From 754e8f214b940e05298cb360ed829f5c685d55a5 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 25 Jul 2024 11:07:33 -0500
Subject: Rename module: qc_app --> uploader
---
.../rqtl2/create-geno-dataset-success.html | 55 ++++
.../rqtl2/create-probe-dataset-success.html | 59 +++++
.../rqtl2/create-probe-study-success.html | 49 ++++
.../templates/rqtl2/create-tissue-success.html | 106 ++++++++
uploader/templates/rqtl2/index.html | 36 +++
uploader/templates/rqtl2/no-such-job.html | 13 +
uploader/templates/rqtl2/rqtl2-job-error.html | 39 +++
uploader/templates/rqtl2/rqtl2-job-results.html | 24 ++
uploader/templates/rqtl2/rqtl2-job-status.html | 20 ++
uploader/templates/rqtl2/rqtl2-qc-job-error.html | 120 +++++++++
uploader/templates/rqtl2/rqtl2-qc-job-results.html | 66 +++++
uploader/templates/rqtl2/rqtl2-qc-job-status.html | 41 +++
uploader/templates/rqtl2/rqtl2-qc-job-success.html | 37 +++
uploader/templates/rqtl2/select-geno-dataset.html | 144 +++++++++++
uploader/templates/rqtl2/select-population.html | 136 ++++++++++
.../templates/rqtl2/select-probeset-dataset.html | 191 ++++++++++++++
.../templates/rqtl2/select-probeset-study-id.html | 143 +++++++++++
uploader/templates/rqtl2/select-tissue.html | 115 +++++++++
uploader/templates/rqtl2/summary-info.html | 65 +++++
.../rqtl2/upload-rqtl2-bundle-step-01.html | 276 +++++++++++++++++++++
.../rqtl2/upload-rqtl2-bundle-step-02.html | 33 +++
21 files changed, 1768 insertions(+)
create mode 100644 uploader/templates/rqtl2/create-geno-dataset-success.html
create mode 100644 uploader/templates/rqtl2/create-probe-dataset-success.html
create mode 100644 uploader/templates/rqtl2/create-probe-study-success.html
create mode 100644 uploader/templates/rqtl2/create-tissue-success.html
create mode 100644 uploader/templates/rqtl2/index.html
create mode 100644 uploader/templates/rqtl2/no-such-job.html
create mode 100644 uploader/templates/rqtl2/rqtl2-job-error.html
create mode 100644 uploader/templates/rqtl2/rqtl2-job-results.html
create mode 100644 uploader/templates/rqtl2/rqtl2-job-status.html
create mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-error.html
create mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-results.html
create mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-status.html
create mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-success.html
create mode 100644 uploader/templates/rqtl2/select-geno-dataset.html
create mode 100644 uploader/templates/rqtl2/select-population.html
create mode 100644 uploader/templates/rqtl2/select-probeset-dataset.html
create mode 100644 uploader/templates/rqtl2/select-probeset-study-id.html
create mode 100644 uploader/templates/rqtl2/select-tissue.html
create mode 100644 uploader/templates/rqtl2/summary-info.html
create mode 100644 uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
create mode 100644 uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
(limited to 'uploader/templates/rqtl2')
diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
new file mode 100644
index 0000000..1b50221
--- /dev/null
+++ b/uploader/templates/rqtl2/create-geno-dataset-success.html
@@ -0,0 +1,55 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+
Select Genotypes Dataset
+
+
+
You successfully created the genotype dataset with the following
+ information.
+
+ ID
+ {{geno_dataset.id}}
+
+ Name
+ {{geno_dataset.name}}
+
+ Full Name
+ {{geno_dataset.fname}}
+
+ Short Name
+ {{geno_dataset.sname}}
+
+ Created On
+ {{geno_dataset.today}}
+
+ Public?
+ {%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}
+
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
new file mode 100644
index 0000000..790d174
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-dataset-success.html
@@ -0,0 +1,59 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Create ProbeSet Dataset
+
+
+
You successfully created the ProbeSet dataset with the following
+ information.
+
+ Averaging Method
+ {{avgmethod.Name}}
+
+ ID
+ {{dataset.datasetid}}
+
+ Name
+ {{dataset.name2}}
+
+ Full Name
+ {{dataset.fname}}
+
+ Short Name
+ {{dataset.sname}}
+
+ Created On
+ {{dataset.today}}
+
+ DataScale
+ {{dataset.datascale}}
+
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
new file mode 100644
index 0000000..d0ee508
--- /dev/null
+++ b/uploader/templates/rqtl2/create-probe-study-success.html
@@ -0,0 +1,49 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Create ProbeSet Study
+
+
+
You successfully created the ProbeSet study with the following
+ information.
