From b7891c5a3c655898f726ec365e49529b283b0177 Mon Sep 17 00:00:00 2001 From: chunwei Date: Mon, 21 Aug 2023 18:41:26 -0400 Subject: [PATCH] update sidarthe demo with ta1 service --- .../mit-aug-demo-data-model-cards.ipynb | 35 +++--- ...aly-s41591-020-0883-7.pdf => sidarthe.pdf} | Bin demos/extract_vars_example.ipynb | 118 +++++++++++++++++- src/xdd/xdd_parser.py | 2 +- 4 files changed, 133 insertions(+), 22 deletions(-) rename demos/2023-08/{2020-Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy-s41591-020-0883-7.pdf => sidarthe.pdf} (100%) diff --git a/demos/2023-08/mit-aug-demo-data-model-cards.ipynb b/demos/2023-08/mit-aug-demo-data-model-cards.ipynb index 2f83645..d474920 100644 --- a/demos/2023-08/mit-aug-demo-data-model-cards.ipynb +++ b/demos/2023-08/mit-aug-demo-data-model-cards.ipynb @@ -26,7 +26,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 2, "id": "d07d53d5", "metadata": { "pycharm": { @@ -37,14 +37,15 @@ "source": [ "import ast, json, requests, os\n", "from gpt_key import *\n", - "API_ROOT = \"http://3.83.68.208/\"\n", + "API_ROOT = \"https://api.askem.lum.ai/\"\n", + "# API_ROOT = \"https://api.askem.lum.ai/\"\n", "# \"http://localhost:8000/\" #" ] }, { "cell_type": "markdown", "source": [ - "## 1. MIT annotation end to end pipeline" + "## 1. TA1 text extraction end to end pipeline" ], "metadata": { "collapsed": false, @@ -56,8 +57,7 @@ { "cell_type": "markdown", "source": [ - "#### We bring every annotation step together: for the original paper text, let's integrate all the extraction modules and output the MIT extraction:\n", - "[http://3.83.68.208/#/Paper-2-annotated-vars/upload_file_annotate_annotation_upload_file_extract__post](http://3.83.68.208/#/Paper-2-annotated-vars/upload_file_annotate_annotation_upload_file_extract__post)" + "#### We bring every annotation step together: for the original paper pdf, let's integrate all the extraction modules and output the TA1 extraction:" ], "metadata": { "collapsed": false, @@ -68,23 +68,25 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 3, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - 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(chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"value_specs\":[{\"id\":{\"id\":\"v26-value\"},\"value\":{\"source\":\"0.0100\",\"grounding\":null,\"extraction_source\":null},\"units\":null,\"type\":null,\"bounds\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"groundings\":[{\"grounding_text\":\"recovered population\",\"grounding_id\":\"apollosv:00000163\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}},{\"grounding_text\":\"AE recovery rate\",\"grounding_id\":\"oae:0001869\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"data_columns\":[]}},{\"type\":\"anchored_extraction\",\"amr_element_id\":null,\"payload\":{\"id\":{\"id\":\"v27\"},\"names\":[{\"id\":{\"id\":\"v27\"},\"name\":\"τ\",\"extraction_source\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"descriptions\":[{\"id\":{\"id\":\"v27\"},\"source\":\"mortality rate\",\"grounding\":null,\"extraction_source\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}},{\"id\":{\"id\":\"v27\"},\"source\":\"Healing parameter\",\"grounding\":null,\"extraction_source\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"value_specs\":[{\"id\":{\"id\":\"v27-value\"},\"value\":{\"source\":\"0.0100\",\"grounding\":null,\"extraction_source\":null},\"units\":null,\"type\":null,\"bounds\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"groundings\":[{\"grounding_text\":\"mortality rate\",\"grounding_id\":\"stato:0000414\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}},{\"grounding_text\":\"neonatal mortality rate\",\"grounding_id\":\"sdgio:00020030\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"data_columns\":[]}},{\"type\":\"anchored_extraction\",\"amr_element_id\":null,\"payload\":{\"id\":{\"id\":\"v28\"},\"names\":[{\"id\":{\"id\":\"v28\"},\"name\":\"S*\",\"extraction_source\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"descriptions\":[{\"id\":{\"id\":\"v28\"},\"source\":\"threshold value\",\"grounding\":null,\"extraction_source\":null,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"value_specs\":null,\"groundings\":[{\"grounding_text\":\"has