npm - @cyanheads/interpro-mcp-server - Versions diffs - 0.1.1 → 0.1.3 - Mend

@cyanheads/interpro-mcp-server 0.1.1 → 0.1.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (40) hide show

package/dist/services/interpro/description-text.js ADDED Viewed

@@ -0,0 +1,179 @@
+/**
+ * @fileoverview Readable projection of InterPro HTML description fragments.
+ * @module services/interpro/description-text
+ */
+import { Tokenizer } from 'htmlparser2';
+const PARAGRAPHS = new Set([
+    'p',
+    'div',
+    'section',
+    'article',
+    'blockquote',
+    'pre',
+    'h1',
+    'h2',
+    'h3',
+    'h4',
+    'h5',
+    'h6',
+    'table',
+    'dl',
+]);
+const REFERENCES = /\b(?:IPR[0-9]{6}|PUB[0-9]+)\b/gi;
+/** Decode description fragments without executing markup or changing the source description. */
+export function descriptionText(description) {
+    const fragments = typeof description === 'string'
+        ? [description]
+        : Array.isArray(description)
+            ? description.flatMap((item) => item && typeof item === 'object' && 'text' in item && typeof item.text === 'string'
+                ? [item.text]
+                : [])
+            : [];
+    const rendered = fragments
+        .map((fragment) => {
+        const chunks = [];
+        let pending = '';
+        let bullet = false;
+        let listDepth = 0;
+        let suppressed;
+        let openingTag = '';
+        let attributeName = '';
+        let attributeChunks = [];
+        let href;
+        let anchor;
+        const boundary = (separator) => {
+            const rank = (value) => value === '\n\n' ? 4 : value === '\n' ? 3 : value === '\t' ? 2 : value === ' ' ? 1 : 0;
+            if (rank(separator) > rank(pending))
+                pending = separator;
+        };
+        const open = (name) => {
+            if (name === 'script' || name === 'style')
+                suppressed = name;
+            if (suppressed)
+                return;
+            if (name === 'a') {
+                closeAnchor();
+                if (href)
+                    anchor = { href, text: [] };
+            }
+            if (name === 'ul' || name === 'ol') {
+                if (!listDepth)
+                    boundary('\n\n');
+                listDepth += 1;
+            }
+            else if (name === 'li') {
+                boundary('\n');
+                bullet = true;
+            }
+            else if (PARAGRAPHS.has(name))
+                boundary('\n\n');
+            else if (name === 'br' || name === 'tr' || name === 'dt' || name === 'dd')
+                boundary('\n');
+        };
+        const append = (value) => {
+            if (suppressed)
+                return;
+            anchor?.text.push(value);
+            const normalized = value.replace(/[\t\n\f\r ]+/g, ' ');
+            const text = normalized.trim();
+            if (text) {
+                if (chunks.length)
+                    chunks.push(pending || (normalized.startsWith(' ') ? ' ' : ''));
+                if (bullet)
+                    chunks.push('- ');
+                chunks.push(text);
+                pending = normalized.endsWith(' ') ? ' ' : '';
+                bullet = false;
+            }
+            else if (normalized)
+                boundary(' ');
+        };
+        const closeAnchor = () => {
+            if (!anchor)
+                return;
+            const visible = new Set([...anchor.text.join('').matchAll(REFERENCES)].map(([token]) => token.toUpperCase()));
+            const references = new Set([...anchor.href.matchAll(REFERENCES)].map(([token]) => token.toUpperCase()));
+            anchor = undefined;
+            const missing = [...references].filter((token) => !visible.has(token));
+            if (missing.length)
+                append(` (${missing.join(', ')})`);
+        };
+        const close = (name) => {
+            if (name === suppressed) {
+                suppressed = undefined;
+                return;
+            }
+            if (suppressed)
+                return;
+            if (name === 'a')
+                closeAnchor();
+            if (name === 'ul' || name === 'ol') {
+                listDepth = Math.max(0, listDepth - 1);
+                boundary(listDepth ? '\n' : '\n\n');
+            }
+            else if (name === 'li') {
+                bullet = false;
+                boundary('\n');
+            }
+            else if (PARAGRAPHS.has(name))
+                boundary('\n\n');
+            else if (name === 'tr' || name === 'dt' || name === 'dd')
+                boundary('\n');
+            else if (name === 'td' || name === 'th')
+                boundary('\t');
+        };
+        /** Token callbacks need no open-element stack; even deeply nested fragments stay streaming. */
+        const tokenizer = new Tokenizer({ decodeEntities: true }, {
+            onopentagname(start, end) {
+                openingTag = fragment.slice(start, end).toLowerCase();
+                href = undefined;
+            },
+            onopentagend() {
+                open(openingTag);
+            },
+            onselfclosingtag() {
+                open(openingTag);
+                if (openingTag !== 'script' && openingTag !== 'style')
+                    close(openingTag);
+            },
+            onclosetag(start, end) {
+                close(fragment.slice(start, end).toLowerCase());
+            },
+            ontext(start, end) {
+                append(fragment.slice(start, end));
+            },
+            ontextentity(codepoint) {
+                append(String.fromCodePoint(codepoint));
+            },
+            onattribdata(start, end) {
+                if (attributeName === 'href')
+                    attributeChunks.push(fragment.slice(start, end));
+            },
+            onattribentity(codepoint) {
+                if (attributeName === 'href')
+                    attributeChunks.push(String.fromCodePoint(codepoint));
+            },
+            onattribend() {
+                if (attributeName === 'href')
+                    href = attributeChunks.join('');
+            },
+            onattribname(start, end) {
+                attributeName = fragment.slice(start, end).toLowerCase();
+                attributeChunks = [];
+            },
+            oncdata() { },
+            oncomment() { },
+            ondeclaration() { },
+            onprocessinginstruction() { },
+            onend() {
+                closeAnchor();
+            },
+        });
+        tokenizer.write(fragment);
+        tokenizer.end();
+        return chunks.join('');
+    })
+        .filter(Boolean);
+    return rendered.length ? rendered.join('\n\n') : undefined;
+}
+//# sourceMappingURL=description-text.js.map

