DSM Lab Extract: Difference between revisions

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We are working on a way to get DSM to extract Labs for import to our DB.
The DSM Lab Extract is a set of data we receive from Diagnostic Services of Manitoba. It is requested and processed by [[DSM Labs Consistency check.accdb]] and stored in the [[L_Labs_DSM table]].
It is requested via [[Instructions for requesting a batch of data from DSM]] and imported via  [[Instructions for importing a batch of DSM Data]].
See [[DSM data]] for more info on the data once imported.  


== Outstanding Issues ==
== Things we still want to implement/fix ==
=== additional labs ===
None currently
*we want at least NA, K, Lactate but Allan Garland is consulting with colleagues to find out if we need additional
** Lactacte, NA and K are included with current output.


=== cultures ===
== Known Issues ==
When DSM sent the original batch of data they were not sure yet about how to extract cultures. We discussed this on the phone on our meeting on Aug 14 but I have not followed this up with an email and will not right now because the data looks so bad I don't know if we will want to pursue this.
=== Aliases ===
 
There might be some inconsistencies in how the labs are re-linked to patients who arrive as Jon Doe or have aliases in PHIN or Chart for other reason. If we want to include all patients with Aliases, we will need to do something to reconcile with [[Alias ID collection]].
==== Blood ====
 
==== Sputum ====
Site = Sputum? There are a lot
 
==== Urine ====
Site = Urine? There are a handful 18
 
=== missing PHINs ===
We did not receive data for patients where we don't have PHINs. Emailed Loretta 2014-09-05
 
Could they give us chart #s? If we had those + hosp we could link conclusively. How do they do it for EMR/EPR, they must have a solid linking variable?
 
=== missing collecteddate field in returned data ===
Some of the data that was returned had blank collecteddate field. this means we can't match it to distinct admission.
 
She said they have "arrival time" - presumably they always have an entry for that, so it might be better. Are there circumstances where the diff between these would be so great to make arrival time useless? Maybe get both and use arrival time if collected time is blank?
 
=== Special Cases in results ===
What is?
: *&DEL
 
=== duplicate records ===
There were 1,865,570 records in the export.
There were 1,863,373 unique records.  
Why the duplicates?


== Requesting data ==
== Requesting data ==
Query ''Labs_requester'' in [[Centralized data front end.mdb]] will generate a list of patients we have encountered in '''<what cycle time?>'''.
A file is exported to [[#File Share]], and we ask [[#DSM Contacts]] to provide a new extract. See [[Instructions for requesting a batch of data from DSM]] for details.
 
The list includes:
*Hosp mrn
*Phin
*Admit date time
*Discharge date time
 
The file will need to be extracted to the [[#File Share]]. We could automate the process but it'll be manual for now.


== Actions by DSM ==
== Actions by DSM ==
DSM will take our file and generate an output of all labs for those patients for the admission. They will return it to us via the file share.  
DSM will take our file and generate an output of all labs for those patients for the admission. They will return it to us via the file share.  


== Data we will receive ==
== Processing data received from DSM ==
The ABGs will not be complete, are only entered at STB and used to be at HSC but flakey lately. More info to come. Ttenbergen 13:17, 2014 August 14 (CDT)
See
 
* [[Instructions for importing a batch of DSM Data]]
See also [[DSM exchange file details]]
* [[Lab identification in the DSM data]]
 
== Processing data on receipt ==
Open and run Module DSM_Processor Sub DSM_Data_prepper.
 
If there is a problem, clear out all tables (empty 0_TrialExport and run clear_made_tables), run compact and repair, try again.
 
The last column of the data can have problematic content. Last time it contained something that line-broke but wasn't a carriage return or line break. Finding short lines allowed detection and correction.


== File Share ==
== File Share ==
\\ad.wrha.mb.ca\wrha\REGION\Shared\CCMDB_Lab_Exchange
\\ad.wrha.mb.ca\wrha\REGION\Shared\CCMDB_Lab_Exchange


== Contacts ==
== DSM Contacts ==
* data guy is Alun Carter
* main contact: Alun Carter
* Mark Curtis 9267014
* Loretta Eng 9261406 Leng @ dsmanitoba.CA
* Loretta Eng 9261406 Leng @ dsmanitoba.CA  
 
