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2015-11-02 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients In comment:9 this was marked as public-web so I will removing the sensitive flag. Nathan (owner) confirmed over my shoulder. data-repository major mhoag 11/02/15 defect 07/20/15

2015-10-29 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2318 refactor medication modifiers so "items instance will be the same" will work Ticket retargeted after milestone closed data-repository minor ngraham 10/29/15 enhancement 10/01/13
#2301 constraining birth-date by date doesn't work - HERON uses sysdate for start_date in demographics Ticket retargeted after milestone closed data-repository minor ngraham 10/29/15 problem 09/24/13
#2278 Epic-internal RxNORM mapping Ticket retargeted after milestone closed data-repository minor ngraham 10/29/15 design-issue 09/11/13
#2059 Medications mapped to Other Medication Concepts folder belong elsewhere in the hierarchy Ticket retargeted after milestone closed data-repository minor ngraham 10/29/15 enhancement 05/20/13

2015-10-28 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) data-repository major dconnolly 10/28/15 design-issue 07/02/13

2015-10-25 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#2617 Saved searches not updated in REDCap projects after Arkansas release bumping minor technical debt (or similar) data-repository minor dconnolly 10/25/15 defect 04/01/14

2015-10-21 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#2713 Bring Cardiology labs data into HERON data-repository major bzschoche 10/21/15 enhancement 05/15/14

2015-10-12 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. data-repository major dconnolly 10/12/15 enhancement 05/21/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients data-repository major dconnolly 10/12/15 defect 07/20/15

2015-10-07 (3 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) heron-weekly: DC: I'm overcommitted; bariatric study depends on CDM v3 which depends on this BZ: study is on hold pending PCORI contracting streamlining DC: and next month is technical-debt, so... Butternut/Dec data-repository major dconnolly 10/07/15 design-issue 07/02/13
#2713 Bring Cardiology labs data into HERON heron-weekly: SC: After getting the lab hierarchy updated, I'd like to tackle this one as it is relevant to ADAPTABLE. I have a meeting with Dr. Gupta today and will ask for specific use cases for this. data-repository major ngraham 10/07/15 enhancement 05/15/14
#2713 Bring Cardiology labs data into HERON data-repository major bzschoche 10/07/15 enhancement 05/15/14

2015-10-06 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#3487 Clicking "Other Medication Concepts" in the i2b2 webclient results in "Database Error" message I addressed a latent TODO in [13ca435e2045] - move the dup test to run on DEID rather than ID. This resulted in significant performance gains in the per-developer docker containers (#1318). Matt reviewed over my shoulder - merged to default in [2508cbd7879b]. data-repository major ngraham 10/06/15 problem 05/12/15

2015-09-29 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2318 refactor medication modifiers so "items instance will be the same" will work Ticket retargeted after milestone closed data-repository minor ngraham 09/29/15 enhancement 10/01/13
#2301 constraining birth-date by date doesn't work - HERON uses sysdate for start_date in demographics Ticket retargeted after milestone closed data-repository minor ngraham 09/29/15 problem 09/24/13
#2278 Epic-internal RxNORM mapping Ticket retargeted after milestone closed data-repository minor ngraham 09/29/15 design-issue 09/11/13
#2059 Medications mapped to Other Medication Concepts folder belong elsewhere in the hierarchy Ticket retargeted after milestone closed data-repository minor ngraham 09/29/15 enhancement 05/20/13

2015-09-23 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) data-repository major dconnolly 09/23/15 design-issue 07/02/13

2015-09-11 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) scheduled for Oct (Michigan) in HeronProjectTimeline#August2015Planning data-repository major dconnolly 09/11/15 design-issue 07/02/13

2015-09-09 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2713 Bring Cardiology labs data into HERON heron-weekly: postpone data-repository major dconnolly 09/09/15 enhancement 05/15/14
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) not sure where this fits... data-repository major dconnolly 09/09/15 design-issue 07/02/13

2015-09-02 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) data-repository major dconnolly 09/02/15 design-issue 07/02/13
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) data-repository major dconnolly 09/02/15 design-issue 07/02/13

