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#L50>For the second error, you need to create a new 'data validation type'. You go <your_site>/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#L50>https://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 <[email protected]> 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 GitHub<#8 (comment)>, or mute the thread<https://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