Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+--
 Reporter:  dconnolly |   Owner:  lv
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  grouse-resdac-2
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+--
Changes (by dconnolly):

 * cc: gpc-dev@…, badagarla (removed)
 * cc: lv, gkowalski, Phillip.Reeder@… (added)
 * owner:  lpatel => lv


Comment:

 LV to investigate at MCRF the week of 6 Jun (#12). Other notes from the
 call:
   - the list of tables GK used (comment:9) - is that OK?
   - DC: yes, that meets all requirements I’m aware of

 MCW is done; how long did that take?
  - Dump DB tables - mostly waiting
  - Re-map patients - some thinking (a few hours)

 PR: UTSW can start soon.

 questions from MCRF, IU, WISC show they’re thinking about it.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+--
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  grouse-resdac-2
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+--
Changes (by dconnolly):

 * milestone:  gpc-phase2-h4 => grouse-resdac-2


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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by dconnolly):

 The normal place to find a ticket's due date is the milestone that it's
 attached to. HackathonFour discussion was "by summer?" so this ticket is
 on milestone:gpc-phase2-h4, which is due July 31.

 Meanwhile, I think it's fair to ask each site to find 2 to 4 hours to give
 it a try and at least report where you get stuck within six weeks of when
 I asked for it (comment:3 May 8, discussed in the May 9 call); so that's
 June 20.

 George, I see you got it done within two weeks of when we assigned it to
 you; did it take you more than 2 hours? More than 4 hours?

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by bgryzlak):

 Can someone please clarify what the expected due date is for this ticket?

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by lpatel):

 crosswalk file has been received.
 {{{
 FCIV -sha1 grouse_crosswalk_mcw.zip
 7c0324d068a1639caf190581a506134c842df3c1 grouse_crosswalk_mcw.zip
 }}}

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 Uploaded crosswalk file to secureflles site . Done

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 From: Dan Connolly <dconno...@kumc.edu>
 Date: Thursday, May 25, 2017 at 5:39 PM
 To: "Kowalski, George" <gkowal...@mcw.edu>, Lav Patel <lpa...@kumc.edu>
 Subject: RE: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

 George, the hashes are already computed as part of the finder file you
 sent to GDIT Jan 30.

 https://informatics.gpcnetwork.org/trac/Project/ticket/595

 What we need now is a crosswalk from the patient_num in the datamart you
 sent us to the patient_num_hash you sent to GDIT Jan 30. As well as the
 date-shift for each patient_num.

 --
 Dan

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/595#comment:19>
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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by gkowalski):

 * owner:  gkowalski => lpatel


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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  gkowalski
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 Sorry about that . I'll be using the code from :  https://github.com/kumc-
 bmi/heron/blob/grouse_finder_g526/grouse/obfuscate.py to generate this .
 But looking at that code it requires a  HASH KEY , It says it is to be
 found in this ticket:
 https://informatics.gpcnetwork.org/trac/Project/ticket/401 . there is says
 :

  You should be able to get KUMC's hash key from: GPC GROUSE Key
 Distribution redcap project 65

 I don't have access to that Redcap project.  Or am I completely missing
 something ?

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  gkowalski
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by lpatel):

 * owner:  lpatel => gkowalski


Comment:

 Hi George,
 As mention in the comment:3, Can you also send the cross-walk file?

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by lpatel):

 * cc: badagarla (added)


Comment:

 Checked both files SHA1 and it matches with comment:14, and currently
 moving both files to ID server.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 FYI : there are 2 DMP files , first is I2B2 core data , the second is the
 METADATA Schema .

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  lpatel
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by dconnolly):

 * owner:  dconnolly => lpatel


Comment:

 Thanks, George!

 Lav, please confirm receipt of MCW's dump file (e.g. post a sha1 hash) and
 copy it to the GROUSE ID server. I'm not sure which DB we should import it
 into. Let's talk with Russ.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by gkowalski):

 * owner:  gkowalski => dconnolly


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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  gkowalski
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 MCW Completed uploading DMP files and password to load them into Oracle.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  gkowalski
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+

Comment (by gkowalski):

 Tables we're going to extract from i2b2 :

 OBSERVATION_FACT
 MODIFIER_DIMENSION
 CONCEPT_DIMENSION
 PATIENT_DIMENSION
 PROVIDER_DIMENSION
 VISIT_DIMENSION

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  gkowalski
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:  597
 Blocking:|
--+
Changes (by dconnolly):

 * owner:  rwaitman => gkowalski


Comment:

 Sounds like GK / MCW is in a good position to go first / soon.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  rwaitman
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+
Changes (by dconnolly):

 * owner:  rfothergill => rwaitman


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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  rfothergill
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by dconnolly):

 We expect you to include a `date_shift` column in your crosswalk; I edited
 comment:3 to include this briefly; stand by for further clarification.

 I hope the [[GROUSE#Agreements]] make it unnecessary for you to generate
 new patient IDs. The crosswalk does mean it won't matter to us on the
 receiving end, but it seems like considerable work on your end and I hope
 this submission is a relatively simple task.

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  rfothergill
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by lv):

 In terms of patient_num, I know that KUMC generates new IDs at each data
 load. Marshfield persists our IDs across refreshes (preferred by PCORnet).
 I'm not sure I'd want to send our i2b2 specific IDs out for this
 repository.

 Is this what other sites would do... or would sites generate new IDs for
 GROUSE? It shouldn't matter as long as a map is provided to get from the
 hashed IDs sent to CMS and the i2b2 data sent to KUMC.

 Are we expecting dates to be shifted? Will this cause issues matching with
 the CMS data (and/or would matching to CMS break our date shift
 obfuscation)?

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Re: [gpc-informatics] #595: collect i2b2 datamarts for GROUSE

[GPC Informatics]

#595: collect i2b2 datamarts for GROUSE
--+
 Reporter:  dconnolly |   Owner:  rfothergill
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+
Changes (by dconnolly):

 * cc: ngraham (removed)
 * cc: lpatel, gpc-dev@… (added)
 * keywords:   => all-sites
 * status:  new => assigned
 * owner:  dconnolly => rfothergill
 * priority:  minor => major


Comment:

 Rita, would you please send us a copy of your i2b2 data repository?

 I'm asking all-sites to do this in the coming weeks, but DevTeams#cmh is
 nominated by die roll to take the ball first.

 In detail:
   1. Make a back-up including your star schema (`observation_fact`,
 `concept_dimension`, etc. but not necessarily your `qt_query_master` and
 other `qt_...` logging tables) and preferably your metadata schema (tables
 with `c_fullname`, `c_hlevel`, `c_basecode` etc.).
  a. Oracle sites, please make an Oracle `.dmp` file
  b. sqlserver sites, please use whatever backup tool seems
 appropriate. If it produces multiple files, combine them into a `.zip`
 archive.
   2. Make a cross-walk between the `patient_num`s in that backup and the
 `patient_num_hash` from your finder file (#401). A two-column CSV file
 should do.
   3. Upload these files using https://securefiles.kumc.edu/ ; address the
 submission to `lpa...@kumc.edu, badaga...@kumc.edu`

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