package/dist/services/interpro/description-text.js.map ADDED Viewed

@@ -0,0 +1 @@

+ 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package/dist/services/interpro/format.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"format.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAyBA,2GAA2G;AAC3G,wBAAgB,eAAe,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAW9C;AAED;;;;GAIG;AACH,wBAAgB,0BAA0B,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC1E,QAAQ,EAAE,CAAC,EACX,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,MAAM,GACf;IAAE,QAAQ,EAAE,CAAC,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAoBlC;AAED,qGAAqG;AACrG,wBAAgB,cAAc,CAAC,KAAK,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,EAAE,~~CA4D~~/E"}
1	+ {"version":3,"file":"format.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAyBA,2GAA2G;AAC3G,wBAAgB,eAAe,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,CAW9C;AAED;;;;GAIG;AACH,wBAAgB,0BAA0B,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC1E,QAAQ,EAAE,CAAC,EACX,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,MAAM,GACf;IAAE,QAAQ,EAAE,CAAC,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAoBlC;AAED,qGAAqG;AACrG,wBAAgB,cAAc,CAAC,KAAK,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,EAAE,CAiD/E"}

package/dist/services/interpro/format.js CHANGED Viewed

@@ -2,7 +2,7 @@
  * @fileoverview Reversible JSON output with usable source URL and image indexes.
  * @module services/interpro/format
  */
-import { markdown } from '@cyanheads/mcp-ts-core/utils';
+import { markdown, markdownImage, markdownLink } from '@cyanheads/mcp-ts-core/utils';
 /** Base64 prefixes of the image formats Wikipedia thumbnails arrive in, with their media types. */
 const THUMBNAIL_SIGNATURES = [
     ['iVBORw0KGgo', 'image/png'],
@@ -104,26 +104,17 @@ export function formatInterpro(value) {
         .replace(/\u2028/g, '\\u2028')
         .replace(/\u2029/g, '\\u2029');
     const output = markdown().codeBlock(json, 'json');
-    /**
-     * CommonMark angle destinations retain parentheses, and entities decode to the original URL.
-     * Whitespace and control characters, which no indexed URL holds, are percent-encoded as a
-     * backstop so no destination can span a line.
-     */
-    const destination = (url) => url
-        .replace(/&/g, '&amp;')
-        .replace(/</g, '&lt;')
-        .replace(/>/g, '&gt;')
-        .replace(/\\/g, '&#92;')
-        .replace(/[\s\p{Cc}]/gu, encodeURIComponent);
     if (urls.size)
         output
             .raw('\n\nSources and links:\n')
-            .raw([...urls].map((url, index) => `[Link ${index + 1}](<${destination(url)}>)`).join('\n\n'));
+            .raw([...urls].map((url, index) => markdownLink(`Link ${index + 1}`, url)).join('\n\n'));
     if (images.size)
-        output
-            .raw('\n\nImages:\n')
-            .raw([...images]
-            .map((url, index) => `![Image ${index + 1}](<${destination(url)}>)`)
+        output.raw('\n\nImages:\n').raw([...images]
+            .map((url, index) =>
+        /** Validated base64 thumbnails intentionally render as images; the framework accepts only HTTP(S). */
+        DATA_IMAGE.test(url)
+            ? `![Image ${index + 1}](<${url}>)`
+            : markdownImage(`Image ${index + 1}`, url))
             .join('\n\n'));
     return [{ type: 'text', text: output.build() }];
 }