value\",\"grounding_id\":\"stato:0000129\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}},{\"grounding_text\":\"has value specification\",\"grounding_id\":\"obi:0001938\",\"source\":[],\"score\":1.0,\"provenance\":{\"method\":\"MIT extractor V1.0 - text, dataset, formula annotation (chunwei@mit.edu)\",\"timestamp\":\"2023-08-21T22:37:55.722018\"}}],\"data_columns\":[]}},{\"type\":\"document_collection\",\"amr_element_id\":null,\"payload\":{\"documents\":[{\"id\":{\"id\":\"1\"},\"source_file\":\"9e8f0a3deb7dfd30091c2d585190565e__file\",\"doi\":\"\"}]}}]},\"errors\":null}],\"generalized_errors\":[{\"pipeline\":\"SKEMA\",\"message\":\"Problem annotating with SKEMA: Calling http://hopper.sista.arizona.edu/cosmosJsonToMentions failed with HTTP code 502\"}]}\n" ] } ], "source": [ - "# We assume plain text from arizona team.\n", - "scenario_1_paper = \"sidarthe.txt\"\n", - "with open(scenario_1_paper, 'rb') as f:\n", - " files = {'file': ('filename', f)}\n", - " params = {\"gpt_key\": GPT_KEY}\n", - " response = requests.post(API_ROOT + \"annotation/upload_file_extract/\", params=params, files=files)\n", + "paper_pdf = \"sidarthe.pdf\"\n", + "with open(paper_pdf, 'rb') as f:\n", + " params = {\n", + " \"annotate_skema\":True,\n", + " \"annotate_mit\": True\n", + " }\n", + " files = [(\"pdfs\", (paper_pdf, f))]\n", + " response = requests.post(API_ROOT + \"text-reading/integrated-pdf-extractions\", params=params, files=files)\n", " json_str = response.text\n", "print(json_str)\n" ], @@ -110,8 +112,7 @@ { "cell_type": "markdown", "source": [ - "#### Model cards provide general information about the model.\n", - "[http://3.83.68.208/#/Data-and-model-cards/get_model_card_cards_get_model_card_post](http://3.83.68.208/#/Data-and-model-cards/get_model_card_cards_get_model_card_post)" + "#### Model cards provide general information about the model." ], "metadata": { "collapsed": false, @@ -139,8 +140,7 @@ "\n", "with open(text_name, 'rb') as f_text, open(code_name, 'rb') as f_code:\n", " files = { 'text_file': ('filename', f_text),'code_file': ('filename', f_code)}\n", - " params = {\"gpt_key\": GPT_KEY}\n", - " response = requests.post(API_ROOT + \"cards/get_model_card\", params=params, files=files)\n", + " response = requests.post(API_ROOT + \"text-reading/cards/get_model_card\", files=files)\n", "# print(response.text)\n", "\n", "ast.literal_eval(response.text)" @@ -169,7 +169,6 @@ "source": [ "#### TODO (we need to find the corresponding dataset)\n", "Data cards summarize general information about the dataset.\n", - "[http://3.83.68.208/#/Data-and-model-cards/get_data_card_cards_get_data_card_post](http://3.83.68.208/#/Data-and-model-cards/get_data_card_cards_get_data_card_post)\n", "\n", "The data card endpoint supports both tabular and matrix (e.g. transmission probabilities) data.\n", "It will automatically detect which one has been passed, based on whether or not the first row in the dataset contains purely numeric data.\n", diff --git a/demos/2023-08/2020-Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy-s41591-020-0883-7.pdf b/demos/2023-08/sidarthe.pdf similarity index 100% rename from demos/2023-08/2020-Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy-s41591-020-0883-7.pdf rename to demos/2023-08/sidarthe.pdf diff --git a/demos/extract_vars_example.ipynb b/demos/extract_vars_example.ipynb index ba19742..5e8104f 100644 --- a/demos/extract_vars_example.ipynb +++ b/demos/extract_vars_example.ipynb @@ -12,7 +12,10 @@ "shell.execute_reply": "2023-07-11T16:02:24.134500Z", "shell.execute_reply.started": "2023-07-11T16:02:24.123275Z" }, - "tags": [] + "tags": [], + "pycharm": { + "name": "#%%\n" + } }, "outputs": [], "source": [ @@ -34,6 +37,9 @@ "iopub.status.idle": "2023-07-11T16:02:25.102485Z", "shell.execute_reply": "2023-07-11T16:02:25.102041Z", "shell.execute_reply.started": "2023-07-11T16:02:24.144245Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -52,6 +58,9 @@ "iopub.status.idle": "2023-07-11T16:09:37.531739Z", "shell.execute_reply": "2023-07-11T16:09:37.531033Z", "shell.execute_reply.started": "2023-07-11T16:09:37.524656Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -76,6 +85,9 @@ "iopub.status.idle": "2023-07-11T16:02:25.352277Z", "shell.execute_reply": "2023-07-11T16:02:25.351864Z", "shell.execute_reply.started": "2023-07-11T16:02:25.348849Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -95,6 +107,9 @@ "iopub.status.idle": "2023-07-11T16:02:25.658409Z", "shell.execute_reply": "2023-07-11T16:02:25.657608Z", "shell.execute_reply.started": "2023-07-11T16:02:25.654792Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -113,6 +128,9 @@ "iopub.status.idle": "2023-07-11T16:02:32.968263Z", "shell.execute_reply": "2023-07-11T16:02:32.967248Z", "shell.execute_reply.started": "2023-07-11T16:02:32.964017Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -131,6 +149,9 @@ "iopub.status.idle": "2023-07-11T16:10:41.152175Z", "shell.execute_reply": "2023-07-11T16:10:41.151527Z", "shell.execute_reply.started": "2023-07-11T16:10:24.156244Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -150,6 +171,9 @@ "iopub.status.idle": "2023-07-11T16:10:44.415537Z", "shell.execute_reply": "2023-07-11T16:10:44.414974Z", "shell.execute_reply.started": "2023-07-11T16:10:44.409732Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -204,6 +228,9 @@ "iopub.status.idle": "2023-07-11T16:04:40.391159Z", "shell.execute_reply": "2023-07-11T16:04:40.390371Z", "shell.execute_reply.started": "2023-07-11T16:04:40.387219Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -222,6 +249,9 @@ "iopub.status.idle": "2023-07-11T15:54:59.557247Z", "shell.execute_reply": "2023-07-11T15:54:59.556493Z", "shell.execute_reply.started": "2023-07-11T15:54:59.542853Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -251,6 +281,9 @@ "iopub.status.idle": "2023-07-11T15:55:28.660114Z", "shell.execute_reply": "2023-07-11T15:55:28.659649Z", "shell.execute_reply.started": "2023-07-11T15:55:28.591129Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -280,6 +313,9 @@ "iopub.status.idle": "2023-07-11T15:33:56.145057Z", "shell.execute_reply": "2023-07-11T15:33:56.144327Z", "shell.execute_reply.started": "2023-07-11T15:33:56.140338Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -299,6 +335,9 @@ "iopub.status.idle": "2023-07-11T15:34:00.662425Z", "shell.execute_reply": "2023-07-11T15:34:00.661734Z", "shell.execute_reply.started": "2023-07-11T15:34:00.658594Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -329,6 +368,9 @@ "iopub.status.idle": "2023-07-11T15:00:13.333046Z", "shell.execute_reply": "2023-07-11T15:00:13.332666Z", "shell.execute_reply.started": "2023-07-11T15:00:13.248300Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -531,6 +573,9 @@ "iopub.status.idle": "2023-07-10T21:44:09.328972Z", "shell.execute_reply": "2023-07-10T21:44:09.328192Z", "shell.execute_reply.started": "2023-07-10T21:44:09.321677Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -552,6 +597,9 @@ "iopub.status.idle": "2023-07-11T14:55:15.364057Z", "shell.execute_reply": "2023-07-11T14:55:15.363361Z", "shell.execute_reply.started": "2023-07-11T14:55:15.360527Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -570,6 +618,9 @@ "iopub.status.idle": "2023-07-11T14:56:20.099130Z", "shell.execute_reply": "2023-07-11T14:56:20.098256Z", "shell.execute_reply.started": "2023-07-11T14:56:20.095258Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -589,6 +640,9 @@ "iopub.status.idle": "2023-07-11T16:10:19.437463Z", "shell.execute_reply": "2023-07-11T16:10:19.436852Z", "shell.execute_reply.started": "2023-07-11T16:10:19.433453Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -608,6 +662,9 @@ "iopub.status.idle": "2023-07-11T14:56:25.675638Z", "shell.execute_reply": "2023-07-11T14:56:25.674767Z", "shell.execute_reply.started": "2023-07-11T14:56:25.671504Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -818,6 +875,9 @@ "iopub.status.idle": "2023-07-09T03:20:21.640719Z", "shell.execute_reply": "2023-07-09T03:20:21.640329Z", "shell.execute_reply.started": "2023-07-09T03:20:21.604089Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -842,6 +902,9 @@ "iopub.status.idle": "2023-07-09T03:20:32.277515Z", "shell.execute_reply": "2023-07-09T03:20:32.276686Z", "shell.execute_reply.started": "2023-07-09T03:20:32.274315Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -860,6 +923,9 @@ "iopub.status.idle": "2023-07-10T19:44:50.800018Z", "shell.execute_reply": "2023-07-10T19:44:50.799200Z", "shell.execute_reply.started": "2023-07-10T19:44:50.794682Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -878,7 +944,11 @@ "cell_type": "code", "execution_count": 14, "id": "7d72796d", - "metadata": {}, + "metadata": { + "pycharm": { + "name": "#%%\n" + } + }, "outputs": [], "source": [ "#os.environ['OPENAI_API_KEY']" @@ -895,6 +965,9 @@ "iopub.status.idle": "2023-07-05T15:46:08.882776Z", "shell.execute_reply": "2023-07-05T15:46:08.881823Z", "shell.execute_reply.started": "2023-07-05T15:46:08.877979Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -913,6 +986,9 @@ "iopub.status.idle": "2023-07-10T19:42:29.870784Z", "shell.execute_reply": "2023-07-10T19:42:29.869350Z", "shell.execute_reply.started": "2023-07-10T19:42:19.201975Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -942,6 +1018,9 @@ "iopub.status.idle": "2023-07-10T19:20:18.951735Z", "shell.execute_reply": "2023-07-10T19:20:18.950827Z", "shell.execute_reply.started": "2023-07-10T19:20:01.423748Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -970,6 +1049,9 @@ "iopub.status.idle": "2023-07-10T19:22:14.058735Z", "shell.execute_reply": "2023-07-10T19:22:14.057443Z", "shell.execute_reply.started": "2023-07-10T19:21:58.723306Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -997,6 +1079,9 @@ "iopub.status.idle": "2023-07-05T15:46:30.375913Z", "shell.execute_reply": "2023-07-05T15:46:30.375259Z", "shell.execute_reply.started": "2023-07-05T15:46:30.371890Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1016,6 +1101,9 @@ "iopub.status.idle": "2023-07-10T19:23:29.129796Z", "shell.execute_reply": "2023-07-10T19:23:29.128774Z", "shell.execute_reply.started": "2023-07-10T19:23:13.782353Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -1045,6 +1133,9 @@ "iopub.status.idle": "2023-07-05T15:46:59.312211Z", "shell.execute_reply": "2023-07-05T15:46:59.311424Z", "shell.execute_reply.started": "2023-07-05T15:46:59.307950Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1070,6 +1161,9 @@ "iopub.status.idle": "2023-07-05T15:47:12.030693Z", "shell.execute_reply": "2023-07-05T15:47:12.028863Z", "shell.execute_reply.started": "2023-07-05T15:47:12.025721Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1088,6 +1182,9 @@ "iopub.status.idle": "2023-07-05T15:48:16.500408Z", "shell.execute_reply": "2023-07-05T15:48:16.498292Z", "shell.execute_reply.started": "2023-07-05T15:48:16.488175Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1107,6 +1204,9 @@ "iopub.status.idle": "2023-07-05T15:48:46.336796Z", "shell.execute_reply": "2023-07-05T15:48:46.335206Z", "shell.execute_reply.started": "2023-07-05T15:48:46.329876Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1125,6 +1225,9 @@ "iopub.status.idle": "2023-07-05T15:48:53.441866Z", "shell.execute_reply": "2023-07-05T15:48:53.440991Z", "shell.execute_reply.started": "2023-07-05T15:48:53.437089Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -1154,6 +1257,9 @@ "iopub.status.idle": "2023-07-05T15:49:02.313156Z", "shell.execute_reply": "2023-07-05T15:49:02.312317Z", "shell.execute_reply.started": "2023-07-05T15:49:02.308574Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1172,6 +1278,9 @@ "iopub.status.idle": "2023-07-05T15:49:30.957414Z", "shell.execute_reply": "2023-07-05T15:49:30.956622Z", "shell.execute_reply.started": "2023-07-05T15:49:30.951587Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [], @@ -1190,6 +1299,9 @@ "iopub.status.idle": "2023-07-05T15:49:31.643917Z", "shell.execute_reply": "2023-07-05T15:49:31.642537Z", "shell.execute_reply.started": "2023-07-05T15:49:31.622891Z" + }, + "pycharm": { + "name": "#%%\n" } }, "outputs": [ @@ -1325,4 +1437,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} +} \ No newline at end of file diff --git a/src/xdd/xdd_parser.py b/src/xdd/xdd_parser.py index 7dfcbce..13b65aa 100644 --- a/src/xdd/xdd_parser.py +++ b/src/xdd/xdd_parser.py @@ -177,7 +177,7 @@ def main(file_path, output_dir): if __name__ == "__main__": parser = argparse.ArgumentParser(description='Process a PDF file.') - parser.add_argument('--file', type=str, default="/Users/chunwei/Documents/paper/LLM/Flamingo.pdf", + parser.add_argument('--file', type=str, default="/Users/chunwei/Downloads/sidarthe.pdf", help='The path to the PDF file to process.') parser.add_argument('--output_dir', type=str, default="/Users/chunwei/Downloads/", help='The directory to save the extraction results.')