== Related articles ==
{{Related Articles}}


== Log ==
* 2015-09-28 can’t see directory that Alun made;
** asked him to copy content to a diff directory I made.
** Launched ticket with eHealth to fix underlying issue.
* 2015-09-24 Alun emailed that new data is ready
* 2015-09-21 replied busy but will get me a timeline.
* 2015-09-21 emailed Alun f/u
* 2015-08-13 finished first round of http://ccmdb.kuality.ca/index.php?title=DSM_Labs_Importer.mdb waiting for data for further tests
* 2015-08-06 Alun is on vacation until Aug 24; no new import from him
* '''2015-07-22''' requested a new output from Alun because missing time for "arrived" means comparisons will always be off
* 2015-06-29 working...
* 2015-06-25 re-starting; found erroneous line because it causes a short line.
* 2014-12-29 importing new export into test tool; there were problems with the data file, then other things became higher priority
* 2014-12-24 received new export from Alun
* 2014-12-15 fu email to Alun; he figures won’t get to it till after Christmas… * 2014-12-05 provided new extract, updated wiki
*2014-11-20 Loretta emailed me to find out details… emailed her some. We are set to meet Dec 1, will need to review before then.
* 2014-11-06 Allan will book meeting with Lab folk, hopefully over next week or so, snooze for 10days
* 2014/Oct/20 no news from, whatever…
* 2014/Oct/16 emailed Allan for update
* Sept 2014 received extract from Alun carter, some good some bad
* week of 2014-12-05 met with Loretta, Alun and Allan; agreed on next round of tests; Send new test data to Alun today. Ttenbergen 11:28, 2014 December 5 (CST)
* 2014/09/25 met with Allan Garland, discussed. he was going to talk to DSM. Ttenbergen 12:56, 2014 September 29 (CDT)
* email to put this on the Task group's agenda for this Thursday. Ttenbergen 10:39, 2014 September 22 (CDT)
*did an initial analysis which doesn't look good. emailed to Allan and Julie for comment Ttenbergen 17:00, 2014 September 8 (CDT)
*discussed labs list with Allan, now need to do some more validationTtenbergen 17:09, 2014 September 4 (CDT)
*2014/aug/25  started to review data, stuck on matching labs now, will need to talk with Trish when back. Also emailed Allan with some weirdness in the data. Ttenbergen 19:38, 2014 August 25 (CDT)
*2014/Aug/21 we received data last week, but have not formally reviewed it. Ttenbergen 10:39, 2014 August 21 (CDT) Sent list of labs to Allan, he offered to review... Ttenbergen 20:59, 2014 August 21 (CDT)
*2014/Aug/14 phone call with Loretta to confirm what is needed. Requested early sample data so we can start our processing... Ttenbergen 13:17, 2014 August 14 (CDT)
*2014/Aug/07 submitted test data at Loretta’s request
*2014/Jul/31 emailed Loretta again, since no news from Alun; ooomsg says back Tue Aug 5
*2014/Jul/21 We have a file share. Alun will hopefully have test data by end of week, or early next week
*2014/Jul/17 Email from Chad Kitching re. share folder description
*2014-07-14 emailed Alun and Loretta re progress
*2014-06-16 talked with Loretta on Friday. She said Alun Carter is the data guy we will work with. She suggested a different format and requested a list of labs we want, which I gave her. Also emailed Alun to get this moving. However, he is on vacation for 3 weeks, will f/u when he is back
*2014-06-12 emailed Loretta a test extract;
*2014-06-12 emailed Loretta a sample request file. Ttenbergen 17:47, 2014 June 12 (CDT)


[[Category: DSM Labs Extract]]
[[Category: DSM Labs Extract]]
[[Category: Data Sources]]

Revision as of 17:35, 2019 December 9

The DSM Lab Extract is a set of data we receive from Diagnostic Services of Manitoba. It is requested and processed by DSM Labs Consistency check.accdb and stored in the L_Labs_DSM table. It is requested via Instructions for requesting a batch of data from DSM and imported via Instructions for importing a batch of DSM Data. See DSM data for more info on the data once imported.

Things we still want to implement/fix

None currently

Known Issues

Aliases

There might be some inconsistencies in how the labs are re-linked to patients who arrive as Jon Doe or have aliases in PHIN or Chart for other reason. If we want to include all patients with Aliases, we will need to do something to reconcile with Alias ID collection.

Requesting data

A file is exported to #File Share, and we ask #DSM Contacts to provide a new extract. See Instructions for requesting a batch of data from DSM for details.

Actions by DSM

DSM will take our file and generate an output of all labs for those patients for the admission. They will return it to us via the file share.

Processing data received from DSM

See

File Share

\\ad.wrha.mb.ca\wrha\REGION\Shared\CCMDB_Lab_Exchange

DSM Contacts

  • main contact: Alun Carter
  • Loretta Eng 9261406 Leng @ dsmanitoba.CA

Related articles

Related articles: