From e82d73fc39f126ceb86ab3ff6ece97a770de1b02 Mon Sep 17 00:00:00 2001 From: Aidan Cooper <30752032+AidanCooper@users.noreply.github.com> Date: Tue, 20 Aug 2024 16:32:13 +0100 Subject: [PATCH 1/4] Fix clinicaltrials error by adding missing kwargs (#482) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ClinicalTrials.call() raises an error due an unexpected keyword argument, 'session'. Resolved by adding **kwargs to the call method. This PR also converts the method to async for consistency with the other community tools. Co-authored-by: Luísa Moura Co-authored-by: Tianjing Li --- src/community/tools/clinicaltrials.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/community/tools/clinicaltrials.py b/src/community/tools/clinicaltrials.py index 99cce410f6..52a0a16444 100644 --- a/src/community/tools/clinicaltrials.py +++ b/src/community/tools/clinicaltrials.py @@ -21,11 +21,8 @@ def __init__(self, url="https://clinicaltrials.gov/api/v2/studies"): def is_available(cls) -> bool: return True - def call( - self, - parameters: Dict[str, Any], - ctx: Any, - n_max_studies: int = 10, + async def call( + self, parameters: Dict[str, Any], ctx: Any, n_max_studies: int = 10, **kwargs ) -> List[Dict[str, Any]]: query_params = {"sort": "LastUpdatePostDate"} if condition := parameters.get("condition", ""): From 8fe22db21cc4657f70842b405c0b6b9691c5cde6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 20 Aug 2024 14:12:45 -0400 Subject: [PATCH 2/4] chore(deps-dev): bump nltk from 3.8.1 to 3.9 (#715) Bumps [nltk](https://github.com/nltk/nltk) from 3.8.1 to 3.9. - [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog) - [Commits](https://github.com/nltk/nltk/compare/3.8.1...3.9) --- updated-dependencies: - dependency-name: nltk dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 08f51b16a9..8cdc1b4a85 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3388,13 +3388,13 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"] [[package]] name = "nltk" -version = "3.8.1" +version = "3.9" description = "Natural Language Toolkit" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "nltk-3.8.1-py3-none-any.whl", hash = "sha256:fd5c9109f976fa86bcadba8f91e47f5e9293bd034474752e92a520f81c93dda5"}, - {file = "nltk-3.8.1.zip", hash = "sha256:1834da3d0682cba4f2cede2f9aad6b0fafb6461ba451db0efb6f9c39798d64d3"}, + {file = "nltk-3.9-py3-none-any.whl", hash = "sha256:d17863e861bb33ac617893329d71d06a3dfb7e3eb9ee0b8105281c53944a45a1"}, + {file = "nltk-3.9.tar.gz", hash = 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b/src/interfaces/assistants_web/package-lock.json index 1a136a1735..da9faddd6a 100644 --- a/src/interfaces/assistants_web/package-lock.json +++ b/src/interfaces/assistants_web/package-lock.json @@ -83,6 +83,8 @@ "@storybook/react": "^8.2.6", "@storybook/test": "^8.2.6", "@tailwindcss/typography": "^0.5.9", + "@testing-library/dom": "^10.4.0", + "@testing-library/react": "^16.0.0", "@trivago/prettier-plugin-sort-imports": "^4.1.1", "@types/js-cookie": "^3.0.6", "@types/lodash": "^4.14.185", @@ -91,14 +93,17 @@ "@types/react-syntax-highlighter": "^15.5.11", "@typescript-eslint/eslint-plugin": "^6.7.4", "@typescript-eslint/parser": "^6.7.4", + "@vitejs/plugin-react": "^4.3.1", "eslint": "^8.50.0", "eslint-config-next": "^13.5.4", "eslint-config-prettier": "^9.0.0", "eslint-plugin-storybook": "^0.8.0", + "jsdom": "^24.1.1", "postcss-100vh-fix": "^1.0.2", "prettier": "2.8.7", "prettier-plugin-tailwindcss": "0.4.1", - "storybook": "^8.2.6" + "storybook": "^8.2.6", + "vitest": "^2.0.5" }, 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true + }, "node_modules/xtend": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", diff --git a/src/interfaces/assistants_web/package.json b/src/interfaces/assistants_web/package.json index da4263ebe4..2669fa5e05 100644 --- a/src/interfaces/assistants_web/package.json +++ b/src/interfaces/assistants_web/package.json @@ -15,6 +15,7 @@ "ts-lint": "tsc -noEmit -incremental -watch", "format": "prettier --check \"**/*.