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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file. Dates are displayed in UTC.

Generated by auto-changelog, with manual clean-up after.

Preparing for "Nine Additional Tables" 8/2018 AllOfUs deadline

  • forgot to delete from provider in run. fixed. 5b6710d
  • fixed typo in run script, needed to put OMOPprovider afrer OMOP clear. c2195fe
  • added provider to the transform as well as the run script. e961a70
  • not sure what is being committed.... 6143756
  • New OMOPprocedure_secondary adds to all other procedure tables; procedures mappings generated on-the-fly! 559ed8d
  • New procedures transform, gets mappings on the fly! 19762db
  • Diagnosis transform upgrade! Now builds mappings on the fly from concept and targets all four tables. d096b0f
  • Update README.md bbcbc55
  • Update README.md 62086fe
  • i2o mapping now only in one place, updated condition which was very incomplete 58234ce
  • Added some internal testing code, not needed to update. 6aedf1d
  • Add observation to run script cea0f7b
  • OMOPDeath procedure for PHS codes. Not for other sites. 882aba5
  • changed i2b2patient_list to i2b2patient in the i2b2loyalty_patients views 8e3c1f2
  • Removing this eMERGE specific script. Relocated into our partners dropbox. 2e572f0
  • updated run script for OMOPdeath 2eee50a
  • Fixed issues that left out RxNorm codes in drug_exposure, made condition_occurrence more inclusive, if a condition-domain code exists the record is now included even without a snomed mapping 04cb103
  • workedon OMOPdeath proc, still need to test d43550a
  • Added initial observation transform, cleaned up report procedure a bit 3a2b591
  • Adding multi-domain support for procedure with omop_targettable column. e228058
  • added death procedure, still needs updating for OMOP 0b32fa6
  • Updated the view to the current irb_protocol number ca93151

Updates for OMOP 5.2 and bugfixes

  • Updated table definition d7e4999
  • OMOPdrug procedure updated for removed columns in 5.2= b47e259
  • updated report procedure 2dc485e
  • updated loaded, fixed bugs in person import, removed visit dimension constraint on i2b2patient list in run script. also adding other useful OMOP files 4ef36f6
  • Another instance of the entire fact table being copied into a temp table. Fixed. 40218b9
  • Major bug! Procedures transform was trying to copy all data into a temporary table! 5a60d9d
  • Added era to run script 0a6cc19
  • Added Columbia's era table transform dc9e812
  • Bugfixes to add OMOP codes to old ontologies with terminology prefix in pcori_basecode. f941a2a
  • Update OMOPLoader.sql 79e5164

Initial release.

  • Moved old files. 4c86be0
  • Update README.md 2e75983
  • Update README.md e74a5c1
  • Update README.md 0696224
  • Little Cleanups b2715b3
  • Supporting obs period. ac0c1c8
  • Added Patient_num_to_aou_id mapping logic b6437e3
  • Fixed demo procedure to grab only patient_dimesion ontology values 31762fc
  • bug fix in demographics of transform for birth_date. Also adding i2ounitsmap table file for MSSQL 4fa2b5c
  • Got rid of some pcori isms 3090e2c
  • Updated the database names 06af20f
  • i2o_mapping table for MSSQL in pipe delimited format 77c48a8
  • Fixed removal of a couple procedures from OMOPLoader 7b4bc6d
  • Cleaned up OMOPClear and OMOPLoader procedures b996885
  • Added if exists/select + drop statement for the i2b2concept synonym. Added if exists/select + drop statements for the primary key constraints on the measurement, drug exposure, procedure occurrence and condition occurrence tables d9926af
  • Add scripts to load HealthPro data into Constrack and check and map AoU IDs to Constrack MRNs 7959d0c
  • Update README.md d362b90
  • Fix up some comments 6d57fd0
  • cleaned up i2o transform and run script comments. Removed unused procedures. 78d7c77
  • Create README.md dd49564
  • Added prelim drug exposure. 2cdfbb5
  • Needed for transforming vitals. 9422ff4
  • commented out unused blocks 0ee8142
  • updated transform to conform to OMOP v5.1 spcifications 17ccd5c
  • filled in a couple of columns in drug_exposure procedure, and I updated the run script. 7abef91
  • pushing Kevin Embree's update to the transform 629067a
  • fixed the last _concept_id fields in labs 1b0e512
  • deleted old vitals procedure, and changed %_concept_id fields to insert '0' instead of null in vitals and labs de09cbe
  • Bugfix to insert 0 instead of null c06b30a
  • added more joins to vitals and lab results procs, and remapped units_concept_cd 8c01fbe
  • Typo in i2o_unitsmap proc 6dfd5f4
  • Now adds omop codes for vitals & labs and generates a unit conversion table. 056e473
  • configured vitals procedure to work with OMOP. ec1f9e0
  • fixed some small bugs in lab results procedure. Lab results is now configured and working for OMOP d154240
  • bug fix, and replacing lab normal table 624ce68
  • re-added jeff's bugfix from 2 weeks ago. It got destroyed by my latest update somehow... 7ae144f
  • changed measurement procedure to have fields that match omop fields 359e952
  • Pushing up Kevin's changes to the loader: procedures proc modified to work with omop. 6d2d2e3
  • Bugfix 9116b6c
  • Export of ontology and mapping tables for demographics, encounters, diagnoses, and procedures. 66ddd52
  • Modified to support multiple target codes in OMOP. 3e4a087
  • Developer code to insert OMOP mappings. 3c3ae09
  • deleted 'condition' procedure from loader. Deleted corresponding delete from and execute lines from run script. a9f3dd7
  • added a case statement in the diagnosis transform for condition_type_concept_id 6db76a4
  • modofied run script to match OMOP names accosiated with diagnosis procedure. 33bc44c
  • Fixed issues with Hispanic and Unknown in demographics source value. de38436
  • fixed qoute numbers for %source_value field inserts in demographics 056e597
  • fixed typo in demographics 43b1c5e
  • changed input for %source_value fields in demographics. Still debugging 8bff496
  • File rename= e5c0a4a
  • Working on adding OMOP codes to condition & procedure. 191de86
  • Uploading modified ontology tables with OMOP_BASECODE 2f5fbbe
  • wrong file 8a3d265
  • wrong file 15ef4bf
  • uploaded updated onotology files that have a new OMOP_BASECODE column b542be9
  • fixed problems with dates. Now the loader will not put in null end dates or times, and instead substitutes the start_date / time. Add visit_source_value. 58b46b7
  • changed pcori_enctype to omop_enctype, modified case statement, changed select to find just omop_basecode. cb3dcce
  • worked more on encounter procedure. Removed junk. Fixed some of the column names. Hardcoded 'visit_type_concept_id'. Encounters is not working yet... 57950e3
  • changed demographics and encounter procedures to use OMOP references and column names. Changed PCORI_basecode to OMOP_basecode in these procs c2c11e0
  • modified OMOP loader to refer to OMOP instead of PCORNET, 9a3f78f
  • Update README.md 0f4088e
  • Removed junk b41dc2e
  • Git Ignore. a04f2e1
  • Initial commit. Fork of i2p-transform. b00fac2
  • Initial commit d9ded56