@yeyuan98/opencode-bioresearcher-plugin 1.6.8 → 1.7.1-alpha.0

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 (14) hide show
  1. package/dist/skills/bioresearcher-tests/SKILL.md +46 -4
  2. package/dist/skills/bioresearcher-tests/test_cases/table_tests.md +347 -9
  3. package/dist/skills/bioresearcher-tests/test_runner.py +36 -1
  4. package/dist/tools/parser/pubmed/utils.js +1 -1
  5. package/dist/tools/table/index.d.ts +35 -7
  6. package/dist/tools/table/tools.d.ts +36 -8
  7. package/dist/tools/table/tools.js +270 -118
  8. package/dist/tools/table/utils.d.ts +8 -2
  9. package/dist/tools/table/utils.js +56 -2
  10. package/dist/vendor/xlsx.d.mts +1 -0
  11. package/dist/vendor/xlsx.mjs +33989 -0
  12. package/dist/version.d.ts +1 -1
  13. package/dist/version.js +1 -1
  14. package/package.json +6 -5
package/dist/tools/table/index.d.ts CHANGED
@@ -4,9 +4,11 @@ export declare const tableTools: {
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  args: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
8
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -14,9 +16,11 @@ export declare const tableTools: {
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  description: string;
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  args: {
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  file_path: import("zod").ZodString;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
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  tableGetHeaders: {
@@ -24,9 +28,11 @@ export declare const tableTools: {
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  args: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -36,10 +42,12 @@ export declare const tableTools: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  cell_address: import("zod").ZodString;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  cell_address: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -57,16 +65,20 @@ export declare const tableTools: {
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  ">=": ">=";
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  "<=": "<=";
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  contains: "contains";
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+ starts_with: "starts_with";
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+ ends_with: "ends_with";
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  }>;
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- value: import("zod").ZodAny;
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+ value: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber, import("zod").ZodBoolean]>;
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  max_results: import("zod").ZodDefault<import("zod").ZodNumber>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  column: string;
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- operator: "=" | "!=" | ">" | "<" | ">=" | "<=" | "contains";
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- value: any;
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+ operator: "=" | "!=" | ">" | "<" | ">=" | "<=" | "contains" | "starts_with" | "ends_with";
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+ value: string | number | boolean;
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  max_results: number;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -77,11 +89,13 @@ export declare const tableTools: {
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  search_term: import("zod").ZodString;
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  max_results: import("zod").ZodDefault<import("zod").ZodNumber>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  search_term: string;
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  max_results: number;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -91,10 +105,12 @@ export declare const tableTools: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  range: import("zod").ZodString;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  range: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -104,9 +120,11 @@ export declare const tableTools: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  columns: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  columns?: string[] | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
@@ -125,12 +143,14 @@ export declare const tableTools: {
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  min: "min";
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  max: "max";
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  }>>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  group_column: string;
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  agg_column: string;
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  agg_type: "sum" | "count" | "avg" | "min" | "max";
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -149,6 +169,7 @@ export declare const tableTools: {
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  min: "min";
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  max: "max";
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  }>>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
@@ -156,6 +177,7 @@ export declare const tableTools: {
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  col_field: string;
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  value_field: string;
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  agg: "sum" | "count" | "avg" | "min" | "max";
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -165,10 +187,12 @@ export declare const tableTools: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  rows: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodArray<import("zod").ZodAny>, import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodAny>]>>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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  };