{js,json,ts,tsx,md}\"", "format:write": "prettier --write \"**/*.{js,json,ts,tsx,md}\"", + "test": "vitest", "next:build": "next build", "start": "next start --port 4444", "start:single-docker": "next start --port 4444", @@ -99,6 +100,8 @@ "@storybook/react": "^8.2.6", "@storybook/test": "^8.2.6", "@tailwindcss/typography": "^0.5.9", + "@testing-library/dom": "^10.4.0", + "@testing-library/react": "^16.0.0", "@trivago/prettier-plugin-sort-imports": "^4.1.1", "@types/js-cookie": "^3.0.6", "@types/lodash": "^4.14.185", @@ -107,13 +110,16 @@ "@types/react-syntax-highlighter": "^15.5.11", "@typescript-eslint/eslint-plugin": "^6.7.4", "@typescript-eslint/parser": "^6.7.4", + "@vitejs/plugin-react": "^4.3.1", "eslint": "^8.50.0", "eslint-config-next": "^13.5.4", "eslint-config-prettier": "^9.0.0", "eslint-plugin-storybook": "^0.8.0", + "jsdom": "^24.1.1", "postcss-100vh-fix": "^1.0.2", "prettier": "2.8.7", "prettier-plugin-tailwindcss": "0.4.1", - "storybook": "^8.2.6" + "storybook": "^8.2.6", + "vitest": "^2.0.5" } -} +} \ No newline at end of file diff --git a/src/interfaces/assistants_web/src/hooks/chat.ts b/src/interfaces/assistants_web/src/hooks/chat.ts index 3f149a9678..19ffdd9152 100644 --- a/src/interfaces/assistants_web/src/hooks/chat.ts +++ b/src/interfaces/assistants_web/src/hooks/chat.ts @@ -37,7 +37,7 @@ import { } from '@/types/message'; import { createStartEndKey, - fixMarkdownImagesInText, + fixMarkdown, isGroundingOn, replaceTextWithCitations, shouldUpdateConversationTitle, @@ -453,7 +453,7 @@ export const useChat = (config?: { onSend?: (msg: string) => void }) => { // TODO(@wujessica): TEMPORARY - we don't pass citations for langchain multihop right now // so we need to manually apply this fix. Otherwise, this comes for free when we call // `replaceTextWithCitations`. - text: citations.length > 0 ? finalText : fixMarkdownImagesInText(transformedText), + text: citations.length > 0 ? finalText : fixMarkdown(transformedText), citations, isRAGOn, originalText: isRAGOn ? responseText : botResponse, diff --git a/src/interfaces/assistants_web/src/utils/citations.test.ts b/src/interfaces/assistants_web/src/utils/citations.test.ts new file mode 100644 index 0000000000..bcfd58f796 --- /dev/null +++ b/src/interfaces/assistants_web/src/utils/citations.test.ts @@ -0,0 +1,86 @@ +import { describe, expect, test } from 'vitest'; + +import { Citation } from '@/cohere-client'; +import { replaceTextWithCitations } from '@/utils/citations'; + +describe('replaceTextWithCitations', () => { + test('should replace text with citations', () => { + const citations: Citation[] = [ + { + start: 0, + end: 4, + text: 'test', + document_ids: ['12345'], + }, + ]; + const text = 'This is a test text'; + const generationId = '12345'; + const result = replaceTextWithCitations(text, citations, generationId); + expect(result).toBe(':cite[test]{generationId="12345" start="0" end="4"} is a test text'); + }); + + test('should return text if citations are empty', () => { + const citations: Citation[] = []; + const text = 'This is a test text'; + const generationId = '12345'; + const result = replaceTextWithCitations(text, citations, generationId); + expect(result).toBe(text); + }); + + test('should avoid add citations inside of iframes', () => { + const citations: Citation[] = [ + { + start: 14, + end: 21, + text: 'Kadabra', + document_ids: ['12345'], + }, + ]; + const text = 'Abra Alakazam'; + const generationId = '12345'; + const result = replaceTextWithCitations(text, citations, generationId); + expect(result).toBe( + 'From: :cite[Reference #1]{generationId="12345" start="14" end="21"}\nAbra Alakazam' + ); + }); + + test('should avoid to break markdown images', () => { + const citations: Citation[] = [ + { + start: 0, + end: 26, + text: '! [test](https://test.com)', + document_ids: ['12345'], + }, + ]; + const text = '![test](https://test.com)'; + const generationId = '12345'; + const result = replaceTextWithCitations(text, citations, generationId); + expect(result).toBe( + ':cite[![test](https://test.com)]{generationId="12345" start="0" end="26"}' + ); + }); + + test('should handle extra space when fixing markdown images', () => { + const citations: Citation[] = [ + { + start: 5, + end: 31, + text: '! [test](https://test.com)', + document_ids: ['12345'], + }, + { + start: 32, + end: 39, + text: 'Kadabra', + document_ids: ['44444'], + }, + ]; + const text = 'Abra ![test](https://test.com) Kadabra'; + const generationId = '12345'; + const result = replaceTextWithCitations(text, citations, generationId); + expect(result).toBe( + 'Abra :cite[![test](https://test.com)]{generationId="12345" start="5" end="31"} :cite[Kadabra]{generationId="12345" start="32" end="39"}' + ); + }); +}); diff --git a/src/interfaces/assistants_web/src/utils/citations.ts b/src/interfaces/assistants_web/src/utils/citations.ts index 5562ae4bb4..26eb3145f6 100644 --- a/src/interfaces/assistants_web/src/utils/citations.ts +++ b/src/interfaces/assistants_web/src/utils/citations.ts @@ -29,11 +29,12 @@ export const replaceTextWithCitations = ( let lengthDifference = 0; // Track the cumulative length difference let notFoundReferences: string[] = []; + let carryOver = 0; citations .filter((citation) => citation.document_ids.length) .forEach(({ start = 0, end = 0, text: citationText }, index) => { - const citeStart = start + lengthDifference; - const citeEnd = end + lengthDifference; + let citeStart = start + lengthDifference + carryOver; + let citeEnd = end + lengthDifference + carryOver; // if citeStart is higher than the length of the text, add it to the bottom of the text as "Reference #n" if (start >= text.length || isReferenceBetweenIframes(replacedText, start)) { @@ -45,6 +46,12 @@ export const replaceTextWithCitations = ( } const fixedText = fixMarkdownImagesInText(citationText); + const isFixedText = fixedText.length !== citationText.length; + + if (isFixedText) { + citeEnd += fixedText.length - citationText.length; + carryOver += fixedText.length - citationText.length; + } // Encode the citationText in case there are any weird characters or unclosed brackets that will // interfere with parsing the markdown. However, let markdown images through so they may be properly diff --git a/src/interfaces/assistants_web/vitest.config.ts b/src/interfaces/assistants_web/vitest.config.ts new file mode 100644 index 0000000000..bb33e19c16 --- /dev/null +++ b/src/interfaces/assistants_web/vitest.config.ts @@ -0,0 +1,15 @@ +import react from '@vitejs/plugin-react'; +import path from 'path'; +import { defineConfig } from 'vitest/config'; + +export default defineConfig({ + plugins: [react()], + test: { + environment: 'jsdom', + }, + resolve: { + alias: { + '@': path.resolve(__dirname, './src'), + }, + }, +}); From a16fa2e859e6dba04ebc48e42e6539af7c25bd5a Mon Sep 17 00:00:00 2001 From: Scott <146760070+scott-cohere@users.noreply.github.com> Date: Tue, 20 Aug 2024 14:57:09 -0400 Subject: [PATCH 4/4] fix compass params (#716) fix --- src/backend/services/file.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/backend/services/file.py b/src/backend/services/file.py index 50915d9bfe..16d19585ce 100644 --- a/src/backend/services/file.py +++ b/src/backend/services/file.py @@ -487,6 +487,7 @@ async def consolidate_agent_files_in_compass( "index": agent_id, "file_id": file_id, "file_bytes": fetched_doc["text"], + "filename": fetched_doc["file_name"], "custom_context": { "file_id": file_id, "file_name": fetched_doc["file_name"], @@ -569,6 +570,7 @@ async def insert_files_in_compass( "index": new_file_id if index is None else index, "file_id": new_file_id, "file_bytes": file_bytes, + "filename": filename, "custom_context": { "file_id": new_file_id, "file_name": filename,