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ClinicalTrialsDataProcessing
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Code Issues 3 Pull Requests Packages Projects Releases 6 Wiki Activity
107 Commits
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llm-extraction
parser
history-download
v1.0.1
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107 Commits (llm-extraction)
 

Author SHA1 Message Date
Will King eca4795d2f Began redoing lost formularies work 
I lost some work on USP formularies and those are crucial for my analysis.
So, I began reworking them. In the process, I:

- Created a new formularies schema and added a table and some views
  - new file:   Scripts/ConfiguringFormularies.sql
- exported the schema
  - new file:   Scripts/export_tables.sh
  - new file:   export/export_data_postgres_materialized_views.sql
  - new file:   export/export_data_postgres_tables.sql
  - new file:   export/export_data_postgres_views.sql
  - new file:   export/output_2025-01-06_export_data_postgres_materialized_views.sql
  - new file:   export/output_2025-01-06_export_data_postgres_tables.sql
  - new file:   export/output_2025-01-06_export_data_postgres_views.sql
  - new file:   Scripts/Extracting Tables Views and MatViews.sql
- created a new checkpoint/backup of my work
  - modified:   .gitattributes
  - new file:   containers/AACT_Reloader/backup/aact_db_backup_20250106_184236.sql.gz
  - new file:   Scripts/Backup_AACT_work.sh
 1 year ago
Will King 87074aa42b Worked on error preventing restore 
Turns out that the code for checking if the database was up was wrong. I think I fixed it but am not sure.
 1 year ago
Will King 79902f400a added some work on extracting data with LLMs 2 years ago
Will King b4a3cec7e6 Updated modefile 2 years ago
Will King 211151e223 added modelfile for llama3.1-extractor:2024-08-28.1 2 years ago
Will King d90539a679 updated data-restoration script. Currently working 2 years ago
Will King 142670d08a added some data that had been left untracked 2 years ago
youainti 6a931b3a49 added USP MMG data 3 years ago
youainti 1c3d749ef4 added VA and USP DC datasets 3 years ago
youainti ef68adae89 Added backup of the aact_db 3 years ago
youainti a336fb92d9 Linking again after changing remotes 
Merge branch 'main' of https://git.youainti.com/youainti/ClinicalTrialsDataProcessing into main
 3 years ago
will king 05a96a3a29 adding scripts 3 years ago
will king 256177e569 Updated to what I am using so far 3 years ago
youainti b7290c271b Merge branch 'main' of ssh://gitea.kgjk.icu:3022/Research/ClinicalTrialsDataProcessing into main 3 years ago
will king c4b8484cab added submission date to extractor 3 years ago
youainti 2a9b8349ba storing local details 3 years ago
will king 9a718f72a0 Adding sql queries that I need for the analysis 3 years ago
will king e88f450b8c minor updates 3 years ago
will king 4643351305 minor adjustments to improve workflow 3 years ago
will king c1f9f6e528 Updated to be able to run as webpage. 3 years ago
will king 277b5b9bd5 Working validation tool 3 years ago
will king 1de1ff9e4a Minor updates to umls_... to add progress bars. Got the main features of validation running. 3 years ago
will king 47996ba607 updated import-icd10... to use execute_values to speed up insert. 3 years ago
will king 9ac4cffe61 Nearly finished interface to manually review icd-10 codes. 3 years ago
will king 5600ad932d Got the basics for matching and importing icd->GBD data 3 years ago
youainti d1edac3c4f Merge branch 'main' of ssh://gitea.kgjk.icu:3022/Research/ClinicalTrialsDataProcessing into main 3 years ago
youainti e2edf1eb6b created base of umls linking script 3 years ago
will king c5f3bfcdec Merging work from other computer into home. 
Merge branch 'main' of ssh://gitea.kgjk.icu:3022/Research/ClinicalTrialsDataProcessing
 3 years ago
will king 12c3c69304 added Glbal burden fo disease data 3 years ago
youainti 29644a0ad5 Connected Global Burdens of Disease Data to ICD-10 Codes 3 years ago
youainti 123fe3b5e4 Merge completed: Merged working versions from home and office PCs 3 years ago
youainti 470dfc2611 got a working merge of the who icd10 and cms icd10cm code spaces. This merge has a single entry for each code, prefering the WHO version when available. 3 years ago
youainti 6876779c17 Merged two commits because I initially forgot to include the deleted 
paths.

fixed some paths, added the CMS version of icd10cm, and added the downloaded source for the CMS data

forgot to remove old paths
 3 years ago
youainti bbdd7552a8 adding various changed for which I don't remember the details. I'm adding it to avoid loosing it. 3 years ago
youainti 4831864805 adjusted paths and started writing something to link GBD and ICD10 3 years ago
youainti 6b5a48c77a added GlobalBurden of Disease connections to ICD-10 3 years ago
youainti 2aba3469d3 adding WHO ICD-10 Data 3 years ago
will king ef7ed7001b added info for setting up the db from DrugCentral.org 3 years ago
Will King 2ec314180f Merge remote-tracking branch 'refs/remotes/origin/main' 3 years ago
Will King f6b56da261 Got working connection between trials and NDA/ANDA start times 3 years ago
Will King ed49d8728a Update 'README.md' 3 years ago
youainti 39397cc224 reorganized python scripts into package, added requisit sql, and added shell scripts to notify me when the systems are up again. 3 years ago
youainti 804a90c247 lots of updates while integrating rxnav and aact into one dockerfile 3 years ago
youainti 8dbf4e8c2e removed unused files, began adjusting docker-composes so that they will work together. 3 years ago
youainti 1a106a553e moved containers to single location, ignored raw data 3 years ago
youainti f6f687fff5 removed old code (orangebook and old rxnorm_mappings) and adjusted the AACT_downloader to use a local directory when launching 3 years ago
youainti 016a449258 merged the two settings 3 years ago
youainti 091fd63366 committing results 3 years ago
will king bbf8c77e6d more work on linking market data 3 years ago
youainti 4283719d3d added stashed changes 3 years ago