATCH_CODE = "W_COUNT_MISMATCH";
+/** The producer marked the document as failed (CX `status.success: false`): it is incomplete (fatal). */
+export const STATUS_FAILED_CODE = "E_STATUS_FAILED";
+/** The producer marked the document as successful but attached an error text. */
+export const STATUS_WARNING_CODE = "W_STATUS_WARNING";
+/**
+ * The input is beyond a size limit (a zip's uncompressed total or ratio, a document longer than
+ * one string); the same string as graph-format's E_TOO_LARGE, recorded with category "unsupported".
+ */
+export const TOO_LARGE_CODE = "E_TOO_LARGE";
+/** `graphIndex` is beyond the graphs of the input, or `graphName` names none of them (fatal). */
+export const GRAPH_NOT_FOUND_CODE = "E_GRAPH_NOT_FOUND";
+/** `graphName` names more than one graph of the input; the message lists their indexes (fatal). */
+export const AMBIGUOUS_GRAPH_NAME_CODE = "E_AMBIGUOUS_GRAPH_NAME";
 // ============================================================ exporter loss notes
 /** A role column the format has no slot for is written as a plain attribute (the role is lost). */
 export const ROLE_DROPPED_CODE = "W_ROLE_DROPPED";

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

@@ -1 +1 @@
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package/dist/src/common/input.d.ts

@@ -42,6 +42,15 @@ export interface ReadOptions {
  * @returns the canonical name ("windows-1252", "utf-16le", ...) or null
  */
 export declare function canonicalEncoding(label: string): string | null;
+/**
+ * A zip entry name as text (APPNOTE 4.4.17): UTF-8 when the bytes are valid UTF-8, whether or not
+ * the entry sets the language-encoding flag (bit 11), else windows-1252 (WHATWG has no CP437, and
+ * session entry names are ASCII in practice). Never throws: a name is a matching key, never a path,
+ * so an undecodable one still has to name its entry.
+ * @param bytes - the name bytes from the central directory or a local header
+ * @returns the name
+ */
+export declare function decodeEntryName(bytes: Uint8Array): string;
 /**
  * Whether a value is an ImportInput this module can read.
  * @param input - any value

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

@@ -1 +1 @@
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+{"version":3,"file":"input.d.ts","sourceRoot":"","sources":["../../../src/common/input.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAIH,OAAO,EAAE,KAAK,WAAW,EAAE,MAAM,aAAa,CAAC;AAC/C,OAAO,EAAiD,iBAAiB,EAAyB,MAAM,YAAY,CAAC;AACrH,OAAO,EAAE,KAAK,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAEvD,OAAO,EAAE,iBAAiB,EAAE,CAAC;AAE7B;;;;GAIG;AACH,MAAM,WAAW,WAAW;IACxB,6DAA6D;IAC7D,QAAQ,CAAC,MAAM,CAAC,EAAE,WAAW,GAAG,IAAI,GAAG,SAAS,CAAC;IACjD,2DAA2D;IAC3D,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,KAAK,IAAI,CAAC,GAAG,IAAI,GAAG,SAAS,CAAC;IAC5F,qGAAqG;IACrG,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C;;;OAGG;IACH,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,GAAG,IAAI,CAAC,GAAG,SAAS,CAAC;CAC7E;AAQD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAM9D;AA2MD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,UAAU,GAAG,MAAM,CAMzD;AA8BD;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,WAAW,CAQlE;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,WAAW,GAAG,MAAM,GAAG,IAAI,CAQ7D;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,WAAW,GAAG,IAAI,GAAG,SAAS,GAAG,IAAI,CAU3E;AAgBD;;;;;;;;;;GAUG;AACH,wBAAuB,UAAU,CAC7B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,OAAO,GAAE,WAAgB,GAC1B,cAAc,CAAC,MAAM,EAAE,IAAI,EAAE,SAAS,CAAC,CAmGzC;AA4CD;;;;;;GAMG;AACH,wBAAsB,QAAQ,CAC1B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,OAAO,GAAE,WAAgB,GAC1B,OAAO,CAAC,MAAM,CAAC,CAWjB;AAED;;;;;;GAMG;AACH,qBAAa,UAAW,YAAW,aAAa,CAAC,MAAM,CAAC;IACpD,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAc;IAEpC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAsB;IAE7C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAc;IAEtC,OAAO,CAAC,UAAU,CAAK;IAEvB;;;;;OAKG;gBACS,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,mBAAmB,EAAE,OAAO,GAAE,WAAgB;IAMtF;;;OAGG;IACH,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED;;;;OAIG;IACI,CAAC,MAAM,CAAC,aAAa,CAAC,IAAI,cAAc,CAAC,MAAM,EAAE,IAAI,EAAE,SAAS,CAAC;CAoE3E"}

package/dist/src/common/input.js

@@ -208,6 +208,22 @@ function startsWithUtf8(bytes) {
         return false;
     }
 }
+/**
+ * A zip entry name as text (APPNOTE 4.4.17): UTF-8 when the bytes are valid UTF-8, whether or not
+ * the entry sets the language-encoding flag (bit 11), else windows-1252 (WHATWG has no CP437, and
+ * session entry names are ASCII in practice). Never throws: a name is a matching key, never a path,
+ * so an undecodable one still has to name its entry.
+ * @param bytes - the name bytes from the central directory or a local header
+ * @returns the name
+ */
+export function decodeEntryName(bytes) {
+    try {
+        return new TextDecoder("utf-8", { fatal: true, ignoreBOM: true }).decode(bytes);
+    }
+    catch {
+        return new TextDecoder("windows-1252").decode(bytes);
+    }
+}
 /**
  * Join byte chunks.
  * @param chunks - the chunks

