Sample collection #26
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Thanks @MiguelAHPpih ... I made a few comments, and also pushed up a couple proposed changes to the identifier configuration. I made comments where I made the changes, let me know if it looks good to you!
fyi @brandones
configuration/concepts/seslab.csv
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| @@ -0,0 +1,266 @@ | |||
| uuid,Void/Retire,Same as mappings,Fully specified name:es,Fully specified name:en,Data class,Data type,_version:1,_order:1000 | |||
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I'm getting the following Iniz error when trying to parse this file... are others seeing the same thing?
`ERROR - BaseFileLoader.loadUnsafe(47) |2021-06-23 10:54:34,272| The loading of the 'concepts' configuration file was aborted:
/home/mgoodrich/openmrs/ses/configuration/concepts/seslab.csv
java.lang.IllegalArgumentException:
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+-+-+-+-- BEGINNING OF CSV FILE ERROR SUMMARY --+-+-+-+
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
seslab.csv ('concepts' domain) was processed and 11 out of 265 entities were not saved.
The CSV line(s) corresponding to those entities are listed below:
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| uuid | Void/Retire | Same as mappings | Fully specified name:es | Fully specified name:en | Data class | Data type | _version:1 | _order:1000 |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 0b6f8714-6cd5-4da7-b89b-5649d6855259 | | SES Lab:SAMPLE_Plasma | Plasma | Plasma | Specimen | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 27b9eb31-6c54-4079-8079-c5ddc133fe75 | | SES Lab:SAMPLE_Whole blood | Sangre Total | Whole blood | Specimen | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| a6fd7ad8-b892-410e-b966-42df37467a80 | | SES Lab:SAMPLE_Biopsy | Biopsia | Biopsy | Specimen | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| fe9b668e-c360-4d6a-87b0-d1cf99bbe3bd | | SES Lab:SAMPLE_Ulcer | Ulcera | Ulcer | Specimen | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 8d3d888d-f71d-4120-9131-1dd2f85da36f | | SES Lab:PRESENTATION_Tube | Tubo | Tube | Medical Supply | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| c4437a04-8426-43c5-a0d3-5c931f954b85 | | SES Lab:locations_Hospital | Hospital | Hospital | Misc | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 25ee65ec-0b42-462d-8b1e-84191f1c0059 | | SES Lab:Exam_039 | Glucosa | | Test | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 8aaa4950-3944-4beb-baed-a711bdc1378e | | SES Lab:Exam_046 | PBMC | | Test | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 5c268d62-09de-4aa2-b70d-803cfc8c6655 | | SES Lab:Exam_055 | GeneXpert MTB/RIF Ultra | | Test | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 40b486bf-e08d-482d-934c-0e95082a1fad | | SES Lab:Exam_071 | PCR IS6110 para Deteccion de M. Tuberculosis | | Test | N/A | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
| 9d6b0934-b517-47cf-b5ff-07a90530fcad | | SES Lab:Exam_072 | Prueba de Sensibilidad a drogas Antituberculosas de 1ra Línea en medio | | Test | N/A | | |
| | | | Lowenstein Jensen (SIRE) (v1.0) | | | | | |
+--------------------------------------+-------------+----------------------------+--------------------------------------------------------------------------------+-------------------------+----------------+-----------+------------+-------------+
Paste print for spreadsheets... etc:
uuid,Void/Retire,Same as mappings,Fully specified name:es,Fully specified name:en,Data class,Data type,_version:1,_order:1000
0b6f8714-6cd5-4da7-b89b-5649d6855259,,SES Lab:SAMPLE_Plasma,Plasma,Plasma,Specimen,N/A,,
27b9eb31-6c54-4079-8079-c5ddc133fe75,,SES Lab:SAMPLE_Whole blood,Sangre Total,Whole blood,Specimen,N/A,,
a6fd7ad8-b892-410e-b966-42df37467a80,,SES Lab:SAMPLE_Biopsy,Biopsia,Biopsy,Specimen,N/A,,
fe9b668e-c360-4d6a-87b0-d1cf99bbe3bd,,SES Lab:SAMPLE_Ulcer,Ulcera,Ulcer,Specimen,N/A,,
8d3d888d-f71d-4120-9131-1dd2f85da36f,,SES Lab:PRESENTATION_Tube,Tubo,Tube,Medical Supply,N/A,,
c4437a04-8426-43c5-a0d3-5c931f954b85,,SES Lab:locations_Hospital,Hospital,Hospital,Misc,N/A,,
25ee65ec-0b42-462d-8b1e-84191f1c0059,,SES Lab:Exam_039,Glucosa,,Test,N/A,,
8aaa4950-3944-4beb-baed-a711bdc1378e,,SES Lab:Exam_046,PBMC,,Test,N/A,,
