@inflexa-ai/harness 0.11.0 → 0.12.0
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@@ -40,7 +40,8 @@ export const searchGeoDatasetsTool = defineTool({
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id: "search_geo_datasets",
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description: "Search NCBI GEO for public gene-expression datasets by disease, tissue, or experimental condition — use it to find external validation cohorts or to cite published data. " +
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"Returns totalFound plus datasets[]: { accession (GSE…/GDS…), title, summary (truncated to 500 chars), platform, sampleCount, organism, pubmedIds }. " +
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"HARD CAVEAT:
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"HARD CAVEAT: this tool returns metadata only, and sandbox containers have no network — never plan an in-sandbox step that downloads a GEO dataset. " +
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"Bringing the data itself in is a capability of the surrounding environment, not of this tool: consult the tools you actually have rather than assuming it is possible or that it is not. " +
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"An empty datasets array is a valid 'nothing matched' — do not retry the identical query.",
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inputSchema: z.object({
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query: z
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@@ -19,9 +19,10 @@ const ListFilesInputSchema = z.object({
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export function createListFilesTool(fs, workingDir) {
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return defineTool({
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id: "list_files",
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description: "List the entries (files and directories, with file sizes) in a " +
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"workspace
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"
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description: "List the entries (files and directories, with file sizes) in a directory of the analysis's " +
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"own workspace tree. Faster than `ls` via execute_command. Its scope is that tree and nothing " +
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"else: it never reaches a directory outside the analysis, including the host process's current " +
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"working directory. Missing and out-of-scope paths return a data variant, not an error.",
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inputSchema: ListFilesInputSchema,
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execute: async ({ path }, ctx) => {
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const result = unwrapOrThrow(await fs.list({ session: ctx.session, path, workingDir }));
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package/package.json
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