@graphty/graph-io 0.3.32 → 0.3.34

package/dist/chunks/{exporter-BOLJIzvA.js → exporter-CkPnJCXU.js}

@@ -1,6 +1,6 @@
 import { GraphFormatError, INVALID_INDEX } from "@graphty/graph-format";
-import { S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, R as ROLE_TAKEN_CODE, ay as RENAMED_CODE, I as ID_MERGED_CODE, i as DANGLING_REFERENCE_CODE, g as UNKNOWN_ELEMENT_CODE, o as DUPLICATE_ATTRIBUTE_CODE, n as DUPLICATE_NODE_CODE, a3 as BAD_VALUE_CODE, t as MISSING_ID_CODE, w as UNKNOWN_ENCODING_CODE, x as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, E as EMPTY_INPUT_CODE, F as ELEMENT_ISSUE, G as INPUT_ISSUE, al as resolveImportOptions, a8 as ImportReportBuilder, ao as reportSinkOptions, an as reportUnusedOptions, am as throwIfAborted, b as plural, a1 as declareResolved, ar as IdCoercer, aq as DirectionResolver, $ as agree, az as LineReader, c as capabilities, L as LOSS, au as ROLE_ASSUMED_CODE, aA as NODE_ORDER_CODE, aB as GRAPH_COLUMN_AS_METADATA_CODE, aC as TYPEDEF_NODES_CODE, aD as RELATION_ASSUMED_CODE, at as COLUMN_AS_PROPERTY_VALUE_CODE, r as resolveExportOptions, p as pairFolding, e as explicitWeights, av as formatNumber } from "./export-ZucVKiU4.js";
-import { S as SYNONYM_SCOPES, O as OBO_NODE_COLUMNS, o as oboColumnDecl, P as PLACEHOLDER_COLUMN, f as framelessNodes, m as movedNodes, s as slotColumn, c as capabilityNotes, e as emptyColumnNotes, a as cellOf, F as FRAME_KINDS$1, U as UNWRITTEN_ROLES, n as notePropertyColumn, b as fitsVocabulary, i as isQualifierRecord, t as textOf } from "./ontology-export-BRErBO6J.js";
+import { S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, R as ROLE_TAKEN_CODE, ay as RENAMED_CODE, I as ID_MERGED_CODE, i as DANGLING_REFERENCE_CODE, g as UNKNOWN_ELEMENT_CODE, o as DUPLICATE_ATTRIBUTE_CODE, n as DUPLICATE_NODE_CODE, a3 as BAD_VALUE_CODE, t as MISSING_ID_CODE, w as UNKNOWN_ENCODING_CODE, x as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, E as EMPTY_INPUT_CODE, F as ELEMENT_ISSUE, G as INPUT_ISSUE, al as resolveImportOptions, a8 as ImportReportBuilder, ao as reportSinkOptions, an as reportUnusedOptions, am as throwIfAborted, b as plural, a1 as declareResolved, ar as IdCoercer, aq as DirectionResolver, $ as agree, az as LineReader, c as capabilities, L as LOSS, au as ROLE_ASSUMED_CODE, aA as NODE_ORDER_CODE, aB as GRAPH_COLUMN_AS_METADATA_CODE, aC as TYPEDEF_NODES_CODE, aD as RELATION_ASSUMED_CODE, at as COLUMN_AS_PROPERTY_VALUE_CODE, r as resolveExportOptions, p as pairFolding, e as explicitWeights, av as formatNumber } from "./export-Cbt4h_0n.js";
+import { S as SYNONYM_SCOPES, O as OBO_NODE_COLUMNS, o as oboColumnDecl, P as PLACEHOLDER_COLUMN, f as framelessNodes, m as movedNodes, s as slotColumn, c as capabilityNotes, e as emptyColumnNotes, a as cellOf, F as FRAME_KINDS$1, U as UNWRITTEN_ROLES, n as notePropertyColumn, b as fitsVocabulary, i as isQualifierRecord, t as textOf } from "./ontology-export-p1PsPenq.js";
 import { j as joinText, e as encodeChunks } from "./writer-DxjgHwSe.js";
 const ESCAPES = Object.freeze({
   n: "\n",
@@ -68,23 +68,36 @@ function splitTagValue(line) {