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  execute(args: {
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  file_path: string;
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  rows: (any[] | Record<string, any>)[];
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -178,12 +202,14 @@ export declare const tableTools: {
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodOptional<import("zod").ZodString>;
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  cell_address: import("zod").ZodString;
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- value: import("zod").ZodAny;
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+ value: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber, import("zod").ZodBoolean, import("zod").ZodNull]>;
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+ force: import("zod").ZodDefault<import("zod").ZodBoolean>;
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207
  };
183
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  execute(args: {
184
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  file_path: string;
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  cell_address: string;
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- value: any;
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+ value: string | number | boolean | null;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -192,12 +218,14 @@ export declare const tableTools: {
192
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  args: {
193
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  file_path: import("zod").ZodString;
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  sheet_name: import("zod").ZodDefault<import("zod").ZodString>;
195
- data: import("zod").ZodAny;
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+ data: import("zod").ZodUnion<readonly [import("zod").ZodArray<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodAny>>, import("zod").ZodArray<import("zod").ZodArray<import("zod").ZodAny>>, import("zod").ZodString]>;
222
+ overwrite: import("zod").ZodDefault<import("zod").ZodBoolean>;
196
223
  };
197
224
  execute(args: {
198
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  file_path: string;
199
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  sheet_name: string;
200
- data: any;
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+ data: string | any[][] | Record<string, any>[];
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+ overwrite: boolean;
201
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  }, context: import("@opencode-ai/plugin").ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
202
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  };
203
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  };
package/dist/tools/table/tools.d.ts CHANGED
@@ -1,13 +1,15 @@
1
1
  import { ToolContext } from '@opencode-ai/plugin/tool';
2
- import { z } from 'zod';
2
+ import * as z from 'zod';
3
3
  export declare const tableGetSheetPreview: {
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  description: string;
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  args: {
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  file_path: z.ZodString;
7
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  sheet_name: z.ZodOptional<z.ZodString>;
8
+ force: z.ZodDefault<z.ZodBoolean>;
8
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  };
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -15,9 +17,11 @@ export declare const tableListSheets: {
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  description: string;
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  args: {
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  file_path: z.ZodString;
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+ force: z.ZodDefault<z.ZodBoolean>;
18
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  };
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  execute(args: {
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  file_path: string;
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+ force: boolean;
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  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
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  export declare const tableGetHeaders: {
@@ -25,9 +29,11 @@ export declare const tableGetHeaders: {
25
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  args: {
26
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  file_path: z.ZodString;
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  sheet_name: z.ZodOptional<z.ZodString>;
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+ force: z.ZodDefault<z.ZodBoolean>;
28
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  };
29
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  execute(args: {
30
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  file_path: string;
36
+ force: boolean;
31
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  sheet_name?: string | undefined;
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  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -37,10 +43,12 @@ export declare const tableGetCell: {
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  file_path: z.ZodString;
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  sheet_name: z.ZodOptional<z.ZodString>;
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  cell_address: z.ZodString;
46
+ force: z.ZodDefault<z.ZodBoolean>;
40
47
  };
41
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  execute(args: {
42
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  file_path: string;
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  cell_address: string;
51
+ force: boolean;
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  sheet_name?: string | undefined;
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  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