5c268d62-09de-4aa2-b70d-803cfc8c6655,,SES Lab:Exam_055,GeneXpert MTB/RIF Ultra,,Test,N/A,,
40b486bf-e08d-482d-934c-0e95082a1fad,,SES Lab:Exam_071,PCR IS6110 para Deteccion de M. Tuberculosis,,Test,N/A,,
9d6b0934-b517-47cf-b5ff-07a90530fcad,,SES Lab:Exam_072,Prueba de Sensibilidad a drogas Antituberculosas de 1ra Línea en medio Lowenstein Jensen (SIRE) (v1.0),,Test,N/A,,
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+-+-+-+-+-- END OF CSV FILE ERROR SUMMARY --+-+-+-+-+
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
`
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I think this is because they already exist on the concept server, but since this csv was made for only Perú i decided to leave it like that and fix it on the future
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I'm not sure if it's because of the concept server... I tried to run it on my local SES dev environment and got the error... and unfortunately we changed how things work now so that startup fails entirely if something can't be installed.
I'm trying rerunning again now because it looks like the above message I pasted doesn't include the underlying error.
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@mogoodrich , did you have any troubles with this again?
| "${patientIdentifierType.Passport.uuid}" | ||
| ], | ||
| "dispositionConfig": "file:configuration/pih/pih-dispositions-default.json", | ||
| "findPatientColumnConfig": [ |
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I made a couple changes here, see below... instead of a "type of identifier" column and a "identifier" column, this renders a separate column for DNI and Passport (feel free to adjust the labels as you see fit).
I believe this isn't exactly what you wanted, but it seemed good to do this as a start as we work through potential changes to the Core Apps module.
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This could be a nice workaround. But i think in the future we might add more document types, therefore having more columns.
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Cool, yeah, makes sense @MiguelAHPpih see my updated comments on the coreapps pull request about moving forward with supporting multiple identifiers per column:
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I'm ok with this, until we get the coreapps function. Mergin it!
| "dispositionConfig": "file:configuration/pih/pih-dispositions-default.json" | ||
| "extraIdentifierTypes": [ | ||
| "${patientIdentifierType.DNI.uuid}", | ||
| "${patientIdentifierType.Passport.uuid}" |
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These two lines add the DNI and Passport to the patient header (and make them editable via the header). Not sure if that's what you want, but I wanted to add it in as a example.
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
Co-authored-by: Brandon Istenes <[email protected]>
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I think we can merge this now. ¿Any thoughts? |
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@brandones @MiguelAHPpih did you want me to test this again? |
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@mogoodrich Yes, please. |
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@MiguelAHPpih will do! won't get to it today, but hopefully tomorrow! |
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@brandones @MiguelAHPpih not sure if I'm working off the branch or something, but I'm still getting a bunch of duplicate concept name exceptions: +--------------------------------------+-------------+-----------------------+-------------------------+-------------------------+------------+-----------+------------+-------------+ Paste print for spreadsheets... etc: uuid,Void/Retire,Same as mappings,Fully specified name:es,Fully specified name:en,Data class,Data type,_version:1,_order:1000 Paste print for spreadsheets... etc: uuid,Void/Retire,Same as mappings,Fully specified name:es,Fully specified name:en,Data class,Data type,_version:1,_order:1000 Paste print for spreadsheets... etc: uuid,Void/Retire,Same as mappings,Fully specified name:es,Fully specified name:en,Data class,Data type,_version:1,_order:1000 |
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Maybe we can remove |
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@brandones Yeah,that's better. |
National document configurations