@graphty/graph-io 0.3.18 → 0.3.20

package/dist/src/formats/cx2/exporter.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/cx2/importer.d.ts

@@ -0,0 +1,169 @@
+/**
+ * The CX2 importer (design/graph-io/cytoscape-and-obo/design.md section 1.3; the feature and error
+ * inventory is research-cx2.md): the JSON exchange format of NDEx, Cytoscape 3.10+ and Cytoscape
+ * Web. A CX2 document is one array: a descriptor (`CXVersion`), aspect blocks (`nodes`, `edges`,
+ * `attributeDeclarations`, `networkAttributes`, `nodeBypasses`, `visualProperties`, opaque
+ * aspects) and a final `status`.
+ *
+ * The document is read through the streaming scanner of common/json-elements.ts, so its text is
+ * never held as one string; the parsed aspect elements are collected and the graph is built at the
+ * end, which makes every aspect order the format allows (declarations after the nodes, edges
+ * before their nodes) read the same.
+ *
+ * Mapping: every edge is directed (CX2 has no undirected edge); node ids follow the CX id rule
+ * (design section 1.0.2); declared attributes become typed columns named by their full name, with
+ * the alias in `origin.id` and the declared default in `meta.default`; `name` is the label; node
+ * `x` / `y` become the position column with y flipped to y-up, `z` the `z` column; per-element
+ * bypasses become one column per visual property (origin namespace "cx2.bypass"); style rules
+ * (`visualProperties`, `visualEditorProperties`) and every opaque aspect are kept verbatim in
+ * `meta.extra.cx2.opaque` and are not applied (W_STYLES_NOT_IMPORTED, issue #706).
+ */
+import { type GraphImporter } from "../../types.js";
+/** The format name. */
+export declare const CX2_FORMAT = "cx2";
+/** The node attribute the exporter's `sanitizeIds: "mangle"` keeps an original id in. */
+export declare const ORIGINAL_ID_ATTRIBUTE = "graphty:originalId";
+/** The origin namespace of the per-element visual property columns. */
+export declare const BYPASS_NAMESPACE = "cx2.bypass";
+/** The format-specific options of the CX2 importer. */
+export interface Cx2ImportOptions {
+    /**
+     * Where a node's `z` goes: "column" (default) keeps it in the f64 node column `z` (Cytoscape
+     * writes a stacking order there); "position" makes it the third component of the position.
+     */
+    zAs?: "column" | "position" | undefined;
+}
+/**
+ * The issue codes the CX2 importer records (design section 1.3), by name: the codes shared with
+ * the other importers (src/common/codes.ts) and the CX2-specific ones. A key is the code without
+ * its severity and format prefixes.
+ */
+export declare const CX2_ISSUE: Readonly<{
+    /** The input is empty (fatal). */
+    EMPTY_INPUT: "E_EMPTY_INPUT";
+    /** The text is not JSON (fatal). */
+    SYNTAX: "E_SYNTAX";
+    /** Invalid UTF-8 (fatal). */
+    INVALID_UTF8: "E_INVALID_UTF8";
+    /** Invalid bytes in the encoding a BOM or the encoding option chose (fatal). */
+    INVALID_ENCODING: "E_INVALID_ENCODING";
+    /** Bytes that are not UTF-8 were read as windows-1252. */
+    ENCODING_FALLBACK: "W_ENCODING_FALLBACK";
+    /** An encoding the platform cannot decode was ignored. */
+    UNKNOWN_ENCODING: "W_UNKNOWN_ENCODING";
+    /** The document is not an array or does not start with a descriptor holding CXVersion (fatal). */
+    NO_DESCRIPTOR: "E_CX2_NO_DESCRIPTOR";
+    /** CXVersion names a major version other than 2 (fatal); "1.x" says the file is CX1. */
+    VERSION: "E_CX2_VERSION";
+    /** CXVersion is a 2.x other than "2.0" (or not a string); the document is read. */
+    MINOR_VERSION: "W_CX2_MINOR_VERSION";
+    /** The document has no status block, or a malformed one. */
+    NO_STATUS: "E_CX2_NO_STATUS";
+    /** The producer marked the document as failed (fatal). */
+    STATUS_FAILED: "E_STATUS_FAILED";
+    /** The producer marked the document as successful with an error text. */
+    STATUS_WARNING: "W_STATUS_WARNING";
+    /** An aspect appears in several blocks although the descriptor does not declare fragments. */
+    UNDECLARED_FRAGMENTS: "W_CX2_UNDECLARED_FRAGMENTS";
+    /** An attribute declared twice with two different types; the first declaration wins. */
+    DECLARATION_CONFLICT: "E_CX2_DECLARATION_CONFLICT";
+    /** An attribute value whose name no declaration covers; its column is inferred. */
+    UNDECLARED_ATTRIBUTE: "W_CX2_UNDECLARED_ATTRIBUTE";
+    /** A node or edge attribute named `id`, which the specification reserves. */
+    RESERVED_KEY: "W_CX2_RESERVED_KEY";
+    /** An alias that is another attribute's name or another attribute's alias; the alias is ignored. */