2015-08-31 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Dr.Gupta finally got a chance to look at the NCDR hierarchy in HERON. He provided me with the below use cases that I can use to validate NCDR on HERON. - All patients with > 70% stenosis in atleast one artery(CIRC/Mid Distal LAD/Proximal). This information could be found in NCDR\Coronary Anatomy. - All patients with > 70% stenosis in two arteries(CIRC/Mid Distal LAD/Proximal). - All patients with LVEF<=35%, no acute STEMI,>70% stenosis in 3 arteries and no prior CABG. data-repository major schandaka 08/31/15 enhancement 02/03/15

2015-08-28 (5 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2713 Bring Cardiology labs data into HERON Ticket retargeted after milestone closed data-repository major mhoag 08/28/15 enhancement 05/15/14
#2318 refactor medication modifiers so "items instance will be the same" will work Ticket retargeted after milestone closed data-repository minor mhoag 08/28/15 enhancement 10/01/13
#2301 constraining birth-date by date doesn't work - HERON uses sysdate for start_date in demographics Ticket retargeted after milestone closed data-repository minor mhoag 08/28/15 problem 09/24/13
#2278 Epic-internal RxNORM mapping Ticket retargeted after milestone closed data-repository minor mhoag 08/28/15 design-issue 09/11/13
#2059 Medications mapped to Other Medication Concepts folder belong elsewhere in the hierarchy Ticket retargeted after milestone closed data-repository minor mhoag 08/28/15 enhancement 05/20/13

2015-08-24 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Thanks Matt! I ran the block of code in PROD_ID_DB (ran in 174.464 sec ~2.9 min), missing concept_cd are being created, number of rows extracted is appropriate. Merged with heron-riverwalk (8bd89cbb60f8), and I will close the ticket. data-repository major ssuman 08/24/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. closed data-repository major ssuman 08/24/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Replying to [comment:22 ssuman]: > Concept_cd for non-alplanumeric alert_desc were missing, checked in the code (9a6f5a6f9efd)...Thanks Matt and Bhargav! Missing concept_cd are being created. Suman, some of the code in (9a6f5a6f9efd) was not as we discussed, particularly the use of the first character bucketing being duplicated in two place. Additionally, there is a needless `join` in the construction of `alert_concepts_with_alpha` because `al_hash_value` already has the `first_char`. I went ahead and fixed these issues in (c155eb0fa511), but I will re-open the ticket so that you can look it over before you merge it in. Here is a successful build (`heron_etl_tiny_no_DBA/1023`) as well. data-repository major mhoag 08/24/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. reopened data-repository major mhoag 08/24/15 enhancement 05/21/15

2015-08-21 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Concept_cd for non-alplanumeric alert_desc were missing, checked in the code (9a6f5a6f9efd)...Thanks Matt and Bhargav! Missing concept_cd are being created. {{{ #!CSV "KUH|DI:A770BA495967B59BEEAE40D95DA771F81084CB3B","\i2b2\Alerts\3\6\I\A770BA495967B59BEEAE40D95DA771F81084CB3B\" "KUH|DI:38878B58F6E82DBB57303F18EB5714A01BF6A05F","\i2b2\Alerts\3\10\I\38878B58F6E82DBB57303F18EB5714A01BF6A05F\" }}} data-repository major ssuman 08/21/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. closed data-repository major ssuman 08/21/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. All facts use known concepts test fell over...reference ticket:3677#comment:6 data-repository major ssuman 08/21/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. reopened data-repository major ssuman 08/21/15 enhancement 05/21/15

2015-08-20 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2617 Saved searches not updated in REDCap projects after Arkansas release move with #2646 data-repository minor dconnolly 08/20/15 defect 04/01/14
#3458 identified data with MRN only; no contact info data-repository major badagarla 08/20/15 enhancement 04/30/15

2015-08-19 (8 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2868 Document the DUA process We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 enhancement 08/01/14
#2947 search HERON labs by LOINC terminology including GPC usability design We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository critical badagarla 08/19/15 enhancement 09/12/14
#3275 Missing Expected LOS facts (UHC) for patients beginning Oct 2013 We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 problem 02/24/15
#3397 previous queries with Encounter Type (DRAFT) result in a popup message showing "ERROR: ERROR" We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 problem 04/02/15
#3418 Portable DataBuilder uses different filename suffixes for CSVs We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository minor badagarla 08/19/15 defect 04/14/15
#3417 Portable DataBuilder does not use jobname file prefixes for CSVs We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 defect 04/14/15
#3357 Query by drug-drug interaction alert description (BPA) We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 enhancement 03/19/15
#3458 identified data with MRN only; no contact info We got permission during heron-weekly from team and documented it in ticket:3557#comment:7. data-repository major badagarla 08/19/15 enhancement 04/30/15

2015-08-14 (5 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I data-repository major schandaka 08/14/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I closed data-repository major schandaka 08/14/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Thanks for the review, Matt. I addressed some of your comments in [e428a2813bf8]. Merged to default in [3cfa2468a4be]. Credit to Sravani for all her hard work to add the ability to search NCDR facts in HERON. ==== details Replying to [comment:80 mhoag]: > === concepts_merge.sql > Nathan, I remember you showing me on test that some of the hidden concepts actually had facts associated with them. Did that get fixed? Otherwise looks good to me. ...answered by Sravani in comment:81 > === ncdr_manual_selections.csv > Any documentation on where these come from, why they were created? Pointer to a ticket comment would be nice. I tried to explain this better in the comment. > === epic_etl.py > 279: Erroneous tab Fixed. > === heron_build.py > 517: Not sure why an NCDR specific curated data is not in kumc_etl.py instead. I don't think we are intending to use this curated data in any other ETL piece (i.e. epic) Hmm, I guess I'm not sure which is better - I guess the rest of the NCDR stuff is in the KUMC file so maybe it does make sense. However, I'm not inspired to move it at this point. > === ncdr_concepts_load.sql > 9-26: there is an implicit dependency on this part of ncdr concept load that Age at Visit has also been loaded. I guess that is captured well enough in `heron_build.py`. But I think it is important to note that we are sacrificing code portability for and edge on code reuse. I agree - I went back and forth on this for a while. In the end, though, I decided to make the portability/order dependency sacrifice to avoid copy/pasting a bunch of code. > === ncdr_constants.sql > 21: s/dasta/data I de-dastafied the comment. > === ncdr_facts_load.sql > 19: Pivot looks as I described... maybe though you don't need a seq num for each line and instead kind of group them by paragraph bases on their category (e.g. `/*Cath Lab Visit*/`) Yeah, we could have saved some screen real estate, but I'm not inclined to change it at this point. > 225-227: Code duplication here is mildly annoying, but is isolated to a single place (unlike before) and DRY SQL code might actually add more lines than it removes... Oops - I agree - seems we could have factored them out. Don't think I'll do it now though - I don't feel like making too many changes this close to ETL after Sravani has already done quite a bit of validateion. > 341: Why not commit after the update of upload status? Hmm, maybe that would be a good idea, but I think db_util will commit once it's done with running the file anyway. The commit right after the insert into observation_fact_upload is there (I think) so that if the following statement (primary key constraint) fails, we can easily tell which rows were duplicated without having to re-run the insert. > === test_heron_query.py > 18: Not sure why the typo was added here... Not sure either - I fixed it. data-repository major ngraham 08/14/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Code Review done (comment:80). I think this is ready for merge, but you might want to address some of the non-critical comments. data-repository major mhoag 08/14/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Matt, Hidden concepts having facts issue has been fixed. data-repository major schandaka 08/14/15 enhancement 02/03/15

2015-08-13 (10 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. took care of the magic 3, checked first_char of alert_desc for alphanumeric, removed extra distinct, added alt_history table to clarity_import.par, checked in the code (982fe29a3330), ran `heron_etl_tiny_no_DBA/1019`, and merged to default...closing the ticket. data-repository major ssuman 08/13/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. closed data-repository major ssuman 08/13/15 enhancement 05/21/15
#3224 Bring NCDR(v4) data into HERON - Phase I Code reviewing changes between b71217e9f53c (default) and e3bdf0d7a96c (latest NCDR): '''Overall, I didn't see anything that worries me. I think this is okay to merge.''' == By File Review === concepts_merge.sql Nathan, I remember you showing me on test that some of the hidden concepts actually had facts associated with them. Did that get fixed? Otherwise looks good to me. === code_sync_ex.csv No comment. === ncdr_manual_selections.csv Any documentation on where these come from, why they were created? Pointer to a ticket comment would be nice. === source_master.csv No comment. === epic_etl.py 279: Erroneous tab === heron_build.py 517: Not sure why an NCDR specific curated data is not in kumc_etl.py instead. I don't think we are intending to use this curated data in any other ETL piece (i.e. epic) === kumc_etl.py Looks good. === ncdr_concepts_load.sql 9-26: there is an implicit dependency on this part of ncdr concept load that Age at Visit has also been loaded. I guess that is captured well enough in `heron_build.py`. But I think it is important to note that we are sacrificing code portability for and edge on code reuse. Otherwise this looks good. === ncdr_constants.sql 21: s/dasta/data Looks good. I love that this file exists! So that there is a source of truth for concept code generation. === ncdr_facts_load.sql 19: Pivot looks as I described... maybe though you don't need a seq num for each line and instead kind of group them by paragraph bases on their category (e.g. `/*Cath Lab Visit*/`) 225-227: Code duplication here is mildly annoying, but is isolated to a single place (unlike before) and DRY SQL code might actually add more lines than it removes... 341: Why not commit after the update of upload status? === test_heron_query.py 18: Not sure why the typo was added here... === ncdr_dictionary.ctl === ncdr_dictionary.sql Looks good. === ncdr_stage_prep.py === ncdr_to_i2b2_paths.py Looks pretty good to me. I know that it does what it is supposed to do and and has good unit test coverage. === sample_ncdr_dict yeah for rich test data data-repository major mhoag 08/13/15 enhancement 02/03/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients Thanks Sravani, I ran a query against the `epic_billing_diag_discharge` view with production data and it completed in what I consider to be a reasonable amount of time (<30 seconds): {{{ select count(*) from epic_billing_diag_discharge; }}} Merged in [27acba45d38c]. data-repository major ngraham 08/13/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients closed data-repository major ngraham 08/13/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients Nathan briefly walked me through the code and it is pretty straight forward. == Feature Checklist ||= Item =||= Ready? =|| || Use Case Clear? || Yes || Automated Feature Tests? || Yes || Usable by Peer Developers? || Yes || Code Secure? || N/A || Performance OK? || Not Checked(Will check with Nathan about this) || Deployment OK? || N/A || Copyright and Acknowledgements? || Yes || Happy to Maintain? || Yes Assigning this back to Nathan. data-repository major schandaka 08/13/15 defect 07/20/15
#3224 Bring NCDR(v4) data into HERON - Phase I Modified test queries for the new paths in (e3bdf0d7a96c). Assigning to Matt to code-review. data-repository major schandaka 08/13/15 enhancement 02/03/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients Matt is pretty busy now with Flowsheet deid just now - Sravani agreed to review instead. data-repository major ngraham 08/13/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients Matt, My first attempt at modifying test data to result in a POA fact failed as I didn't end up picking an encounter that got mapped in HERON. I fixed the test data - see [4c7aa32e1829]. Ran `heron_etl_tiny_no_DBA/1010`. Now, the test passes: {{{ python test_heron_query.py http://TEST-HOST.kumc.edu/i2b2/webclient --demo INFO:__main__:opening Heron homepage... INFO:__main__:Found page with title: i2b2 Web Client INFO:__main__:Getting user configuration... INFO:__main__:Got it. INFO:__main__: Testing: Billing Diagnosis - Present on Admission INFO:__main__:Found: 1 INFO:__main__:timing: 2015-08-13 10:53:58.089000, 2015-08-13 10:54:03.652000, 0:00:05.563000 }}} data-repository major ngraham 08/13/15 defect 07/20/15
#3224 Bring NCDR(v4) data into HERON - Phase I Created a ticket on how to handle NCDR dead patients.(#3694) For heron-riverwalk, added exception to ignore the dead patient facts without concepts in the revision (9a0f59df37f8). data-repository major schandaka 08/13/15 enhancement 02/03/15

2015-08-12 (14 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Thank you Dan! ...working on code review comments ...in progress... I attached the screenshot, used parallel hint enabling a SQL statement to be simultaneously processed by multiple threads or processes...have attached relevant url http://searchitchannel.techtarget.com/feature/Using-parallel-SQL-to-improve-Oracle-database-performance >Why select distinct on line 73? (from ab5b9438ea87) will be removing distinct...since rows are already distinct in alert_recs data-repository major ssuman 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Looks good. Merged in 0535dcf45a82. I made one tweak: 9e4ef0b3c88a. good to know you checked performance in production. You'll take care of that magic 3 as we discussed and then merge again. And do attach that screenshot, please. data-repository major dconnolly 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. assigned data-repository major dconnolly 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. CodeReviewNotes in progress... [https://bmi-work.kumc.edu/work/changeset?old=409ea65931b7&old_path=&new=&new_path= diff from default to branch]. heron_load/epic_alerts_transform.sql?rev=aa3cb5b260f9&annotate=blame why parallel? add a comment? {{{ alert_recs as (select distinct /*+ parallel */ }}} `when (alr.alt_type_c <> 3` what does 3 mean? Why `select distinct` on line 73? (from ab5b9438ea87) data-repository major dconnolly 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. accepted data-repository major dconnolly 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. ...completed automated test...assigning the ticket to Dan for code review data-repository major ssuman 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Dan, I have updated the description...I was wondering if you could help with code review...I am executing `heron_etl_tiny_no_DBA/999` for executing an automated test...Once completed, if I could assign the ticket to you for code-review. '''Details''': Query for drug dosage alert in test: {{{ Finished Query: "DEXTROSE 5% NA@11:28:09" [1.4 secs] Compute Time: 1 secs Number of patients for "DEXTROSE 5% NA@11:28:09" patient_count: 1 Finished Query: "DEXTROSE_AL9" [1.3 secs] Compute Time: 0 secs Number of patients for "DEXTROSE_AL9" patient_count: 1 }}} capture_query: {{{ ssuman@DEV_SERVER:~/bmidev/heron_load> python capture_query.py heron-test.ini 'DEXTROSE_AL9' 'DRUG_DOSAGE_3505' INFO:capture_query.$find_query.deid.bmid:connect(ssuman, oracle://DEV_SERVER:1521/bmid) INFO:capture_query.$find_query.deid.Statement: $find_query:1: INFO:capture_query.$find_query.deid:connection(deid) INFO:capture_query.$find_query:run($find_query) }}} test_heron_query.py updates: (aa3cb5b260f9) added test_queries and updates to test_heron_query.py {{{ Drug-Dosage Alerts (#3505) *************************************** >>> ua.saved_query('DRUG_DOSAGE_3505', ... '2015-08-12_839_demo') > 0 True }}} {{{ ssuman@DEV_SERVER:~/bmidev/heron_load> python test_heron_query.py http://.../i2b2/webclient/ --demo INFO:__main__:opening Heron homepage... INFO:__main__:Found page with title: i2b2 Web Client INFO:__main__:Getting user configuration... INFO:__main__:Got it. INFO:__main__: Testing: DRUG_DOSAGE_3505 INFO:__main__:Found: 1 INFO:__main__:timing: 2015-08-12 12:13:26.559351, 2015-08-12 12:13:26.974730, 0:00:00.415379 INFO:__main__: }}} data-repository major ssuman 08/12/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. data-repository major ssuman 08/12/15 enhancement 05/21/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients Failing test case added in [ae15778241b1]. Update test data so we have one discharge DX flagged as POA [7191eed0e193]. Fixed in [c961c2ec9a6d]. I plan to test it on DEV_SERVER once it's available. Matt agreed to review the `epic_poa_discharge_dx_3640` branch. data-repository major ngraham 08/12/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients assigned data-repository major ngraham 08/12/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients This actually blocks ETL. data-repository major ngraham 08/12/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients data-repository major ngraham 08/12/15 defect 07/20/15
#3640 Epic discharge billing diagnosis modifier "Present on admission" will incorrectly return 0 patients accepted data-repository major ngraham 08/12/15 defect 07/20/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Adding me for any particular reason? The description still says "use case to follow in due course." data-repository major dconnolly 08/12/15 enhancement 05/21/15

