[CGI] Alternative workflow (icke vilt)

Test the workflow in seqdb-beta

Testing the file CGI_II -created by Thomas&Niklas.

1. columns in the xlsx-file should be mapped to (1) Specimen-file and (2) Sample-file
2. there 2 tabs in the file '3000142729' and '3000142896' -> 96 rows in each tab.

The columns in the xlsx-file are the following (mapping by Thomas&Ingimar) :

1. Project = 'diarienummer' such as '4.1-595-2018'
2. Prov-Typ(sample-type) = 'Unio Crassus'
3. Sample-source=M1-till-M31 followed by 150-till-11 followed by 1,2 and NA
4. Prov-Namn (sample-name)= här position A1 till H12 : Remove this column
5. Position -> from the scanner -> put in the 'sample'-template
6. Tube-ID -> from the scanner -> put in the 'sample'-template
7. Container-ID -> from the scanner -> put in the 'sample'-template
8. NRM-ID -> generate an unique identifier, unique for every vile
9. Freezer-room -> in the 'x'-template
10. Freezer-box -> in the 'x'-template 11.Freezer-position -> 2d-position -> in the 'x'-template

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Upload to seqdb-beta

https://seqdb-beta.dina-web.net/login.jsp

1. Mappa kolumn mot kolumn i någon av följande mallar (1) specimen eller (2) sample

Specimen Testing the following mapping.

1. OK-specimen : NRM-CGI2 - i kolumn = 'Group Name'
2. OK-Specimen : 4.1-595-2018 - i kolumn = 'Projects'
3. OK-Specimen : NRM-CGI-ANNAT - i kolumn = 'Collection Code'
4. OK-Specimen : NRM-CGI-909090 (såkallat NRM persistent) - i kolumn = 'Others id'
5. OK-Specimen : Unio Crassus (Prov-typ (el. sample-type)) - i kolumn 'synonym'
6. OK-Specimen : M1-MXX (sample-source) - i kolumn

comments on the mapping

3. 'Collection Code' -> Why ? needs to be in place : 'NRM_-CGI-ANNAT' is a dummy
4. 'Others id' -> We want a persistent NRM-ID, : 'NRM-CGI-909090 is a dummy'

Are these columns in the speciman-templates useful?

1. in the specimen-template we have the following columns 'Tissue type' och 'Extra info'

Sample Testing the following mapping.

1. Position
2. Tube-ID
3. Container-ID
4. NRM-ID
5. Freezer-room
6. Freezer-box
7. Freezer-postition

prova: specimen och sample -> The files should be imported in that order;

1. specimen-file
2. sample-file.

Test A : Specimen-template

1. Logga in på Seqdb -workflow
2. fyll i SeqDB
3. Skapa GROUP = NRM-CGI2 -> DONE
4. Skapa collection code = NRM-CGI-ANNAT -> DONE
5. Skapa project = 4.1-595-2018 -> DONE
6. Försök importera filen 'Specimen-test_a.xlsx' -> https://seqdb-beta.dina-web.net/linkImporter.html
7. klagar på -> Row #3: For input string: "M2"
8. ändrar specimen-identifier till int '22'
9. fungerar nu -> får in

sammanfattning av importen av specimen-mallen

-> group-name = nrm_CGI2, Collection Code = NRM-CGI-ANNAT, Specimen Identifier = 22, sub id = 2 (löpnummer är det tänkt), Other ids = NRM-CGI-909090 (såsom persistent nummer).får inte in -> Projects ????

Test B : Specimen-template

1. Logga in på Seqdb -workflow
2. fyll i SeqDB
3. Skapa GROUP = NRM-CGI2 -> DONE
4. Skapa 'Collection Code' = 4.1-595-2018 -> EJ Möjligt, får inte vara siffror.
5. Skapa project
6. Försök importera filen 'Specimen-test_a.xlsx' -> https://seqdb-beta.dina-web.net/linkImporter.html
7. OBS: Ändrar specimen-identifier till int '22'

Testing C:

1. using the templates from DNA - /home/ingimar/Documents/seqdb/2019-00-27_CGI_Thomas-Niclas/mallar/CGI-test_söndag
2. finetune this example
3. Q: where to store diarienummer, project is not working.
4. exporting from sample or specimen is not working: @TODO mail AAFC