@graphty/graph-io 0.3.25 → 0.3.26

package/dist/src/formats/obo/exporter.d.ts

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+/**
+ * The OBO exporter: writes a snapshot as an OBO 1.4 flat file, the text format of the Gene
+ * Ontology and the OBO Foundry ontologies.
+ *
+ * Every node is a frame (`[Term]`, or `[Instance]` / `[Typedef]` from the `type` column) in node
+ * order; every edge is a clause on its source's frame: `is_a: T` for the relation `is_a`,
+ * `instance_of: T` on an Instance, `relationship: R T` for anything else, an edge without a
+ * relation as `is_a` (the `relation` option). The columns of the OBO vocabulary
+ * (src/common/ontology.ts: `name`, `namespace`, `def`, `synonym`, `xref`, ...) are written back
+ * as their tags; any other node column becomes `property_value: <column> "<value>" xsd:<type>`
+ * lines (with a `[Typedef]` declaring the column as a metadata relation), any other edge column a
+ * qualifier of the edge's clause. A placeholder node (`graphty.placeholder`, a target no frame
+ * declared) gets no frame, so the re-import makes it again. The header, the Typedefs and the
+ * unknown frames an OBO import kept in `meta.extra.obo` are written back.
+ *
+ * check() predicts every difference the OBO importer produces on re-import: a vocabulary column
+ * whose values the file cannot carry exactly is written as `property_value` lines instead and
+ * reported, never written half right.
+ */
+import { type CommonExportOptions, type ExportCapabilities, type GraphExporter } from "../../types.js";
+/**
+ * The format-specific options of the OBO exporter.
+ * @category Built-in formats
+ */
+export interface OboExportOptions extends CommonExportOptions {
+    /**
+     * The relation written for an edge that has none of its own (no `relation` value): an OBO id
+     * such as `is_a` or `part_of`. Reasoners and ROBOT read `is_a` as subclassing.
+     * @defaultValue "is_a"
+     */
+    relation?: string | undefined;
+    /**
+     * The `ontology` id written in the header, such as `go` or `uberon`. It may hold letters,
+     * digits and `_ . - /`; any other character makes checkExport() and the save throw
+     * E_UNSUPPORTED. The default is the id an OBO import read, else the graph name with every other
+     * character replaced by `_`, else no `ontology` line.
+     * @defaultValue as read, else the graph name
+     */
+    ontology?: string | undefined;
+}
+/**
+ * The loss notes the OBO exporter's check() returns, by name. A key is the code without its
+ * severity and format prefixes.
+ * @category Built-in formats
+ */
+export declare const OBO_LOSS: Readonly<{
+    /** A node column outside the OBO vocabulary (or one whose values a tag cannot carry exactly) reads back inside the `property_value` column. */
+    COLUMN_AS_PROPERTY_VALUE: "W_COLUMN_AS_PROPERTY_VALUE";
+    /** An edge column (or the explicit weights) reads back inside the `qualifiers` column. */
+    EDGE_COLUMN_AS_QUALIFIER: "W_OBO_EDGE_COLUMN_AS_QUALIFIER";
+    /** Every edge is written from its source to its target, so an undirected graph reads back as directed. */
+    UNDIRECTED_AS_DIRECTED: "W_OBO_UNDIRECTED_AS_DIRECTED";
+    /** Two identical clauses on one frame (parallel edges with one relation and the same qualifiers, a repeated list item) read back as one. */
+    DUPLICATE_CLAUSE: "W_OBO_DUPLICATE_CLAUSE";
+    /** An edge without a relation is written with the `relation` option (default `is_a`). */
+    RELATION_ASSUMED: "W_RELATION_ASSUMED";
+    /** A relation that is not an OBO id (empty, or holding a space, `!`, `{` or `}`) is written with `_` in place of those characters. */
+    RELATION_RENAMED: "W_OBO_RELATION_RENAMED";
+    /** The graph name is not an ontology id; the header `ontology` is written with `_` in place of the other characters. */
+    ONTOLOGY_NAME: "W_OBO_ONTOLOGY_NAME";
+    /** `[Typedef]` frames read back as nodes only under the importer's `typedefs: "nodes"`; by default they are metadata. */
+    TYPEDEF_NODES: "W_TYPEDEF_NODES";
+    /** Edges are written in the frame of their source node, so they read back grouped by source, in node order. */
+    EDGE_ORDER: "W_OBO_EDGE_ORDER";