2015-08-11 (3 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. Adding Dan. data-repository major ssuman 08/11/15 enhancement 05/21/15
#3505 Alerts 2.0 - Bring in drug dosage, drug allergy and other alert types. - Checked in the source code (46e07b46ddad) `branch:alerts2.0_3505` ...bring in drug dosage, drug allergy and other medical alert types. Doing a test: `heron_etl_tiny_no_DBA/996` data-repository major ssuman 08/11/15 enhancement 05/21/15
#3224 Bring NCDR(v4) data into HERON - Phase I Sravani, I fixed a few bugs with the staging and the ncdr_concepts view (see ticket:3605#comment:7, [235d2c5cb17b]) that caused concept code mismatch for medications and for 7105 Name: Segment Number. I also made a quick tweak in [3500e38766d4] to avoid hard-coded strings. After that, a quick test run seems to indicate that the only facts without concepts we have are `NCDR|CURRENT_AGE:2009` (2 facts - I assume it's due to messy data) and `NCDR|CURRENT_AGE:Dead` (126 facts). data-repository major ngraham 08/11/15 enhancement 02/03/15

2015-08-10 (3 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Sravani, it looks like the "has selections" flag was achievable in SQL. I've added it to the ncdr_concepts view. See [bc1e79d90915]. Also, as we discussed, there's one column per medication - they should be constants (selectable to the user in the webclient) but they aren't "selections" in the NCDR dictionary. So, I added SQL to build the medication hierarchy based on the dictionary column translation table in [f59e48a8628f]. Also, as discussed, I added support for manually curated NCDR selections (specifically, for sequence number 7105) in [2ee6069c79f5]. data-repository major ngraham 08/10/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I After chatting with Sravani, it looks like a large number of missing concepts (in the `ncdrall_nullconcepts` view) are due to the fact that the code is trying to join on both the sequence number _and_ the selection name (except for Labs for which Sravani has made manual exceptions). I'll reopen #3661 to add a column in the dictionary that is a flag to indicate if there are selections for a given sequence number so we'll know whether to join on just sequence number or sequence number and selection. data-repository major ngraham 08/10/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Sravani, Unfortunately, the data seems a bit messy - numbers where there should be text field in places, etc. Also, it appears the data doesn't match the data dictionary. In some cases at least, I think we should make special-case exceptions for the dictionary differences (for example, 'No symptom, no angina' in the dictionary vs. 'No symptom; no angina' in the data). For cases where we have numbers instead of "Yes" and "No", etc., I don't know that we have a choice other than to just not load the rows (assuming of course that it's not a staging problem - preliminary investigation says that what's staged does match the spreadsheet). I'll come chat with you before proceeding to make sure I'm understanding the mismatched concepts report. ==== details Replying to [comment:73 schandaka]: > - Some of the !EntryNumbers are 'No' instead of numbers. Indeed, but it looks like there are only 2 rows: {{{ select count(*) from ( select ltrim(translate(entry_number,'0123456789', ' ')) entry_num FROM ncdrv4.ncdrv4 ) where entry_num is not null ; }}} I double-checked the spreadsheets and indeed, the very last row of "HERON PATS v4 1-2012 to 9-2014.xlsx` (7772) has "No" in the Entry Num field. Same for row 720 of "HERON PATS v4 7-2009 to 12-2011.xlsx". I think we should just ignore these rows in SQL - it's only 2 out of 1000's. > - One of the selections for seq_5000 and seq_5020 is 'No symptom; no angina'(with semi-colon). In the ncdr_concepts view I see it as 'No symptom, no angina'(with comma). The join on ncdr_concepts is failing because of the resulting in null concept_cd. The [https://www.ncdr.com/WebNCDR/docs/public-data-collection-documents/cathpci_v4_codersdictionary_4-4.pdf?sfvrsn=2 data dictionary] has a comma "No symptom, no angina" I plan to make some special case exceptions in the PDF parser such that the resulting dictionary matches the data. > - Race values for some of the rows is numeric. It should be Yes/No. > {{{ > SELECT Entry_number FROM NCDRV4.NCDRV4 WHERE SEQ_2070='180.0' OR SEQ_2070='154.9'; > }}} > - You can see the rows with such anamolies here. > {{{ > select * from schandaka.ncdrall_nullconcepts; > }}} I recreated your view (schandaka.ncdrall_nullconcepts) in my schema and took out the "to_number" calls as I kept getting "invalid number" errors when looking at the concepts. The following produces 692 rows: {{{ select distinct something_name, concept_cd, something_value from ncdrall_nullconcepts order by something_name; --692 }}} data-repository major ngraham 08/10/15 enhancement 02/03/15

