MCL uploading issue

[bluemood2011]

I've created a test template excel file of genotype_snp type which is comprised of db, dataset, stock and genotype_snp sheets. When I uploaded the excel with MCL, it failed with error logs like this:

Error Logs [stock]

row 2 -------------- (name) = () not found in db Invalid stock type : cultivar

For the first error, does it mean the stock name should exist in the db sheet ? But I can't find this header in db. For the second error, is stock type same as germplasm_type? Shouldn't I select from the choices given in the header description?

Thanks

[leetaei]

Could you list 'SITE VARIABLES'? You can find in [your-site]/admin/mcl/global_var?

Thank you.

[bluemood2011]

Hi, Here is my site variables:

And there is no stock_type in admin/mcl/data_valid.

Thank you

[leetaei]

Hi,

row 2 -------------- (name) = () not found in db Invalid stock type : cultivar

https://github.com/tripal/mainlab_chado_loader/blob/2395396462b045d776638be27d0678fc534320d1/includes/class/mcl_chado_class/mcl_chado_db.class.inc#L50For the second error, you need to create a new 'data validation type'. You go /dmin/mcl/data_valid

type 'stock_type' as new data valiattion type and type 'MAIN' as CV name. Once you create 'stock_type', you see new category

'STOCK_TYPE' under DATA VALIDATION fieldset. Now you can add valid stock types for you site there.

I am not sure about the first error since it is empty in the parentheses. If you take a look at the code,

you can see it won't print out error if $db is empty.

https://github.com/tripal/mainlab_chado_loader/blob/2395396462b045d776638be27d0678fc534320d1/includes/class/mcl_chado_class/mcl_chado_db.class.inc#L50https://github.com/tripal/mainlab_chado_loader/blob/d1d160dd5f3be0dedd30d2dc7d14a72b6f1d0819/includes/class/mcl_chado_class/mcl_chado_db.class.inc#L74

You can try to comments out these 3 lines in stock template file.

https://github.com/tripal/mainlab_chado_loader/blob/d1d160dd5f3be0dedd30d2dc7d14a72b6f1d0819/templates/mcl_template_stock.class.inc#L105

https://github.com/tripal/mainlab_chado_loader/blob/d1d160dd5f3be0dedd30d2dc7d14a72b6f1d0819/templates/mcl_template_stock.class.inc#L145

https://github.com/tripal/mainlab_chado_loader/blob/d1d160dd5f3be0dedd30d2dc7d14a72b6f1d0819/templates/mcl_template_stock.class.inc#L146

If you would like, I can meet you in skype or gotomeeting.

Thank you.

• Taein https://github.com/tripal/mainlab_chado_loader/blob/d1d160dd5f3be0dedd30d2dc7d14a72b6f1d0819/templates/mcl_template_stock.class.inc#L146

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From: bluemood2011 notifications@github.com Sent: Monday, August 27, 2018 1:37 AM To: tripal/mainlab_chado_loader Cc: leetaei; Comment Subject: Re: [tripal/mainlab_chado_loader] MCL uploading issue (#8)

Hi, Here is my site variables: [image]https://user-images.githubusercontent.com/42560463/44649689-282fef80-aa17-11e8-83aa-8f668c653e42.png

[https://user-images.githubusercontent.com/42560463/44649689-282fef80-aa17-11e8-83aa-8f668c653e42.png]

And there is no stock_type in admin/mcl/data_valid.

Thank you

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/tripal/mainlab_chado_loader/issues/8#issuecomment-416156552, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVo8CWcSBvimM7x8sm-jeK1YdXp_Gh5Kks5uU6-6gaJpZM4WE-g1.

[bluemood2011]

I created a new stock type and comment out the 3 lines as you suggested, and the errors are fixed. But now I've met another issue: [genotype_snp]

row 2 -------------- (uniquename, type_id) = (AT3G63460_P1-CDS-3-1534499245:23431009..23431101, 2000) not found in feature

this is my genotype_snp template

Actually, I'm quite confused about the template files, as I'm not familiar to a lot of the headers. Thus I'm not clear about how to prepare my data. Could you please give some example data for testing?

By the way, I don't have a skype or gotomeeting.

Thank you