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

@@ -1 +1 @@
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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 @@
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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/common/options.d.ts

@@ -5,7 +5,7 @@
  * `weightFrom`, `addMissingNodes`) supplied by the importer that calls resolveImportOptions().
  */
 import { type DuplicatePolicy, type GraphSink, type IdCoercion } from "@graphty/graph-format";
-import { type CommonExportOptions, type CommonImportOptions } from "../types.js";
+import { type CommonExportOptions, type CommonImportOptions, type GraphChoiceOptions } from "../types.js";
 import { SINK_OPTION_CODE } from "./codes.js";
 import { type ImportReportBuilder } from "./report.js";
 /** The defaults an importer supplies for the options whose default is per format (design section 8.4). */
@@ -93,6 +93,17 @@ export declare function reportSinkOptions(sink: GraphSink, options: CommonImport
  * @returns the number of warnings recorded
  */
 export declare function reportUnusedOptions(options: CommonImportOptions | undefined, report: ImportReportBuilder, used: ReadonlySet<keyof CommonImportOptions>): number;
+/**
+ * The graph an importer reads from an input that holds several: the one `graphIndex` or
+ * `graphName` names, else the first. A choice that names no graph is E_GRAPH_NOT_FOUND, a name two
+ * graphs share is E_AMBIGUOUS_GRAPH_NAME, and an input with no graph at all is E_NO_GRAPH, each
+ * fatal (the report fails with ImportError).
+ * @param names - each graph's name (null for an unnamed graph), in document order
+ * @param options - the caller's graphIndex / graphName
+ * @param report - the report a failure is recorded in
+ * @returns the index of the graph to read; E_UNSUPPORTED for an option of the wrong type, or both
+ */
+export declare function chooseGraph(names: readonly (string | null)[], options: GraphChoiceOptions | undefined, report: ImportReportBuilder): number;
 /**
  * Apply the design section 8.4 defaults to an importer's common options and check every enum
  * value. Format-specific options in the same object are ignored here.

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

@@ -1 +1 @@
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package/dist/src/common/options.js

@@ -5,7 +5,7 @@
  * `weightFrom`, `addMissingNodes`) supplied by the importer that calls resolveImportOptions().
  */
 import { GraphFormatError } from "@graphty/graph-format";
-import { OPTION_IGNORED_CODE, SINK_OPTION_CODE } from "./codes.js";
+import { AMBIGUOUS_GRAPH_NAME_CODE, GRAPH_NOT_FOUND_CODE, NO_GRAPH_CODE, OPTION_IGNORED_CODE, SINK_OPTION_CODE, } from "./codes.js";
 import { canonicalEncoding } from "./input.js";
 const ID_COERCIONS = new Set(["keep", "canonical", "string", "number"]);
 const NODE_ID_SOURCES = new Set(["id", "label", "index"]);
@@ -97,6 +97,56 @@ export function reportUnusedOptions(options, report, used) {
     }
     return recorded;
 }
+/**
+ * The graph an importer reads from an input that holds several: the one `graphIndex` or
+ * `graphName` names, else the first. A choice that names no graph is E_GRAPH_NOT_FOUND, a name two
+ * graphs share is E_AMBIGUOUS_GRAPH_NAME, and an input with no graph at all is E_NO_GRAPH, each
+ * fatal (the report fails with ImportError).
+ * @param names - each graph's name (null for an unnamed graph), in document order
+ * @param options - the caller's graphIndex / graphName
+ * @param report - the report a failure is recorded in
+ * @returns the index of the graph to read; E_UNSUPPORTED for an option of the wrong type, or both
+ */
+export function chooseGraph(names, options, report) {
+    const { graphIndex, graphName } = options ?? {};
+    if (graphIndex !== undefined &&
+        (typeof graphIndex !== "number" || !Number.isInteger(graphIndex) || graphIndex < 0)) {
+        throw new GraphFormatError("E_UNSUPPORTED", `option graphIndex: ${describe(graphIndex)} is not a non-negative integer`, {
+            option: "graphIndex",
+            found: graphIndex,
+        });
+    }
+    if (graphName !== undefined && typeof graphName !== "string") {
+        throw new GraphFormatError("E_UNSUPPORTED", `option graphName: ${describe(graphName)} is not a string`, {
+            option: "graphName",
+            found: graphName,
+        });
+    }
+    if (graphIndex !== undefined && graphName !== undefined) {
+        throw new GraphFormatError("E_UNSUPPORTED", "options graphIndex and graphName both choose a graph; pass one", {
+            option: "graphName",
+            found: graphName,
+        });
+    }
+    if (names.length === 0) {
+        return report.fail(NO_GRAPH_CODE, "the input holds no graph");
+    }
+    if (graphName !== undefined) {
+        const matches = names.flatMap((name, i) => (name === graphName ? [i] : []));
+        if (matches.length > 1) {
+            return report.fail(AMBIGUOUS_GRAPH_NAME_CODE, `graphName ${JSON.stringify(graphName)} names the graphs at indexes ${matches.join(", ")}; pass graphIndex`, { element: graphName });
+        }
+        if (matches.length === 0) {
+            return report.fail(GRAPH_NOT_FOUND_CODE, `graphName ${JSON.stringify(graphName)} names none of the ${names.length} graph(s)`, { element: graphName }, { names: [...names] });
+        }
+        return matches[0];
+    }
+    const index = graphIndex ?? 0;
+    if (index >= names.length) {
+        return report.fail(GRAPH_NOT_FOUND_CODE, `graphIndex ${index} is beyond the ${names.length} graph(s)`);
+    }
+    return index;
+}
 /**
  * Apply the design section 8.4 defaults to an importer's common options and check every enum
  * value. Format-specific options in the same object are ignored here.