+    ALIAS_CONFLICT: "E_CX2_ALIAS_CONFLICT";
+    /** A network attribute declaration with an alias or a default, which CX2 forbids; both ignored. */
+    NETWORK_DECLARATION: "W_CX2_NETWORK_DECLARATION";
+    /** An aspect that holds one element holds several; the first is read. */
+    EXTRA_ELEMENTS: "W_CX2_EXTRA_ELEMENTS";
+    /** Some nodes have coordinates and others none, or a node has x without y. */
+    PARTIAL_LAYOUT: "W_CX2_PARTIAL_LAYOUT";
+    /** A full attribute name used where its alias is declared; read as the same attribute. */
+    ALIAS_BYPASSED: "W_CX2_ALIAS_BYPASSED";
+    /** A CX1 cartesianLayout aspect next to node coordinates; kept, not applied. */
+    LEGACY_LAYOUT: "W_CX2_LEGACY_LAYOUT";
+    /** The file's style rules are not applied (issue #706). */
+    STYLES_NOT_IMPORTED: "W_STYLES_NOT_IMPORTED";
+    /** A member of the top-level array that is not a one-key aspect block, or an element that is not an object. */
+    BAD_ASPECT_BLOCK: "E_BAD_ASPECT_BLOCK";
+    /** An aspect out of its place (after the post-metadata or the status, a third metaData, late declarations). */
+    ASPECT_ORDER: "W_ASPECT_ORDER";
+    /** A metaData element count disagrees with what was read. */
+    COUNT_MISMATCH: "W_COUNT_MISMATCH";
+    /** A value that does not match its declared type; the cell is unset. */
+    BAD_VALUE: "E_BAD_VALUE";
+    /** A declared default that does not match its type. */
+    BAD_DEFAULT: "W_BAD_DEFAULT";
+    /** A declared type CX2 does not define; the column is inferred from the values. */
+    UNKNOWN_ATTR_TYPE: "W_UNKNOWN_ATTR_TYPE";
+    /** A bypass or a layout entry naming no node or edge. */
+    DANGLING_REFERENCE: "W_DANGLING_REFERENCE";
+    /** The same attribute twice on one element (its alias and its full name). */
+    DUPLICATE_ATTRIBUTE: "W_DUPLICATE_ATTRIBUTE";
+    /** A node without an id. */
+    MISSING_ID: "E_MISSING_ID";
+    /** An edge without s or t. */
+    MISSING_ENDPOINT: "E_MISSING_ENDPOINT";
+    /** A node id declared twice; the second merges into the first. */
+    DUPLICATE_NODE: "W_DUPLICATE_NODE";
+    /** An edge id declared twice; the second edge is skipped. */
+    DUPLICATE_EDGE_ID: "E_DUPLICATE_EDGE_ID";
+    /** An id that is not an integer. */
+    INVALID_ID: "E_INVALID_ID";
+    /** An edge endpoint naming no node (addMissingNodes false, the default). */
+    UNKNOWN_NODE: "E_UNKNOWN_NODE";
+    /** A weight that is not a number. */
+    INVALID_WEIGHT: "E_INVALID_WEIGHT";
+    /** An id spelled as a string or a non-integer literal; read as the integer. */
+    ID_TEXT_TYPE: "W_ID_TEXT_TYPE";
+    /** An integer beyond 2^53: an id kept as its digits, a value stored as the nearest f64. */
+    PRECISION: "W_PRECISION";
+    /** Two id texts merged under `ids: "number"`. */
+    ID_MERGED: "W_ID_MERGED";
+    /** An element key CX2 does not define. */
+    UNKNOWN_ELEMENT: "W_UNKNOWN_ELEMENT";
+    /** A column renamed because its name was taken. */
+    COLUMN_RENAMED: "W_COLUMN_RENAMED";
+    /** A column that lost its role because another column holds it. */
+    ROLE_TAKEN: "W_ROLE_TAKEN";
+    /** The sink refused the direction. */
+    DIRECTION_REFUSED: "W_DIRECTION_REFUSED";
+    /** Edges forced to the policy's direction. */
+    DIRECTION_FORCED: "W_DIRECTION_FORCED";
+    /** A common option CX2 has no use for. */
+    OPTION_IGNORED: "W_OPTION_IGNORED";
+    /** A builder option the caller's sink does not honour. */
+    SINK_OPTION: "W_SINK_OPTION";
+    /** The input is beyond a size limit (fatal). */
+    TOO_LARGE: "E_TOO_LARGE";
+}>;
+/** The canonical CX2 scalar types. */
+type Cx2Scalar = "string" | "long" | "integer" | "double" | "boolean";
+/** A declared CX2 type. */
+interface Cx2Type {
+    /** The canonical type text (`list_of_double`). */
+    readonly d: string;
+    /** The scalar (or item) type. */
+    readonly scalar: Cx2Scalar;
+    /** Whether the type is a list. */
+    readonly list: boolean;
+}
+/**
+ * Resolve a declared type text.
+ * @param d - the `d` value
+ * @returns the type, or null when CX2 does not define it
+ */
+export declare function cx2Type(d: string): Cx2Type | null;
+/**
+ * Resolve the zAs option.
+ * @param value - the option
+ * @returns the mode; E_UNSUPPORTED for any other value
+ */
+export declare function zAsOption(value: unknown): "column" | "position";
+/**
+ * The CX2 importer plugin (design section 1.3).
+ */
+export declare const cx2Importer: GraphImporter<Cx2ImportOptions>;
+export {};
+//# sourceMappingURL=importer.d.ts.map

package/dist/src/formats/cx2/importer.d.ts.map

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