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UofS-Pulse-Binfo / analyzedphenotypes

Tripal/Drupal support for analyzed phenotypic data including data loaders, exporters, trait pages and summaries on germplasm pages.
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Cannot upload "stand-alone" phenotypes (without pre-existing) germplasm in db #120

Closed elor77 closed 4 years ago

elor77 commented 4 years ago

Hi @laceysanderson

We're in the process of learning these tools so we went ahead and created a sample site based on TRIPAL tutorial.

We've successfully (i think) installed analyzed phenotypes. However once I tried to upload the file (formatted as specified) we received error that the germplasm in question did not exist.

I went ahead and installed tripal_germplasm_importer When trying to upload my germplasm file I get the following error ERROR: The genus, Citrus, species, sinensis, has no matched organism in chado.organism.

I already created this organism and veryfied it's existence in the db (chado.organism table) so I'm not sure what this error means

I opened this issue under the tripal_germplasm_importer but i'm not sure that page it is very active.. I'm trying to follow your documentation (which is great, by the way) as best I can but maybe we're missing something basic?

Thanks in advance Elad

laceysanderson commented 4 years ago

For our reference, the issue referred to is here: https://github.com/UofS-Pulse-Binfo/tripal_germplasm_importer/issues/21

I've commented on your other issue regarding importing germplasm. We'll get the problem sorted out over there.

We've successfully (i think) installed analyzed phenotypes. However once I tried to upload the file (formatted as specified) we received error that the germplasm in question did not exist.

It sounds like our documentation could use a warning lettings users know that germplasm must already exist. This was done to ensure proper meta-data for the germplasm.