2015-08-08 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Nathan, I have modified the ncdr_facts_load script to point to the newly staged column names. While working on that I have noticed that some of the data in the new table is bad. As in, the selections from the ncdrv4.ncdrv4 do not the match the selections from ncdr_concepts table. Fox example, - Some of the EntryNumbers are 'No' instead of numbers. - One of the selections for seq_5000 and seq_5020 is 'No symptom; no angina'(with semi-colon). In the ncdr_concepts view I see it as 'No symptom, no angina'(with comma). The join on ncdr_concepts is failing because of the resulting in null concept_cd. - Race values for some of the rows is numeric. It should be Yes/No. {{{ SELECT Entry_number FROM NCDRV4.NCDRV4 WHERE SEQ_2070='180.0' OR SEQ_2070='154.9'; }}} - You can see the rows with such anamolies here. {{{ select * from schandaka.ncdrall_nullconcepts; }}} For now i included concept_cd is not null in the script so that it wont error out on observation_fact load due to the null concept_cd. I have pushed the changes that I made in the facts load script so far. data-repository major schandaka 08/08/15 enhancement 02/03/15

2015-08-07 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Replying to [comment:71 schandaka]: > ... because we couldn't map NCDR encounters Why is mapping NCDR encounters necessary for adding age at visit facts? Age at visit is a coherent concept whether it's an Epic visit or not, no? data-repository major dconnolly 08/07/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Discussion about NCDR 'Age' column came up during a meeting with Russ,Dan,Matt,Nathan and Tamara. Nathan and I talked about Age column in NCDR Demographics folder. It is the age at the Cath/PCI Procedure visit. Since we cant obtain that from the Visit Details->Age at Visit(because we couldn't map NCDR encounters),we have decided to retain the NCDR Age terms. However, instead of duplicating the code we will be using something like this from the existing age_terms(from the curated data). {{{ select folder_name, leaf_name, case when concept_cd is null then null else 'NCDR' || substr(concept_cd, instr(concept_cd, '|')) end concept_cd, age, a_min, a_max from age_terms; }}} data-repository major schandaka 08/07/15 enhancement 02/03/15

2015-08-05 (3 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Russ answered Sravani's question (comment:65) data-repository major dconnolly 08/05/15 enhancement 02/03/15
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) heron-weekly: DC: Making progress, but postpone delivery. cf. [http://bmi-ci.kumc.edu:8080/view/GPC/job/scilhs_cdm_prep/ scilhs_cdm_prep] job data-repository major ngraham 08/05/15 design-issue 07/02/13
#2713 Bring Cardiology labs data into HERON heron-weekly: Sravani was reporting for Russ data-repository major dconnolly 08/05/15 enhancement 05/15/14