+
+ ID
+ {{study.id}}
+
+ Name
+ {{study.name}}
+
+ Full Name
+ {{study.fname}}
+
+ Short Name
+ {{study.sname}}
+
+ Created On
+ {{study.today}}
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html
new file mode 100644
index 0000000..5f2c5a0
--- /dev/null
+++ b/uploader/templates/rqtl2/create-tissue-success.html
@@ -0,0 +1,106 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Select Tissue
+
+
+
You have successfully added a new tissue, organ or biological material with
+ the following details:
+
+
+
+ {{flash_all_messages()}}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
new file mode 100644
index 0000000..f3329c2
--- /dev/null
+++ b/uploader/templates/rqtl2/index.html
@@ -0,0 +1,36 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+R/qtl2 data upload
+
+R/qtl2 Upload
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/rqtl2/no-such-job.html
new file mode 100644
index 0000000..b17004f
--- /dev/null
+++ b/uploader/templates/rqtl2/no-such-job.html
@@ -0,0 +1,13 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+R/qtl2 job status
+
+R/qtl2 Upload: No Such Job
+
+No job with ID {{jobid}} was found.
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-error.html b/uploader/templates/rqtl2/rqtl2-job-error.html
new file mode 100644
index 0000000..9817518
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-error.html
@@ -0,0 +1,39 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+R/qtl2 job status
+
+R/qtl2 Upload: Job Status
+
+
+
The processing of the R/qtl2 bundle you uploaded has failed. We have
+ provided some information below to help you figure out what the problem
+ could be.
+
If you find that you cannot figure out what the problem is on your own,
+ please contact the team running the system for assistance, providing the
+ following details:
+
+ R/qtl2 bundle you uploaded
+ This URL: {{request_url()}}
+ (maybe) a screenshot of this page
+
+
+
+
+stdout
+{{cli_output(job, "stdout")}}
+
+stderr
+{{cli_output(job, "stderr")}}
+
+Log
+
+ {%for msg in messages%}
+ {{msg}}
+ {%endfor%}
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-results.html b/uploader/templates/rqtl2/rqtl2-job-results.html
new file mode 100644
index 0000000..4ecd415
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-results.html
@@ -0,0 +1,24 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block contents%}
+R/qtl2 job status
+
+R/qtl2 Upload: Job Status
+
+
+
The processing of the R/qtl2 bundle you uploaded has completed
+ successfully.
+
You should now be able to use GeneNetwork to run analyses on your data.
+
+
+Log
+
+ {%for msg in messages%}
+ {{msg}}
+ {%endfor%}
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-job-status.html b/uploader/templates/rqtl2/rqtl2-job-status.html
new file mode 100644
index 0000000..e896f88
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-job-status.html
@@ -0,0 +1,20 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block extrameta%}
+
+{%endblock%}
+
+{%block contents%}
+R/qtl2 job status
+
+R/qtl2 Upload: Job Status
+
+Log
+
+
{{"\n".join(messages)}}
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
new file mode 100644
index 0000000..90e8887
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
@@ -0,0 +1,120 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
+
+{%macro errors_table(tableid, errors)%}
+
+ {{caption}}
+
+
+ Line
+ Column
+ Value
+ Message
+
+
+
+ {%for error in errors%}
+
+ {{error.line}}
+ {{error.column}}
+ {{error.value}}
+ {{error.message}}
+
+ {%else%}
+
+ No errors to display here.
+
+ {%endfor%}
+
+
+{%endmacro%}
+
+{%block contents%}
+R/qtl2 bundle: QC job Error
+
+
+
The R/qtl2 bundle has failed some Quality Control checks.
+
We list below some of the errors that need to be fixed before the data can
+ be uploaded onto GeneNetwork.