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  };
@@ -58,16 +66,20 @@ export declare const tableFilterRows: {
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  ">=": ">=";
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  "<=": "<=";
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  contains: "contains";
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+ starts_with: "starts_with";
70
+ ends_with: "ends_with";
61
71
  }>;
62
- value: z.ZodAny;
72
+ value: z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean]>;
63
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  max_results: z.ZodDefault<z.ZodNumber>;
74
+ force: z.ZodDefault<z.ZodBoolean>;
64
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  };
65
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  execute(args: {
66
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  file_path: string;
67
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  column: string;
68
- operator: "=" | "!=" | ">" | "<" | ">=" | "<=" | "contains";
69
- value: any;
79
+ operator: "=" | "!=" | ">" | "<" | ">=" | "<=" | "contains" | "starts_with" | "ends_with";
80
+ value: string | number | boolean;
70
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  max_results: number;
82
+ force: boolean;
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  sheet_name?: string | undefined;
72
84
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
73
85
  };
@@ -78,11 +90,13 @@ export declare const tableSearch: {
78
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  sheet_name: z.ZodOptional<z.ZodString>;
79
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  search_term: z.ZodString;
80
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  max_results: z.ZodDefault<z.ZodNumber>;
93
+ force: z.ZodDefault<z.ZodBoolean>;
81
94
  };
82
95
  execute(args: {
83
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  file_path: string;
84
97
  search_term: string;
85
98
  max_results: number;
99
+ force: boolean;
86
100
  sheet_name?: string | undefined;
87
101
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
88
102
  };
@@ -92,10 +106,12 @@ export declare const tableGetRange: {
92
106
  file_path: z.ZodString;
93
107
  sheet_name: z.ZodOptional<z.ZodString>;
94
108
  range: z.ZodString;
109
+ force: z.ZodDefault<z.ZodBoolean>;
95
110
  };
96
111
  execute(args: {
97
112
  file_path: string;
98
113
  range: string;
114
+ force: boolean;
99
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  sheet_name?: string | undefined;
100
116
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
101
117
  };
@@ -105,9 +121,11 @@ export declare const tableSummarize: {
105
121
  file_path: z.ZodString;
106
122
  sheet_name: z.ZodOptional<z.ZodString>;
107
123
  columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
124
+ force: z.ZodDefault<z.ZodBoolean>;
108
125
  };
109
126
  execute(args: {
110
127
  file_path: string;
128
+ force: boolean;
111
129
  sheet_name?: string | undefined;
112
130
  columns?: string[] | undefined;
113
131
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
@@ -126,12 +144,14 @@ export declare const tableGroupBy: {
126
144
  min: "min";
127
145
  max: "max";
128
146
  }>>;
147
+ force: z.ZodDefault<z.ZodBoolean>;
129
148
  };
130
149
  execute(args: {
131
150
  file_path: string;
132
151
  group_column: string;
133
152
  agg_column: string;
134
153
  agg_type: "sum" | "count" | "avg" | "min" | "max";
154
+ force: boolean;
135
155
  sheet_name?: string | undefined;
136
156
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
137
157
  };
@@ -150,6 +170,7 @@ export declare const tablePivotSummary: {
150
170
  min: "min";
151
171
  max: "max";
152
172
  }>>;
173
+ force: z.ZodDefault<z.ZodBoolean>;
153
174
  };
154
175
  execute(args: {
155
176
  file_path: string;
@@ -157,6 +178,7 @@ export declare const tablePivotSummary: {
157
178
  col_field: string;
158
179
  value_field: string;
159
180
  agg: "sum" | "count" | "avg" | "min" | "max";
181
+ force: boolean;
160
182
  sheet_name?: string | undefined;
161
183
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
162
184
  };
@@ -166,10 +188,12 @@ export declare const tableAppendRows: {
166
188
  file_path: z.ZodString;
167
189
  sheet_name: z.ZodOptional<z.ZodString>;
168
190
  rows: z.ZodArray<z.ZodUnion<readonly [z.ZodArray<z.ZodAny>, z.ZodRecord<z.ZodString, z.ZodAny>]>>;
191
+ force: z.ZodDefault<z.ZodBoolean>;
169
192
  };
170
193
  execute(args: {
171
194
  file_path: string;
172
195
  rows: (any[] | Record<string, any>)[];
196
+ force: boolean;
173
197
  sheet_name?: string | undefined;
174
198
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
175
199
  };
@@ -179,12 +203,14 @@ export declare const tableUpdateCell: {
179
203
  file_path: z.ZodString;
180
204
  sheet_name: z.ZodOptional<z.ZodString>;
181
205
  cell_address: z.ZodString;
182
- value: z.ZodAny;
206
+ value: z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean, z.ZodNull]>;
207
+ force: z.ZodDefault<z.ZodBoolean>;
183
208
  };
184
209
  execute(args: {
185
210
  file_path: string;
186
211
  cell_address: string;
187
- value: any;
212
+ value: string | number | boolean | null;
213
+ force: boolean;
188
214
  sheet_name?: string | undefined;
189
215
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
190
216
  };
@@ -193,11 +219,13 @@ export declare const tableCreateFile: {
193
219
  args: {
194
220
  file_path: z.ZodString;
195
221
  sheet_name: z.ZodDefault<z.ZodString>;
196
- data: z.ZodAny;
222
+ data: z.ZodUnion<readonly [z.ZodArray<z.ZodRecord<z.ZodString, z.ZodAny>>, z.ZodArray<z.ZodArray<z.ZodAny>>, z.ZodString]>;
223
+ overwrite: z.ZodDefault<z.ZodBoolean>;
197
224
  };
198
225
  execute(args: {
199
226
  file_path: string;
200
227
  sheet_name: string;
201
- data: any;
228
+ data: string | any[][] | Record<string, any>[];
229
+ overwrite: boolean;
202
230
  }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
203
231
  };