Upload file with WoRMS code

[peterdesmet]

@nicolasvanermen can you test uploading a file where rather than the ESAS code, the AphiaID is provided?

So an observation record with:

• SpeciesCodeType: ERID
• SpeciesCode: 1457401 (this is Vulpes vulpes)

The intent is that this is possible, so users can submit species that are not on the ESAS list but that are on WoRMS, but I don't think this was tested.

• Does not through QA error
• Should be returned by API as:

speciesCodeType: ERID
speciesCode: 1457401
speciesScientificName: Vulpes vulpes (?)
speciesEnglishName: empty
wormsAphiaID: 1457401
wormsScientificName: Vulpes vulpes

Regarding the resubmission, I thought I will check this again yet the earlier accepted ESAS_BE_DATA_test_obis_tab.csv gives an error when screening, while before it did not, how come?

Hi Nicolas,
This is not a valid file:

You are considering that the whole line is a string: "FI 202 BE 202 info@inbo.be"

[nicolasvanermen]

Uploaded a file with ERID instead of ESAS codes. It did not return errors, so this seems to be fine. Failed to check the download though as the download button returns a blank page. @cmspinto how come?

[cmspinto]

Have finally tested this and the import is working fine, like expected!
Can you try to import the file again?

[nicolasvanermen]

Imported again, two of them indeed came through, the resubmission did not it seems? (still the upload of 27/04, although I opted to overwrite).

[nicolasvanermen]

When I download, I get 1 instead of 3 campaign records, yet all three sample records... What went wrong here?

[nicolasvanermen]

[nicolasvanermen]

And why are these campaigns split in two rows?

[cmspinto]

Download and inventory are fixed now :).

Thanks for the heads up:
https://esas.ices.dk/inventory?selectedYear=1996

[nicolasvanermen]

[nicolasvanermen]

In the download page the campaigns are still split into two row, while they should be aggregated in one.

[cmspinto]

thanks for the heads up, it was not grouping correctly.

[nicolasvanermen]

Now I see the 110000155 campaing is no longer in our submissions...? I redirected Peter to this issue, because he wanted to perform some testing on these 3 campaigns...

[nicolasvanermen]

So now there are 2 campaigns in the submission, but three in the download... I don't get this...

[nicolasvanermen]

Regarding the resubmission, I thought I will check this again yet the earlier accepted ESAS_BE_DATA_test_obis_tab.csv gives an error when screening, while before it did not, how come?

[peterdesmet]

😕 this is frustrating. @cmspinto can you check? From the issues here, the (re)submission seems buggy right now.

[cmspinto]

speciesCodeType: ERID
speciesCode: 1457401
speciesScientificName: Vulpes vulpes (?)
speciesEnglishName: empty (this is change to try to find the vernacular name, example bellow... )
wormsAphiaID: 1457401
wormsScientificName: Vulpes vulpes

[peterdesmet]

@cmspinto I don't understand your comment. I mainly want to check records @nicolasvanermen has uploaded, but can't access them via the API, see #76 (comment)

[cmspinto]

Had to re-upload the files, due to a bug in the upload the files were not load correctly.

[peterdesmet]

Test passed, records uploaded with ERID rather than ESAS speciesCodeType are correctly presented by the API: https://esas.ices.dk/api/getObservationRecords?campaignID=110000155

"speciesCodeType": "ERID",
"speciesCode": "137188",
"speciesScientificName": "Gavia stellata",
"speciesEnglishName": "red-throated diver",
"wormsAphiaID": "137188",
"wormsScientificName": "Gavia stellata",

vs e.g record with ESAS:

"speciesCodeType": "ESAS",
"speciesCode": "59",
"speciesScientificName": "Gavia sp.",
"speciesEnglishName": "unidentified diver",
"wormsAphiaID": "137057",
"wormsScientificName": "Gavia",

[peterdesmet]

@nicolasvanermen can this issue be closed? E.g. is #88 (comment) resolved?

[nicolasvanermen]

This comment seems to be resolved... Campaigns aggregated in one line.
Yet when performing the download the observations are not linked to the right observation ID's that were in the three entry files. All data seem to be mingled... @cmspinto please: how is this possible?

[cmspinto]

We are now checking the upload and download.
Data that is uploaded should be the same that is uploaded.

[nicolasvanermen]

We figured this out: the appartent mingling was due to an old file (ESAS_BE_DATA_test_obis_tab_ERID.csv) that was in the database, instead of the most recent upload (ESAS_BE_DATA_test_obis_tab.cs), both with the same campaignID; very glad this was figured out, and that there is a logical explanation... Still very confusing because in the overview of file screenings it seems to suggest that the latter file (88) was uploaded to the database, hereby overwriting the former file (86):

• So concluding: it remains to be tested whether the status "File already uploaded to the database" actually holds true.

[peterdesmet]

A separate issue has been created for testing file overwrites. This issue can be closed.