{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":14119,"defaultBranch":"main","name":"ZIP11","ownerLogin":"lrm22005","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2024-05-06T13:55:52.000Z","ownerAvatar":"https://github.uconn.edu/avatars/u/4583","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1715004055.0","currentOid":""},"activityList":{"items":[{"before":"3a7b4f104f609f9b238e1142eff033d16daaf00d","after":"3a518049980bce091193831bdac525d94a0d46c6","ref":"refs/heads/main","pushedAt":"2024-08-20T17:53:16.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #8 from lrm22005/Luis\n\nPreprocessing updates to ensure recommendations in final file format","shortMessageHtmlLink":"Merge pull request #8 from lrm22005/Luis"}},{"before":"703a8470239aa079246bdb6eeebd7decf1fa07d3","after":"29efc801efb1e53a738a72c398ee3871ea152caf","ref":"refs/heads/Luis","pushedAt":"2024-08-20T17:52:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Preprocessing updates to ensure recommendations in final file format","shortMessageHtmlLink":"Preprocessing updates to ensure recommendations in final file format"}},{"before":"a2e85403c6497a77bd11e96193c556d19744effe","after":"3a7b4f104f609f9b238e1142eff033d16daaf00d","ref":"refs/heads/main","pushedAt":"2024-07-30T19:37:57.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Update .gitignore\n\nCo-Authored-By: Jihye Moon <3928+jim19007@users.noreply.github.uconn.edu>","shortMessageHtmlLink":"Update .gitignore"}},{"before":"6125a680ae1b56d7360521f62b158f96e421500f","after":"a2e85403c6497a77bd11e96193c556d19744effe","ref":"refs/heads/main","pushedAt":"2024-07-30T19:35:08.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #7 from lrm22005/Luis\n\nupdate on step2 and step3","shortMessageHtmlLink":"Merge pull request #7 from lrm22005/Luis"}},{"before":"34e849ff48203214807ec13958a2f479ee7dddfa","after":"703a8470239aa079246bdb6eeebd7decf1fa07d3","ref":"refs/heads/Luis","pushedAt":"2024-07-30T19:34:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"update on step2 and step3\n\nImplementation on genes based in step2 called step2_data_preprocessing_Luis_new.\n\nImplementation of step3_literature_embeding_training_Luis this version allows to train different LLMs of the BERT family and there is working right now I'm creating embeddings for the entire data.\n\nCo-Authored-By: Jihye Moon <3928+jim19007@users.noreply.github.uconn.edu>","shortMessageHtmlLink":"update on step2 and step3"}},{"before":"d60131f7d25973044b844bfc8f26f9d4db3c4466","after":"6125a680ae1b56d7360521f62b158f96e421500f","ref":"refs/heads/main","pushedAt":"2024-07-25T17:10:00.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #6 from lrm22005/Luis\n\ncommiting changes and uploading codes","shortMessageHtmlLink":"Merge pull request #6 from lrm22005/Luis"}},{"before":"1613e6979c3c8bce54b5ea5c24b844bed6c60b4e","after":"34e849ff48203214807ec13958a2f479ee7dddfa","ref":"refs/heads/Luis","pushedAt":"2024-07-25T17:09:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"commiting changes and uploading codes","shortMessageHtmlLink":"commiting changes and uploading codes"}},{"before":"9679d699c66adad396807e11bec3eaf7497363bc","after":"d60131f7d25973044b844bfc8f26f9d4db3c4466","ref":"refs/heads/main","pushedAt":"2024-07-25T17:08:11.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #5 from lrm22005/Luis\n\nLuis updating codes","shortMessageHtmlLink":"Merge pull request #5 from lrm22005/Luis"}},{"before":"f16f5d27a20bf950c8efb023161000013776a62d","after":"1613e6979c3c8bce54b5ea5c24b844bed6c60b4e","ref":"refs/heads/Luis","pushedAt":"2024-05-14T12:12:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Gene downloading\n\nDownloader for Gene data, interact with multiple NCBI sources, without limits for connection.","shortMessageHtmlLink":"Gene downloading"}},{"before":"860d0fe5fe477714cd6bff3737c2ececf6d8af8b","after":"f16f5d27a20bf950c8efb023161000013776a62d","ref":"refs/heads/Luis","pushedAt":"2024-05-08T15:08:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Genes and Query extraction\n\nImplementation of an exogenous gene extraction method.","shortMessageHtmlLink":"Genes and Query extraction"}},{"before":"75ca1ad17f7c19b074097fa14b55bd89a403f932","after":"9679d699c66adad396807e11bec3eaf7497363bc","ref":"refs/heads/main","pushedAt":"2024-05-07T12:34:36.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #4 from lrm22005/Luis\n\nInit updated of security","shortMessageHtmlLink":"Merge pull request #4 from lrm22005/Luis"}},{"before":"0e4993d10da6a695e56fcbe59cfee8cf58f128e7","after":"860d0fe5fe477714cd6bff3737c2ececf6d8af8b","ref":"refs/heads/Luis","pushedAt":"2024-05-07T12:34:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Init updated of security\n\nChanges on files and optimization of downloaders.","shortMessageHtmlLink":"Init updated of security"}},{"before":"16559903c0f701b2e52e59cc4270af31fd1785b5","after":"75ca1ad17f7c19b074097fa14b55bd89a403f932","ref":"refs/heads/main","pushedAt":"2024-05-06T16:47:05.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #3 from lrm22005/Luis\n\nUpdated","shortMessageHtmlLink":"Merge pull request #3 from lrm22005/Luis"}},{"before":"fe9178672376327c88dd075da21ce030b3a598a2","after":"0e4993d10da6a695e56fcbe59cfee8cf58f128e7","ref":"refs/heads/Luis","pushedAt":"2024-05-06T16:46:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Updated\n\nSupport in the files and documents.","shortMessageHtmlLink":"Updated"}},{"before":"e107ed91f515a2f8aea2de9417d0f1c03749efac","after":"16559903c0f701b2e52e59cc4270af31fd1785b5","ref":"refs/heads/main","pushedAt":"2024-05-06T16:31:41.000Z","pushType":"pr_merge","commitsCount":5,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #2 from lrm22005/Luis\n\nLuis","shortMessageHtmlLink":"Merge pull request #2 from lrm22005/Luis"}},{"before":"77d0ba9d54f7a55b3d13dfb4dfda0290a9622c78","after":"fe9178672376327c88dd075da21ce030b3a598a2","ref":"refs/heads/Luis","pushedAt":"2024-05-06T16:31:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Add functionality to fetch and save PubMed records by year\n\nThis commit introduces significant enhancements to the PubMedDownloader class, enabling the automated fetching of PubMed records by topic and year using the NCBI E-utilities API. Each set of records fetched for a specific year is now saved in a dedicated text file formatted in MEDLINE style, facilitating easier access and organization of the data.\n\nKey Changes:\n- Added file saving functionality that organizes records into files named by topic and year.\n- Implemented error handling with retry logic and exponential backoff to manage network and API errors more robustly.\n- Configured the fetch function to retrieve records in MEDLINE format, ensuring that the data is structured according to PubMed's bibliographic standards.\n\nThe records are stored in the './results/baseline_doc' directory, with each file representing a specific year's data on the chosen topic. This update is crucial for researchers needing structured and easily accessible bibliographic information from PubMed.","shortMessageHtmlLink":"Add functionality to fetch and save PubMed records by year"}},{"before":"510e5e21cc3ffedc3633af3f22e9bcd94604d04a","after":"77d0ba9d54f7a55b3d13dfb4dfda0290a9622c78","ref":"refs/heads/Luis","pushedAt":"2024-05-06T16:28:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Delete pubmed_data.txt","shortMessageHtmlLink":"Delete pubmed_data.txt"}},{"before":"abfaa4d9c47513f519cdd5b8ec8f7f5d98915cb8","after":"510e5e21cc3ffedc3633af3f22e9bcd94604d04a","ref":"refs/heads/Luis","pushedAt":"2024-05-06T16:27:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"step_1_data_collection_Luis.py\n\nEnhance PubMed Data Fetching and Saving Mechanism\n\nThis commit introduces several enhancements to the PubMedDownloader class, improving its functionality and usability:\n\n1. **Dynamic Year Querying**: Added support for dynamic querying by year. This allows users to specify a range of years for which the PubMed records should be fetched.\n\n2. **Structured Data Saving**: Implemented functionality to save the fetched PubMed records in MEDLINE format. Each year's data is saved in a separate text file, named according to the query and the year, facilitating easier data management and retrieval.\n\n3. **Error Handling**: Enhanced error handling capabilities to manage network issues and API limitations more robustly. This includes retry mechanisms with exponential backoff and timeout settings to prevent hanging requests.\n\n4. **Directory Management**: Automated directory creation for storing the output files, ensuring that the user does not need to manually create directories before running the script.\n\nThese enhancements make the script more robust and user-friendly, suitable for handling large-scale data retrieval tasks in biomedical research environments.","shortMessageHtmlLink":"step_1_data_collection_Luis.py"}},{"before":"ae973fe87db5f51c4624d33c823cbfd2af78d332","after":"e107ed91f515a2f8aea2de9417d0f1c03749efac","ref":"refs/heads/main","pushedAt":"2024-05-06T14:34:49.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Merge pull request #1 from lrm22005/Luis\n\nCodes update","shortMessageHtmlLink":"Merge pull request #1 from lrm22005/Luis"}},{"before":"ae973fe87db5f51c4624d33c823cbfd2af78d332","after":"abfaa4d9c47513f519cdd5b8ec8f7f5d98915cb8","ref":"refs/heads/Luis","pushedAt":"2024-05-06T14:34:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Codes update\n\nUpdate with debugging changes over the step1_data_collection, step_1_data_collection_Luis and step_1_data_collection_Luis_ looking for a way to download more than 10000 documents.","shortMessageHtmlLink":"Codes update"}},{"before":null,"after":"ae973fe87db5f51c4624d33c823cbfd2af78d332","ref":"refs/heads/Luis","pushedAt":"2024-05-06T14:00:55.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"CAPSULE LOADING\n\nThe following files are the code core, that is going to be defined as relevant on this repository","shortMessageHtmlLink":"CAPSULE LOADING"}},{"before":"9941660a266c749a3b6add38eec30f4b0b736e44","after":"ae973fe87db5f51c4624d33c823cbfd2af78d332","ref":"refs/heads/main","pushedAt":"2024-05-06T14:00:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"CAPSULE LOADING\n\nThe following files are the code core, that is going to be defined as relevant on this repository","shortMessageHtmlLink":"CAPSULE LOADING"}},{"before":null,"after":"9941660a266c749a3b6add38eec30f4b0b736e44","ref":"refs/heads/main","pushedAt":"2024-05-06T13:55:55.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"lrm22005","name":"Luis Roberto Mercado Diaz","path":"/lrm22005","primaryAvatarUrl":"https://github.uconn.edu/avatars/u/4583?s=80"},"commit":{"message":"Initial commit","shortMessageHtmlLink":"Initial commit"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks4AAwhTAA","startCursor":null,"endCursor":null}},"title":"Activity ยท lrm22005/ZIP11"}