Unable to see genotype list/matrix and coloured pie chart

[cornellyujy]

@laceysanderson Hey Lacey, What's kind of theme do you use? we developed our own theme, and the genotype list, matrix with color pie can not display. In this figure, only the fasta and flanking sequence can be displayed. Thanks~

[laceysanderson]

Hi @cornellyujy, we use our own custom theme as well but the default theme for these features is built into this module and its dependencies so you should not run into issues 🤔

Can you provide a screenshot of your site? and/or point me to the address if it's available? I need to know a bit more about how "the genotype list, matrix with colour pie can not display" in order to help you. These features require the data to be imported and for your site to be configured properly.

The data also needs to be "sync'd" with the module which I'm just realizing isn't included in the documentation 😮 I will add it right away but in the meantime, I've included instructions in #60. Sorry!

[cornellyujy]

@laceysanderson Hello Lacey, thanks for your response. My question could be divided into different sections. (i). I have loaded my vcf and sample.txt into chado table using genotype_loader and sync'd the data. Next step, I installed the ND_genotypes module, and here is the screenshot. I have loaded three accessions into table, but there is an error information: no registered. I am not sure the reason. Except that, How to fix the stype of fieldset, textfield, and markup. I checked the css files, but still do not know how to fix. Thanks~

[laceysanderson]

I have loaded three accessions into table, but there is an error information: no registered. I am not sure the reason.

This error message implies it cannot figure out which accession to use because there are 3 with the same name + organism. Is this expected for your data (i.e. do you have three PI173686 records in the chado.stock table with the same organism_id)? This may happen accidentally if you loaded the same genotype VCF file multiple times? 🤔

How to fix the stype of fieldset, textfield, and markup. I checked the css files, but still do not know how to fix.

All the CSS for the genotype matrix is already on your site through this module. Your theme seems to be overriding it 😬 which is hard for me to help you with when I can't inspect the CSS on your site. Here is the CSS for the germplasm field: https://github.com/UofS-Pulse-Binfo/nd_genotypes/blob/7.x-3.x/theme/css/nd_genotypes.multiple_stock_element.css and here is the CSS for the rest of the genotype matrix: https://github.com/UofS-Pulse-Binfo/nd_genotypes/blob/7.x-3.x/theme/css/nd_genotype_matrix.css. I suggest using the developer tools in chrome or firefox to inspect the CSS being applied to those particular fields. You will likely see that the CSS from this module is crossed out --look to see which rules are taking over and either alter them in your module and/or pass them onto me so I can make this module themeing more defensive. It's always a bit of a balance to let your theme take over enough so the matrix looks at home in your site while also ensuring it's still functional.

[cornellyujy]

Hi @laceysanderson , Cool! Yes, I fixed the 'no registered' error, and that's what you said and also fixed the css display. But I have another question. I have loaded vcf and sample data into chado table, but when searching the result, it always display "No variants with genotypes matched the given filter criteria." So, I checked the chado table, and found no record in genotype_call table. Is this the repeat loading leading to this question?
Thanks~

[laceysanderson]

Hi @cornellyujy maybe 😬 it sounds like when you "fixed the no registered error" you may have deleted the associated genotypes as well. I would start the process again with a fresh site to ensure there are no orphaned/missing data problems... and then load the data again.

[laceysanderson]

Also, I think your display issues might be related to using a bootstrap theme as a base for your custom theme? Can you confirm this? If so I may be able to find some time next week to test this module on a bootstrap base and harden the CSS to make filter CSS conflicts less likely.

[cornellyujy]

Thanks @laceysanderson , I am not sure if this issue was from bootstrap. I fixed the css file within the folder (sites/all/modules/nd_genotypes/theme/css). It works (not so much) well. Anyway, it's enough for me. Thanks for your help~

[cornellyujy]

Hey @laceysanderson , I have a simple question. Here is the webpage of genetic marker. In this page, it only displays one section of the left navigation. So how to display all sections at same time. Is this limited by bootstrap css? Thanks~

[laceysanderson]

Hi @cornellyujy, did you ask this in the Tripal Project slack as well and if so, did that conversation help you?