package/dist/services/interpro/format.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"format.js","sourceRoot":"","sources":["../../../src/services/interpro/format.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAErF,mGAAmG;AACnG,MAAM,oBAAoB,GAAG;IAC3B,CAAC,aAAa,EAAE,WAAW,CAAC;IAC5B,CAAC,MAAM,EAAE,YAAY,CAAC;IACtB,CAAC,QAAQ,EAAE,WAAW,CAAC;CACf,CAAC;AACX,mEAAmE;AACnE,MAAM,MAAM,GAAG,wBAAwB,CAAC;AACxC,sGAAsG;AACtG,MAAM,UAAU,GAAG,4DAA4D,CAAC;AAChF,wDAAwD;AACxD,MAAM,UAAU,GAAG,qCAAqC,CAAC;AAEzD,SAAS,gBAAgB,CAAC,IAAY;IACpC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,SAAS,CAAC;IACzC,MAAM,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACxF,OAAO,SAAS,IAAI,QAAQ,SAAS,WAAW,IAAI,EAAE,CAAC;AACzD,CAAC;AAED,2GAA2G;AAC3G,MAAM,UAAU,eAAe,CAAI,KAAQ;IACzC,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,eAAe,CAAM,CAAC;IACjE,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QACpC,OAAO,MAAM,CAAC,WAAW,CACvB,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAoB,EAAE,EAAE,CAAC;YAC5D,GAAG;YACH,CAAC,GAAG,KAAK,WAAW,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,gBAAgB,CAAC,IAAI,CAAC,CAAC;gBACzE,eAAe,CAAC,IAAI,CAAC;SACxB,CAAC,CACE,CAAC;IACT,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,0BAA0B,CACxC,QAAW,EACX,OAAgB,EAChB,QAAgB;IAEhB,IAAI,OAAO;QAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IACjC,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,MAAM,KAAK,GAAG,CAAC,IAAa,EAAW,EAAE;QACvC,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC;QAC1E,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,EAAE,GAAG,IAA+B,CAAC;QAC/D,IAAI,OAAO,SAAS,KAAK,QAAQ,IAAI,SAAS,KAAK,EAAE;YAAE,OAAO,IAAI,CAAC;QACnE,KAAK,IAAI,CAAC,CAAC;QACX,KAAK,IAAI,SAAS,CAAC,MAAM,CAAC;QAC1B,OAAO,IAAI,CAAC;IACd,CAAC,CAAC;IACF,MAAM,EAAE,SAAS,EAAE,GAAG,QAAQ,CAAC;IAC/B,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;IACjF,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IAChC,MAAM,OAAO,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,GAAG,KAAK,uBAAuB,CAAC;IAC1F,OAAO;QACL,QAAQ,EAAE,EAAE,GAAG,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE;QAC3C,MAAM,EAAE,WAAW,OAAO,KAAK,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,wCAAwC,QAAQ,2CAA2C,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG;KACtL,CAAC;AACJ,CAAC;AAED,qGAAqG;AACrG,MAAM,UAAU,cAAc,CAAC,KAAc;IAC3C,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,MAAM,GAAG,IAAI,GAAG,EAAU,CAAC;IACjC;;;OAGG;IACH,MAAM,MAAM,GAAG,CAAC,SAAiB,EAAE,KAAc,EAAW,EAAE;QAC5D,IAAI,CAAC;YACH,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAC;YACxC,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YACpB,IAAI,KAAK,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC;gBAAE,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YAC9D,OAAO,IAAI,CAAC;QACd,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,KAAK,CAAC;QACf,CAAC;IACH,CAAC,CAAC;IACF,MAAM,OAAO,GAAG,CAAC,IAAa,EAAQ,EAAE;QACtC,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE,CAAC;YAC7B,IAAI,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC1B,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBACjB,OAAO;YACT,CAAC;YACD,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC;gBAAE,OAAO;YACzF,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,CAAC,+BAA+B,CAAC;gBAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;QAC9F,CAAC;aAAM,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;YAAE,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;aACjD,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;YAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;IAClF,CAAC,CAAC;IACF,OAAO,CAAC,KAAK,CAAC,CAAC;IACf,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC;SAC/B,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC;SAC7B,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACjC,MAAM,MAAM,GAAG,QAAQ,EAAE,CAAC,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IAClD,IAAI,IAAI,CAAC,IAAI;QACX,MAAM;aACH,GAAG,CAAC,0BAA0B,CAAC;aAC/B,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,YAAY,CAAC,QAAQ,KAAK,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC;IAC7F,IAAI,MAAM,CAAC,IAAI;QACb,MAAM,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,GAAG,CAC7B,CAAC,GAAG,MAAM,CAAC;aACR,GAAG,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;QAClB,sGAAsG;QACtG,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC;YAClB,CAAC,CAAC,WAAW,KAAK,GAAG,CAAC,MAAM,GAAG,IAAI;YACnC,CAAC,CAAC,aAAa,CAAC,SAAS,KAAK,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAC7C;aACA,IAAI,CAAC,MAAM,CAAC,CAChB,CAAC;IACJ,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;AAClD,CAAC"}

