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emo-bon / data-quality-control-action

Action to run the QC on the EMO BON logsheets and transform them
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dealing with blanks in the logsheets #4

Open kmexter opened 3 months ago

kmexter commented 3 months ago

For rows that contain blank replicate types, a number of changes are needed 1) Instead of calling them blank1,2 when repeated, call them just blank but have a _1 and _2 in the source mat id. Need to figure out how to do this - see https://github.com/emo-bon/observatory-hcmr-1-crate/issues/13 2) the only relevant information from the sampling tab for blanks are the following: scientific name --> it's mandatory, so yes. Now it is "unidentified" but I think this is wrong. I added an issue about it. tidal stage --> optional, so no. Also, not relevant. depth --> mandatory, so yes. For now, I have used 0 (there has to be a number). sampl collect device --> optional, so no. Also, not relevant. samp mat process and deviations --> optional, but I would say yes. membr cut --> optional, but I would say yes. size frac low and up --> optional, but I would say yes. time fi --> optional, so no. Also, not relevant. env_material --> it's mandatory, so yes. Right now, for the sediment blanks it is "swab" for the water blanks it is "Milli-Q water" (based on the SOPs). 3) no measurements should be added for these samples

We will need a separate function to deal with blanks for the transformed logsheets OR just for the ttl template. To be taken up after my summer break

kmexter commented 2 months ago

this is not so much to change the values in the transformed logsheets, but rather in the ttls, I would say

kmexter commented 2 months ago

The work to do this should be done via https://github.com/emo-bon/observatory-hcmr-1-crate/issues/13 and the solution proposed there can be adopted. For point 2, I will take this up with @laurianvm first and then maybe Bram

kmexter commented 2 weeks ago

Has no effect on the QC etc but point 2 bring up with @laurianvm