{%extends "base.html"%} {%from "cli-output.html" import cli_output%} {%block title%}R/qtl2 bundle: QC Job Error{%endblock%} {%macro errors_table(tableid, errors)%} <table id="{{tableid}}" class="table error-table"> <caption>{{caption}}</caption> <thead> <tr> <th>Line</th> <th>Column</th> <th>Value</th> <th>Message</th> </tr> </thead> <tbody> {%for error in errors%} <tr> <td>{{error.line}}</td> <td>{{error.column}}</td> <td>{{error.value}}</td> <td>{{error.message}}</td> </tr> {%else%} <tr> <td colspan="4">No errors to display here.</td> </tr> {%endfor%} </tbody> </table> {%endmacro%} {%block contents%} <h1 class="heading">R/qtl2 bundle: QC job Error</h1> <div class="explainer"> <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p> <p>We list below some of the errors that need to be fixed before the data can be uploaded onto GeneNetwork.</p> </div> {%if errorsgeneric | length > 0%} <h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3> <div class="explainer"> We found the following generic errors in your R/qtl2 bundle: </div> <h3>Missing Files</h3> <div class="explainer"> <p>These files are listed in the bundle's control file, but do not actually exist in the bundle</p> </div> <table id="tbl-errors-missing-files" class="table error-table"> <thead> <tr> <th>Control File Key</th> <th>Bundle File Name</th> <th>Message</th> </tr> </thead> <tbody> {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%} <tr> <td>{{error.controlfilekey}}</td> <td>{{error.filename}}</td> <td>{{error.message}}</td> </tr> {%endfor%} </tbody> </table> <h3>Other Generic Errors</h3> {{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}} {%endif%} {%if errorsgeno | length > 0%} <h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3> <div class="explainer"> We found the following errors in the 'geno' file in your R/qtl2 bundle: </div> {{errors_table("tbl-errors-geno", errorsgeno[0:50])}} {%endif%} {%if errorspheno | length > 0%} <h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3> <div class="explainer"> We found the following errors in the 'pheno' file in your R/qtl2 bundle: </div> {{errors_table("tbl-errors-pheno", errorspheno[0:50])}} {%endif%} {%if errorsphenose | length > 0%} <h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3> <div class="explainer"> We found the following errors in the 'phenose' file in your R/qtl2 bundle: </div> {{errors_table("tbl-errors-phenose", errorsphenose[0:50])}} {%endif%} {%if errorsphenocovar | length > 0%} <h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3> <div class="explainer"> We found the following errors in the 'phenocovar' file in your R/qtl2 bundle: </div> {{errorsphenocovar}} {%endif%} <h4>stdout</h4> {{cli_output(job, "stdout")}} <h4>stderr</h4> {{cli_output(job, "stderr")}} <h4>Log</h4> <div class="cli-output"> <pre>{{"\n".join(messages)}}</pre> </div> {%endblock%}