   }
   return null;
 }
+const COMMENT_MARKS = String.raw`\"!`;
+const BRACE_MARKS = String.raw`\"[]{}`;
 function stripComment(rest) {
   let quoted = false;
-  for (let i = 0; i < rest.length; i++) {
+  const found = [-2, -2, -2];
+  let i = nextOf(rest, 0, COMMENT_MARKS, found);
+  while (i >= 0) {
     const ch = rest.charAt(i);
-    if (ch === "\\") {
-      i++;
-      continue;
-    }
     const atStart = i === 0 || rest.charAt(i - 1) === " " || rest.charAt(i - 1) === "	";
     if (ch === '"' && (quoted || atStart)) {
       quoted = !quoted;
     } else if (ch === "!" && !quoted && atStart) {
       return rest.slice(0, i).trimEnd();
     }
+    i = nextOf(rest, ch === "\\" ? i + 2 : i + 1, COMMENT_MARKS, found);
   }
   return rest.trimEnd();
 }
+function nextOf(text, from, marks, found) {
+  let nearest = -1;
+  for (let k = 0; k < marks.length; k++) {
+    if (found[k] !== -1 && found[k] < from) {
+      found[k] = text.indexOf(marks.charAt(k), from);
+    }
+    if (found[k] !== -1 && (nearest === -1 || found[k] < nearest)) {
+      nearest = found[k];
+    }
+  }
+  return nearest;
+}
 function splitQualifiers(value) {
   if (!value.endsWith("}")) {
     return { value, qualifiers: null, badBlock: null };
@@ -338,17 +351,18 @@ function parseXrefList(inner) {
 function hasStrayBrace(value) {
   let quoted = false;
   let listed = false;
-  for (let i = 0; i < value.length; i++) {
+  const found = [-2, -2, -2, -2, -2, -2];
+  let i = nextOf(value, 0, BRACE_MARKS, found);
+  while (i >= 0) {
     const ch = value.charAt(i);
-    if (ch === "\\") {
-      i++;
-    } else if (ch === '"') {
+    if (ch === '"') {
       quoted = !quoted;
     } else if (!quoted && (ch === "[" || ch === "]")) {
       listed = ch === "[";
     } else if (!quoted && !listed && (ch === "{" || ch === "}")) {
       return true;
     }
+    i = nextOf(value, ch === "\\" ? i + 2 : i + 1, BRACE_MARKS, found);
   }
   return false;
 }
@@ -2102,6 +2116,8 @@ const OBO_LOSS = Object.freeze({
   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: TYPEDEF_NODES_CODE,
+  /** A graph without a node `type` column is written as `[Term]` frames and reads back with a `type` column holding Term. */
+  TYPE_GAINED: "W_OBO_TYPE_GAINED",
   /** 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",
   /**
@@ -2691,6 +2707,14 @@ function plan(snapshot, options) {
     }
   }
   const { kinds, type } = planKinds(snapshot, frameless);
+  if (rows.length > 0 && !snapshot.nodes.has("type")) {
+    note(
+      OBO_LOSS.TYPE_GAINED,
+      `${rows.length} node${plural(rows.length)} ${agree(rows.length, "is", "are")} written as [Term] frames and ${agree(rows.length, "reads", "read")} back with the type Term in a new node column "type"`,
+      null,
+      rows.length
+    );
+  }
   const typedefNodes = rows.filter((i) => kinds[i] === "Typedef").length;
   if (typedefNodes > 0) {
     note(
@@ -3462,4 +3486,4 @@ export {
   oboImporter as c,
   oboExporter as o
 };
-//# sourceMappingURL=exporter-BOLJIzvA.js.map
+//# sourceMappingURL=exporter-CkPnJCXU.js.map