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ucsd-ccbb / qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
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Add template for controls #174

Open adswafford opened 5 years ago

adswafford commented 5 years ago

There is no Wizard template for adding controls, following the control branch of EMPO http://www.earthmicrobiome.org/protocols-and-standards/empo/

Unfortunately, because the taxonIDs are different, we'll have to make one for each branch. @stephanieorch do you still have a copy of the blanks prep template fields or do you need one from Carolina to use as a guide?

AmandaBirmingham commented 5 years ago

I have no idea what you mean by a "Wizard template for adding controls". Could you provide some more detail?

adswafford commented 5 years ago

Sure and yes, this is related to #175 . The goal would be to add three more templates nested under "Control" in the Wizard: "Single strain", "Mock community", and "Other"

I've attached the required information to make these in the QIIMP tab of the file here, though I've included the typical implementation for reference as well.

Blank Sample template metadata.xlsx

adswafford commented 5 years ago

Realized that this required an update at the ebi-submittable template, so did this to allow for Control EMPO terms (attached) and created the template for Control->Positive->Single Strain (attached) that branches from EBI-submittable.

Still need to do this for mock communities and negative controls, to be complete by code freeze on Nov 2. Gail provided updated preferred terms for the controls, so implementing these (attached for reference as well.)

ebi-submittable_new.xlsx Blank Sample template metadata_GA.xlsx single-strain.xlsx

AmandaBirmingham commented 5 years ago

@adswafford: If this is to be implemented in time for a code freeze tomorrow, I am going to need considerably more detail IMMEDIATELY about how the interface and templates need to change.

Is the request to make a new "Host/Environment" called "Control" and give it three new "Sample Type"s called "Single strain", "Mock community", and "Other"? If so, what spreadsheet defines the Control host/environment? I assume the single-strain.xlsx spreadsheet defines the "Single strain" sample type? I understand that the spreadsheet for the mock communities is in process; when will it be available? Will there be a spreadsheet defining the "other" sample type for controls, or will it simply inherit one of the other default environments (for example, Other EBI-Submittable Environment)? What is the reference to "still need to do this for ... negative controls"--is there another sample type of control beyond "Single strain", "Mock community", and "Other"? Where does the "Sterile water blank" options that is listed in the ebi-submittable_new.xlsx template fit into the desired changes?

adswafford commented 5 years ago

It looks like we'll miss the code freeze since I've run out of time to prepare them and it looks like we need to discuss the best way to do this since we don't have Stephanie as the main PoC for adding these. I think we should meet with Charlie and Shae to go over what the process is when we need to add new templates as this will likely be an ongoing need with time and as standards are updated.