+
+
+{%if errorsgeneric | length > 0%}
+Generic Errors ({{errorsgeneric | length}})
+
+ We found the following generic errors in your R/qtl2 bundle:
+
+
+Missing Files
+
+
These files are listed in the bundle's control file, but do not actually
+ exist in the bundle
+
+
+
+
+ Control File Key
+ Bundle File Name
+ Message
+
+
+
+ {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%}
+
+ {{error.controlfilekey}}
+ {{error.filename}}
+ {{error.message}}
+
+ {%endfor%}
+
+
+
+Other Generic Errors
+{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}}
+{%endif%}
+
+{%if errorsgeno | length > 0%}
+Geno Errors ({{errorsgeno | length}})
+
+ We found the following errors in the 'geno' file in your R/qtl2 bundle:
+
+{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
+{%endif%}
+
+{%if errorspheno | length > 0%}
+Pheno Errors ({{errorspheno | length}})
+
+ We found the following errors in the 'pheno' file in your R/qtl2 bundle:
+
+{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
+{%endif%}
+
+{%if errorsphenose | length > 0%}
+Phenose Errors ({{errorsphenose | length}})
+
+ We found the following errors in the 'phenose' file in your R/qtl2 bundle:
+
+{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
+{%endif%}
+
+{%if errorsphenocovar | length > 0%}
+Phenocovar Errors ({{errorsphenocovar | length}})
+
+ We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
+
+{{errorsphenocovar}}
+{%endif%}
+
+stdout
+{{cli_output(job, "stdout")}}
+
+stderr
+{{cli_output(job, "stderr")}}
+
+Log
+
+
{{"\n".join(messages)}}
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
new file mode 100644
index 0000000..59bc8cd
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
@@ -0,0 +1,66 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC job results{%endblock%}
+
+{%block contents%}
+R/qtl2 bundle: QC job results
+
+
+
The R/qtl2 bundle you uploaded has passed all automated quality-control
+ checks successfully.
+
You may now continue to load the data into GeneNetwork for the bundle, with
+ the following details:
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
new file mode 100644
index 0000000..f4a6266
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-status.html
@@ -0,0 +1,41 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block extrameta%}
+
+{%endblock%}
+
+{%block contents%}
+R/qtl2 bundle: QC job status
+
+{%if geno_percent%}
+
+
Checking 'geno' file:
+
+ {{geno_percent}}%
+ {{geno_percent}}%
+{%endif%}
+
+{%if pheno_percent%}
+
+
Checking 'pheno' file:
+
+ {{pheno_percent}}%
+ {{pheno_percent}}%
+{%endif%}
+
+{%if phenose_percent%}
+
+
Checking 'phenose' file:
+
+ {{phenose_percent}}%
+ {{phenose_percent}}%
+{%endif%}
+
+Log
+
+
{{"\n".join(messages)}}
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
new file mode 100644
index 0000000..2861a04
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
@@ -0,0 +1,37 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%}
+
+{%block contents%}
+R/qtl2 Bundle: Quality Control Successful
+
+
+
The R/qtl2 bundle you uploaded has passed all quality control
+ checks successfully, and is now ready for uploading into the database.
+
Click "Continue" below to proceed.
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..873f9c3
--- /dev/null
+++ b/uploader/templates/rqtl2/select-geno-dataset.html
@@ -0,0 +1,144 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Select Genotypes Dataset
+
+
+
Your R/qtl2 files bundle contains a "geno" specification. You will
+ therefore need to select from one of the existing Genotype datasets or
+ create a new one.
+
This is the dataset where your data will be organised under.
+
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
new file mode 100644
index 0000000..37731f0
--- /dev/null
+++ b/uploader/templates/rqtl2/select-population.html
@@ -0,0 +1,136 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Select Grouping/Population{%endblock%}
+
+{%block contents%}
+Select grouping/population
+
+
+
The data is organised in a hierarchical form, beginning with
+ species at the very top. Under species the data is
+ organised by population , sometimes referred to as grouping .
+ (In some really old documents/systems, you might see this referred to as
+ InbredSet .)
+
In this section, you get to define what population your data is to be
+ organised by.
+
+
+
+
+OR
+
+
+
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html
new file mode 100644
index 0000000..26f52ed
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-dataset.html
@@ -0,0 +1,191 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Phenotype(ProbeSet) Dataset
+
+
+
The R/qtl2 bundle you uploaded contains (a) "pheno "
+ file(s). This data needs to be organised under a dataset.
+
This page gives you the ability to do that.
+
+
+{%if datasets | length > 0%}
+
+
+ Select from existing ProbeSet datasets
+ {{flash_messages("error-rqtl2")}}
+
+
+
+
+
+
+
+
+
+ Dataset
+
+ Select a dataset
+ {%for dataset in datasets%}
+
+ {{dataset.Name}}
+ {%if dataset.FullName%}
+ -- ({{dataset.FullName}})
+ {%endif%}
+
+ {%endfor%}
+
+
+
+ Select from existing ProbeSet datasets.
+
+
+ select dataset
+
+
+
+
+{%endif%}
+
+
+
Create an entirely new ProbeSet dataset for your data.
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..b9bf52e
--- /dev/null
+++ b/uploader/templates/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,143 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages %}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Phenotype(ProbeSet) Study
+
+
+
The R/qtl2 bundle you uploaded contains (a) "pheno "
+ file(s). This data needs to be organised under a study.
+
In this page, you can either select from a existing dataset:
+
+
+ Select from existing ProbeSet studies
+ {{flash_messages("error-rqtl2-select-probeset-study")}}
+
+
+
+
+
+
+
+
+ Study
+
+ Select a study
+ {%for study in studies%}
+
+ {{study.Name}}
+ {%if study.FullName%}
+ -- ({{study.FullName}})
+ {%endif%}
+
+ {%endfor%}
+
+
+ Select from existing ProbeSet studies.
+
+
+
+ select study
+
+
+
+
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html
new file mode 100644
index 0000000..34e1758
--- /dev/null
+++ b/uploader/templates/rqtl2/select-tissue.html
@@ -0,0 +1,115 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Tissue
+
+
+
The data you are uploading concerns a tissue, cell, organ, or other
+ biological material used in an experiment.
+
Select the appropriate biological material below
+
+
+{%if tissues | length > 0%}
+
+
+ Select from existing ProbeSet datasets
+ {{flash_messages("error-select-tissue")}}
+
+
+
+
+
+
+
+ Tissue
+
+ Select a tissue
+ {%for tissue in tissues%}
+
+ {{tissue.Name}}
+ {%if tissue.Short_Name%}
+ -- ({{tissue.Short_Name}})
+ {%endif%}
+
+ {%endfor%}
+
+
+
+ Select from existing biological material.
+
+
+ use selected
+
+
+
+
+{%endif%}
+
+
+
If you cannot find the biological material in the drop-down above, add it
+ to the system below.
+
+
+ Add new tissue, organ or biological material
+ {{flash_messages("error-create-tissue")}}
+
+
+
+
+
+
+
+ name
+
+
+
+ A name to identify the tissue, organ or biological material.
+
+
+
+
+ short name
+
+
+
+ Provide a short name for the tissue, organ or biological material used in
+ the experiment.
+
+
+
+ add new material
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html
new file mode 100644
index 0000000..1be87fa
--- /dev/null
+++ b/uploader/templates/rqtl2/summary-info.html
@@ -0,0 +1,65 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Summary
+
+
+
This is the information you have provided to accompany the R/qtl2 bundle
+ you have uploaded. Please verify the information is correct before
+ proceeding.
+
+
+
+
+ Species
+ {{species.SpeciesName}} ({{species.FullName}})
+
+ Population
+ {{population.InbredSetName}}
+
+ {%if geno_dataset%}
+ Genotype Dataset
+ {{geno_dataset.Name}} ({{geno_dataset.FullName}})
+ {%endif%}
+
+ {%if tissue%}
+ Tissue
+ {{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})
+ {%endif%}
+
+ {%if probe_study%}
+ ProbeSet Study
+ {{probe_study.Name}} ({{probe_study.FullName}})
+ {%endif%}
+
+ {%if probe_dataset%}
+ ProbeSet Dataset
+ {{probe_dataset.Name2}} ({{probe_dataset.FullName}})
+ {%endif%}
+
+
+
+
+
+ Create ProbeSet dataset
+
+
+
+
+
+
+
+
+ continue
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
new file mode 100644
index 0000000..07c240f
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -0,0 +1,276 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "upload_progress_indicator.html" import upload_progress_indicator%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+{%macro rqtl2_file_help()%}
+
+
+ Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle
+ contains exactly one control file and the corresponding files mentioned in
+ the control file.
+
+
+ The control file can be either a YAML or JSON file. ALL other data
+ files in the zip bundle should be CSV files.
+
+ See the
+
+ R/qtl2 file format specifications
+
+ for more details.
+
+
+{%endmacro%}
+{{upload_progress_indicator()}}
+
+
+
+
+Upload R/qtl2 Bundle
+
+
+
+ Browse
+
+
+ You can drag and drop your file here, or click the browse button.
+ Click on the file to remove it.
+
+ {{rqtl2_file_help()}}
+
+
+ start upload
+ cancel upload
+
+
+
+
+
+
+
+
+ {{flash_all_messages()}}
+
+
+ file upload
+ R/qtl2 bundle
+
+ {{rqtl2_file_help()}}
+
+
+ upload R/qtl2 bundle
+
+
+{%endblock%}
+
+{%block javascript%}
+
+
+
+{%endblock%}
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
new file mode 100644
index 0000000..93b1dc9
--- /dev/null
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -0,0 +1,33 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Upload R/qtl2 Bundle
+
+
+
You have successfully uploaded the zipped bundle of R/qtl2 files.
+
The next step is to select the various extra information we need to figure
+ out what to do with the data. You will select/create the relevant studies
+ and/or datasets to organise the data in the steps that follow.
+
Click "Continue" below to proceed.
+
+
+ {{flash_all_messages()}}
+
+
+
+
+ continue
+
+
+
+{%endblock%}
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