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Problems with import of tutorial subject data #158

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mikkeltullin opened this issue Sep 13, 2016 · 6 comments
Open

Problems with import of tutorial subject data #158

mikkeltullin opened this issue Sep 13, 2016 · 6 comments
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@mikkeltullin
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Hey
We now have our Phenotype Database up and running, both our test node and work node, at the university of Copenhagen. However, I face troubles when trying to import the tutorial subject data and I receive the following message.
validation results

I do not know if it's relevant but the application status is as follow:

App version: 2.0.6.0
Grails version: 2.5.1
Groovy version: 2.4.4
JVM version: 1.8.0_101
Controllers: 44
Domains: 38
Services: 22
Tag Libraries: 26
Environment: PRODUCTION

Best regards
Mikkel Tullin

@ferryjagers
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Edit your study -> subjects -> open the species dropdown and click 'add more...'

The initialisation of species is part of ExampleStudies.addTestData() and only triggered when environment=DEVELOPMENT (see github.com/PhenotypeFoundation/PhenotypeDatabase/blob/master/grails-app/conf/BootStrap.groovy#L79).

Would it be more clear to do this in all environments?

@mikkeltullin
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Dear Ferry
Thank you for your quick response.
I do not have a assess to edit the species dropdown, it is yellow and marked as mandatory to fill in. It seems like it is locked for some reason and it is the only field together with the name field that I am not able to edit. Am I missing something or is there something I do not understand?
subject

@ferryjagers
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The page you are on is the Template Editor, you can find the dropdown I mentioned under Browse -> My/All Studies -> Edit this study -> Subject page.

species_addmore

@mikkeltullin
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Dear Ferry
Thank you for your response.
I don't understand how I can edit species in the subject page when I am not able to import the subjects. I can see that this is possible when they are successfully imported...
I have attached three dumb's before the error message.
subject_1
subject_2
subject_3

@ferryjagers ferryjagers self-assigned this Sep 16, 2016
@ferryjagers
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I'm sorry, I think it would have been more clear if I showed you the steps in an empty study in the first place.

  • Go to Browse -> My/All Studies -> Pencil icon (edit this study) -> Subject page.
  • You will see a screen like this:
    untitled
  • Click Add, a popup window to add subjects will appear.
  • Leave the count at 1, we just need this window to add 'Homo sapiens' as a term, not to add actual subjects.
  • Select a subject template.
  • Click the Species dropdownbox and select add more.
  • Another window will popup, type 'Homo sapiens' in the textfield next to search term.
  • Click the search result (NCBITAXON)
  • Click the add term button
  • Click the close button
  • Click the cancel button

Now you will be able to import your subjects :-)

@mikkeltullin
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Dear Ferry,
Thank you very much. Something is not working correct here, we will update everything and try again.

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