Openbis

Questions

Discussed

we cannot use the API (both as user or admin) see issue on Rostyk
- the creation of a PAT apparently didn't solve the issue

The o.set_token() function should be used o.set_token('pierre-marie.allard_AT_unifr.ch-XXXXXXXXXXX', save_token=True)

have a one2one and a one2many links examples. How to we do this ?

Caterina : this is not doable at the moment through the GUI. Or rather it is but manually. In our case we should take advantage of the pyOpenBis. This is fundamental for the DBGI project. We need to verify that handling of such linked tables is achievable in OpenBIS in a convenient manner. See Todo section for more details.

can we display maps from lat/lon coordinates

No. No geojson handling. We could by screenshoting the maps. Or maybe bettre hyperlinking to an external mapping (e.g. google maps) service

see for upload of a simple csv from the UI TSV is deprecated. This should be done using the Excel template. Caterina will discus with the dev team if a csv import can be maintained.
can we locate individual samples in boxes (e.g. 9*9) in racks, in shelves, in a fridge ?

Yes. What is not doable for now is to define the place of a box of viales inside a rack. An intermediate level should be implemented.

can we barcode a box of vials ?

No. To be implemented.

Should the headers match exactly ? yes
Should ALL fields be present ?

NO if they aren't defined as mandatory in the Object type/OBSERVATION But the depending on the field type they cannot be filled for ex with NA if the field type is digit.

Not discussed / for next time

can we display picture from hyperlinks
updates on QRcodes
why can't properties in General panel (e.g. https://openbis-dbgi.labnotebook.ch/openbis/webapp/openbis-ng-ui/#/object-type/SPECIMEN) be modified. For ex pass from multivarchar to hyperlink ?

Todo

try to pass current Directus tables to OpenBis

Varia

What do you need from us to advance ?

Found one error: Sample type OBSERVATION has no property type ID assigned.

Indeed they are no id field in the OBSERVATION schema (https://openbis-dbgi.labnotebook.ch/openbis/webapp/openbis-ng-ui/#/object-type/OBSERVATION)

Todo

UniFr

create a schema of the tables we want to connect
minimal example of each table
excel sheet for each table
property name / property type for each table

CODE is UPPERCASE and _ instead of space, no special chracter label should match the header Description: free text DATA TYPE: their is a list (where ?)

OpenBIS team

produce pyOpenBis scripts and have the schema and related tables proposed by UniFr implemented in the OpenBIS instance.
implementation of barcodes possibilities at the "box of vials" levels
possibility to track the localisation of boxes of vials within a rack. Creation of an additional and intermediate level in the storage tracking system in openBis.