package/dist/services/interpro/schemas.d.ts CHANGED Viewed

@@ -89,6 +89,16 @@ export declare const EntryMetadataSchema: z.ZodObject<{
         short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>>;
 }, z.core.$catchall<z.ZodJSONSchema>>;
+/** Detail-only output adds readable text without changing upstream description fields. */
+export declare const EntryDetailMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    descriptionText: z.ZodOptional<z.ZodString>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
 /** Complete location fragments retain discontinuity and arbitrary annotations. */
 export declare const LocationSchema: z.ZodObject<{
     fragments: z.ZodArray<z.ZodObject<{
@@ -160,6 +170,21 @@ export declare const ExtraFeaturesSchema: z.ZodRecord<z.ZodString, z.ZodObject<{
         score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>;
 }, z.core.$catchall<z.ZodJSONSchema>>>;
+/** Separate residue-rule annotations retain complete provenance and location records. */
+export declare const ResidueAnnotationsSchema: z.ZodRecord<z.ZodString, z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    locations: z.ZodArray<z.ZodObject<{
+        fragments: z.ZodArray<z.ZodObject<{
+            start: z.ZodNumber;
+            end: z.ZodNumber;
+            'dc-status': z.ZodOptional<z.ZodString>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+        representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+        model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>>;
 /** Standard list envelope; callers select the operation-specific row schema. */
 export declare const listSchema: <T extends z.ZodType>(row: T) => z.ZodObject<{
     count: z.ZodNumber;

package/dist/services/interpro/schemas.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,eAAO,MAAM,eAAe,iBAAiD,CAAC;AAC9E,oEAAoE;AACpE,eAAO,MAAM,gBAAgB,2CAEgB,CAAC;AAC9C,yFAAyF;AACzF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;EAkBe,CAAC;AACjD,mCAAmC;AACnC,eAAO,MAAM,eAAe;;;;;;;;;;;;EAcS,CAAC;AACtC,kCAAkC;AAClC,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIlE,sDAAsD;AACtD,eAAO,MAAM,cAAc,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,+CACjB,CAAC;AAC7C,4FAA4F;AAC5F,eAAO,MAAM,eAAe,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,gCAAoC,CAAC;AACnG,8EAA8E;AAC9E,eAAO,MAAM,eAAe,aAOyC,CAAC;AACtE;;;GAGG;AACH,eAAO,MAAM,WAAW,UAAW,OAAO,KAAG,KAAK,IAAI,MACwB,CAAC;AAC/E,6DAA6D;AAC7D,eAAO,MAAM,sBAAsB,aAIyD,CAAC;AAC7F,0CAA0C;AAC1C,eAAO,MAAM,YAAY;;;;;;;qCAaI,CAAC;AAC9B,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;qCAcH,CAAC;AAC7B,wEAAwE;AACxE,eAAO,MAAM,mBAAmB;;;;;;;qCAcJ,CAAC;AAC7B,0FAA0F;AAC1F,eAAO,MAAM,yBAAyB;;;;;;;;qCAOpC,CAAC;AACH,kFAAkF;AAClF,eAAO,MAAM,cAAc;;;;;;;;;qCAqBqB,CAAC;AACjD,mFAAmF;AACnF,eAAO,MAAM,qBAAqB;;;;;;;;;;;qCAsBN,CAAC;AAC7B,gEAAgE;AAChE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qCAmBI,CAAC;AAC7B,sEAAsE;AACtE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;sCAS/B,CAAC;AACF,yFAAyF;AACzF,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;sCASpC,CAAC;AACF,gFAAgF;AAChF,eAAO,MAAM,UAAU,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,OAAO,CAAC;;;;;qCAQxB,CAAC;AAC/B,gCAAgC;AAChC,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,YAAY,CAAC;;qCACqC,CAAC;AACnG,kCAAkC;AAClC,eAAO,MAAM,UAAU;;;;;;iBAarB,CAAC"}

package/dist/services/interpro/schemas.js CHANGED Viewed

@@ -118,6 +118,13 @@ export const EntryMetadataSchema = z
         .describe('Detail name object.'),
 })
     .catchall(JsonValueSchema);
+/** Detail-only output adds readable text without changing upstream description fields. */
+export const EntryDetailMetadataSchema = EntryMetadataSchema.extend({
+    descriptionText: z
+        .string()
+        .optional()
+        .describe('Readable description text decoded from source HTML fragments; absent without textual content.'),
+});
 /** Complete location fragments retain discontinuity and arbitrary annotations. */
 export const LocationSchema = z
     .object({
@@ -190,6 +197,14 @@ export const ExtraFeaturesSchema = z.record(z.string(), z
     locations: z.array(LocationSchema).describe('Feature locations.'),
 })
     .catchall(JsonValueSchema));
+/** Separate residue-rule annotations retain complete provenance and location records. */
+export const ResidueAnnotationsSchema = z.record(z.string(), z
+    .object({
+    accession: z.string().describe('Residue rule accession.'),
+    source_database: z.string().describe('Rule source database.'),
+    locations: z.array(LocationSchema).describe('Complete rule locations and residue fragments.'),
+})
+    .catchall(JsonValueSchema));
 /** Standard list envelope; callers select the operation-specific row schema. */
 export const listSchema = (row) => z
     .object({
@@ -205,7 +220,11 @@ export const detailSchema = (metadata) => z.object({ metadata: metadata.describe
 export const PageSchema = z.object({
     total: z.number().int().nonnegative().describe('Upstream total records.'),
     returned: z.number().int().nonnegative().describe('Records returned in this page.'),
-    limit: z.number().int().positive().describe('Requested page size.'),
+    limit: z
+        .number()
+        .int()
+        .positive()
+        .describe('Effective page size after clamping to the tool maximum.'),
     hasMore: z.boolean().describe('Whether upstream advertises continuation.'),
     nextCursor: z
         .string()

package/dist/services/interpro/schemas.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/interpro-mcp-server",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "mcpName": "io.github.cyanheads/interpro-mcp-server",
   "description": "Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP.",
   "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
@@ -77,7 +77,7 @@
     "url": "git+https://github.com/cyanheads/interpro-mcp-server.git"
   },
   "license": "Apache-2.0",
-  "packageManager": "bun@1.4.3",
+  "packageManager": "bun@1.4.4",
   "engines": {
     "bun": ">=1.4.0",
     "node": ">=24.0.0"
@@ -86,18 +86,19 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.15",
+    "@cyanheads/mcp-ts-core": "^0.13.16",
+    "htmlparser2": "^12.0.0",
     "pino-pretty": "^13.2.0",
     "zod": "^4.6.7"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.5.15",
+    "@biomejs/biome": "2.6.2",
     "@socketsecurity/bun-security-scanner": "^1.1.3",
     "@types/node": "26.6.5",
     "@vitest/coverage-istanbul": "5.0.5",
     "depcheck": "^1.4.7",
     "fast-check": "^4.10.2",
-    "ignore": "^7.0.12",
+    "ignore": "^7.0.13",
     "tsc-alias": "^1.9.8",
     "typescript": "^7.0.2",
     "vitest": "^5.0.5"

package/server.json CHANGED Viewed

@@ -6,14 +6,20 @@
     "url": "https://github.com/cyanheads/interpro-mcp-server",
     "source": "github"
   },
-  "version": "0.1.1",
+  "version": "0.1.3",
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://interpro.caseyjhand.com/mcp"
+    }
+  ],
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/interpro-mcp-server",
       "runtimeHint": "npx",
-      "version": "0.1.1",
+      "version": "0.1.3",
       "environmentVariables": [
         {
           "name": "MCP_LOG_LEVEL",
@@ -32,7 +38,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/interpro-mcp-server",
       "runtimeHint": "npx",
-      "version": "0.1.1",
+      "version": "0.1.3",
       "environmentVariables": [
         {
           "name": "MCP_TRANSPORT_TYPE",