2015-08-04 (1 match)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I Sravani, I finished up the script/Jenkins jobs to parse/stage the NCDR data dictionary (see ticket:3661#comment:2). Please let me know if you see any issues with the results and/or you want to work together to build the NCDR hierarchy. data-repository major ngraham 08/04/15 enhancement 02/03/15

2015-07-30 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#3224 Bring NCDR(v4) data into HERON - Phase I data-repository major schandaka 07/30/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I assigned data-repository major schandaka 07/30/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Dan, assigning this ticket to you to review the work on test. Please take a look at Coronary Anatomy folder. The numbers that you see are the actual result values. I believe they could be made nval_num. Matt Hoag suggested similar thing with Age folder before and wanted me to check with Russ. I spoke to Russ about it and he was ok with having it as is for now and suggested we could come back to it after reviewing it with the client(Dr.Gupta). I will make sure to bring this discussion during our Tuesday(August 4th) meeting. data-repository major schandaka 07/30/15 enhancement 02/03/15
#3224 Bring NCDR(v4) data into HERON - Phase I Dan, I think I misunderstood you. Since I had insert scripts from the staging on ID server, it wasn't that difficult for me to stage all the data. NCDR data is not that huge either. {{{ select count(*) from ncdrv4.ncdrv4; --16070 rows }}} Let me know if you think otherwise. - As per comment:57, there were some duplicate encounters. Here is the explanation for that. When a patient walks in for a PCI procedure,he/she could be getting multiple PCI procedures done during the same encounter. As in, multiple stents could be placed during the same encounter. I thought EntryNumber in NCDR is unique as the test data lacked patients with multiple stents placed during the same encounter. I was able to fix this error by appending LesionNumber to the EntryNumber to obtain an unique encounterid. LesionNumber is unique within the same encounter. It uniquely identifies the region where a stent is placed. - I also made changes to the ncdr_facts_load script as per comment:52. I used unpivot function 5 times to get 5 different folders. I believe it could still be shortened once Nathan can finish parsing the NCDR data dictionary(PDF file). It doesn't stop my work in anyway though. - I also added a test query for PriorPCI condition. {{{ python test_heron_query.py http://.../i2b2/webclient/ --demo INFO:__main__:opening Heron homepage... INFO:__main__:Found page with title: i2b2 Web Client INFO:__main__:Getting user configuration... INFO:__main__:Got it. INFO:__main__: Testing: NCDR PriorPCI Query #3224 INFO:__main__:Found: 6 INFO:__main__:timing: 2015-07-30 12:42:06.861000, 2015-07-30 12:42:07.262000, 0:00:00.401000 INFO:__main__: Testing: NCDR Query #3224 INFO:__main__:Found: 1 INFO:__main__:timing: 2015-07-30 12:42:07.276000, 2015-07-30 12:42:09.210000, 0:00:01.934000 INFO:__main__: }}} All the above mentioned code modifications are committed in (7286ffeac727). I am proceeding ahead to work on #3563 to bring other NCDR data in. data-repository major schandaka 07/30/15 enhancement 02/03/15

2015-07-29 (2 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) I suppose loading the SCILHS CDRN CDM ontology (GPC:ticket:191) would help with this. data-repository major dconnolly 07/29/15 design-issue 07/02/13
#2138 use SCILHS ontology for HERON ICD9, CPT, HCPCS? (sync with UMLS?) accepted data-repository major dconnolly 07/29/15 design-issue 07/02/13

2015-07-28 (4 matches)

Ticket Summary Comment Component Priority Author Date Type Created
#2713 Bring Cardiology labs data into HERON Ticket retargeted after milestone closed data-repository major ngraham 07/28/15 enhancement 05/15/14
#2617 Saved searches not updated in REDCap projects after Arkansas release Ticket retargeted after milestone closed data-repository minor ngraham 07/28/15 defect 04/01/14
#2318 refactor medication modifiers so "items instance will be the same" will work Ticket retargeted after milestone closed data-repository minor ngraham 07/28/15 enhancement 10/01/13
#2301 constraining birth-date by date doesn't work - HERON uses sysdate for start_date in demographics Ticket retargeted after milestone closed data-repository minor ngraham 07/28/15 problem 09/24/13
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