+    /**
+     * A graph attribute is written as a header `property_value` and reads back in `snapshot.meta.extra.obo.header`,
+     * not as a graph attribute.
+     */
+    GRAPH_COLUMN_AS_METADATA: "W_GRAPH_COLUMN_AS_METADATA";
+    /** A carriage return or form feed in a text cannot be written; it is written as a line feed. */
+    LINE_END: "W_OBO_LINE_END";
+    /** The nodes read back in a different order. */
+    NODE_ORDER: "W_NODE_ORDER";
+    /** A mutual pair is written as two clauses without its mark. */
+    MUTUAL_EXPANDED: "W_MUTUAL_EXPANDED";
+    /**
+     * The undirected edges of a mixed graph are written the way `onMixedDirection` chose ("directed" or "undirected").
+     */
+    MIXED_DIRECTION: "W_MIXED_DIRECTION";
+    /**
+     * The graph has both directed and undirected edges and `onMixedDirection` is "error". An import stops; a save to a
+     * format that holds one direction per file fails with E_DIRECTED. Pass "directed" or "undirected" to read or write
+     * it anyway.
+     */
+    MIXED_DIRECTION_ERROR: "E_MIXED_DIRECTION";
+    /** OBO has no edge ids. */
+    EDGE_IDS_DROPPED: "W_EDGE_IDS_DROPPED";
+    /** OBO has no positions. */
+    POSITIONS_DROPPED: "W_POSITIONS_DROPPED";
+    /** OBO has no containment. */
+    HIERARCHY_DROPPED: "W_HIERARCHY_DROPPED";
+    /** OBO has no time. */
+    TEMPORAL_DROPPED: "W_TEMPORAL_DROPPED";
+    /** OBO has no visual columns. */
+    VIZ_DROPPED: "W_VIZ_DROPPED";
+    /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */
+    ROLE_DROPPED: "W_ROLE_DROPPED";
+    /**
+     * An attribute without a role is written where the format keeps a role (for example, a `name` column as the label), and
+     * reads back with that role.
+     */
+    ROLE_ASSUMED: "W_ROLE_ASSUMED";
+    /**
+     * An attribute with a role (for example, the label) is written where the format keeps that role, and reads back under the
+     * name the format's importer gives it.
+     */
+    COLUMN_NAME_CHANGED: "W_COLUMN_NAME_CHANGED";
+    /**
+     * An OBO attribute stored as text where graph-io uses a dictionary (or the other way round); it reads back with
+     * graph-io's usual type. The values are the same.
+     */
+    DTYPE_UNSUPPORTED: "W_DTYPE_UNSUPPORTED";
+    /** A column without a value on any written element reads back absent. */
+    EMPTY_COLUMN_DROPPED: "W_EMPTY_COLUMN_DROPPED";
+    /** A declared default: OBO has none. */
+    DEFAULT_DROPPED: "W_DEFAULT_DROPPED";
+    /** Declared options: OBO has no enumerations. */
+    OPTIONS_DROPPED: "W_OPTIONS_DROPPED";
+    /** An extension table OBO cannot carry. */
+    EXTENSION_TABLE_DROPPED: "W_EXTENSION_TABLE_DROPPED";
+    /**
+     * Node ids the format cannot write, under `sanitizeIds: "error"`; the save fails with E_INVALID_ID. Pass
+     * `sanitizeIds: "mangle"` to rewrite them.
+     */
+    ID_CHARSET: "E_ID_CHARSET";
+    /** Node ids OBO cannot write as they are, under sanitizeIds "mangle": rewritten, the original kept. */
+    ID_MANGLED: "W_ID_MANGLED";
+    /** Numeric ids are written as text and read back as strings. */
+    ID_TEXT_TYPE: "W_ID_TEXT_TYPE";
+    /**
+     * Two node ids would be written as the same text (the number 5 and the text "5"); the save fails with
+     * E_INVALID_ID.
+     */
+    ID_TEXT_COLLISION: "E_ID_TEXT_COLLISION";
+}>;
+/**
+ * What the OBO flat file keeps: a directed multigraph with self-loops and any id (the exporter's
+ * own rule refuses whitespace, control characters, `!`, `{` and `}`). No column of the snapshot's own reads back as
+ * a column: the file keeps the OBO vocabulary (`name`, `def`, `synonym`, ... with their own
+ * types) and writes every other node column as property values and every edge column as
+ * qualifiers, which check() reports column by column.
+ * @category Built-in formats
+ */
+export declare const OBO_CAPABILITIES: ExportCapabilities;
+/**
+ * The OBO exporter plugin.
+ * @category Built-in formats
+ */
+export declare const oboExporter: GraphExporter<OboExportOptions>;
+//# sourceMappingURL=exporter.d.ts.map

package/dist/src/formats/obo/exporter.d.ts.map

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