From 4285cc10e24d6410206329ba079406e9aa21cc30 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 23 Sep 2024 14:30:15 -0500 Subject: Move R/qtl2 upload code under the populations package. --- .../populations/rqtl2/create-tissue-success.html | 106 ++++++++ uploader/templates/populations/rqtl2/index.html | 54 ++++ .../templates/populations/rqtl2/no-such-job.html | 13 + .../populations/rqtl2/rqtl2-job-error.html | 39 +++ .../populations/rqtl2/rqtl2-job-results.html | 24 ++ .../populations/rqtl2/rqtl2-job-status.html | 20 ++ .../populations/rqtl2/rqtl2-qc-job-error.html | 120 +++++++++ .../populations/rqtl2/rqtl2-qc-job-results.html | 66 +++++ .../populations/rqtl2/rqtl2-qc-job-status.html | 41 +++ .../populations/rqtl2/rqtl2-qc-job-success.html | 37 +++ .../populations/rqtl2/select-geno-dataset.html | 69 ++++++ .../populations/rqtl2/select-population.html | 57 +++++ .../populations/rqtl2/select-probeset-dataset.html | 191 ++++++++++++++ .../rqtl2/select-probeset-study-id.html | 143 +++++++++++ .../templates/populations/rqtl2/select-tissue.html | 115 +++++++++ .../templates/populations/rqtl2/summary-info.html | 65 +++++ .../rqtl2/upload-rqtl2-bundle-step-01.html | 276 +++++++++++++++++++++ .../rqtl2/upload-rqtl2-bundle-step-02.html | 33 +++ .../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 --- 39 files changed, 1469 insertions(+), 1768 deletions(-) create mode 100644 uploader/templates/populations/rqtl2/create-tissue-success.html create mode 100644 uploader/templates/populations/rqtl2/index.html create mode 100644 uploader/templates/populations/rqtl2/no-such-job.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-job-error.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-job-results.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-job-status.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html create mode 100644 uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html create mode 100644 uploader/templates/populations/rqtl2/select-geno-dataset.html create mode 100644 uploader/templates/populations/rqtl2/select-population.html create mode 100644 uploader/templates/populations/rqtl2/select-probeset-dataset.html create mode 100644 uploader/templates/populations/rqtl2/select-probeset-study-id.html create mode 100644 uploader/templates/populations/rqtl2/select-tissue.html create mode 100644 uploader/templates/populations/rqtl2/summary-info.html create mode 100644 uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html create mode 100644 uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html delete mode 100644 uploader/templates/rqtl2/create-geno-dataset-success.html delete mode 100644 uploader/templates/rqtl2/create-probe-dataset-success.html delete mode 100644 uploader/templates/rqtl2/create-probe-study-success.html delete mode 100644 uploader/templates/rqtl2/create-tissue-success.html delete mode 100644 uploader/templates/rqtl2/index.html delete mode 100644 uploader/templates/rqtl2/no-such-job.html delete mode 100644 uploader/templates/rqtl2/rqtl2-job-error.html delete mode 100644 uploader/templates/rqtl2/rqtl2-job-results.html delete mode 100644 uploader/templates/rqtl2/rqtl2-job-status.html delete mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-error.html delete mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-results.html delete mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-status.html delete mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-success.html delete mode 100644 uploader/templates/rqtl2/select-geno-dataset.html delete mode 100644 uploader/templates/rqtl2/select-population.html delete mode 100644 uploader/templates/rqtl2/select-probeset-dataset.html delete mode 100644 uploader/templates/rqtl2/select-probeset-study-id.html delete mode 100644 uploader/templates/rqtl2/select-tissue.html delete mode 100644 uploader/templates/rqtl2/summary-info.html delete mode 100644 uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html delete mode 100644 uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html (limited to 'uploader/templates') diff --git a/uploader/templates/populations/rqtl2/create-tissue-success.html b/uploader/templates/populations/rqtl2/create-tissue-success.html new file mode 100644 index 0000000..d6fe154 --- /dev/null +++ b/uploader/templates/populations/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()}} + +
+ Create Tissue + + + + + + + +
+ + +
+ +
+ + +
+ + {%if tissue.BIRN_lex_ID%} +
+ + +
+ {%endif%} + + {%if tissue.BIRN_lex_Name%} +
+ + +
+ {%endif%} +
+ +
+ +
+ + + + + + + + +
+
+
+ +
+

+ OR +

+
+ +
+
+ + + + + + + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/index.html b/uploader/templates/populations/rqtl2/index.html new file mode 100644 index 0000000..ec6ffb8 --- /dev/null +++ b/uploader/templates/populations/rqtl2/index.html @@ -0,0 +1,54 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Data Upload{%endblock%} + +{%block contents%} +

R/qtl2 data upload

+ +

R/qtl2 Upload

+ +
+
+ upload R/qtl2 bundle + {{flash_messages("error-rqtl2")}} + +
+ + + + Data that you upload to the system should belong to a know species. + Here you can select the species that you wish to upload data for. + +
+ + +
+
+ +
+

R/qtl2 Bundles

+ +
+

This feature combines and extends the two upload methods below. Instead of + uploading one item at a time, the R/qtl2 bundle you upload can contain both + the genotypes data (samples/individuals/cases and their data) and the + expression data.

+

The R/qtl2 bundle, additionally, can contain extra metadata, that neither + of the methods below can handle.

+ + + +
+
+{%endblock%} diff --git a/uploader/templates/populations/rqtl2/no-such-job.html b/uploader/templates/populations/rqtl2/no-such-job.html new file mode 100644 index 0000000..b17004f --- /dev/null +++ b/uploader/templates/populations/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/populations/rqtl2/rqtl2-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-job-error.html new file mode 100644 index 0000000..9817518 --- /dev/null +++ b/uploader/templates/populations/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: +

+

+
+ +

stdout

+{{cli_output(job, "stdout")}} + +

stderr

+{{cli_output(job, "stderr")}} + +

Log

+
+ {%for msg in messages%} + {{msg}}
+ {%endfor%} +
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-job-results.html new file mode 100644 index 0000000..4ecd415 --- /dev/null +++ b/uploader/templates/populations/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/populations/rqtl2/rqtl2-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-job-status.html new file mode 100644 index 0000000..e896f88 --- /dev/null +++ b/uploader/templates/populations/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/populations/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-error.html new file mode 100644 index 0000000..90e8887 --- /dev/null +++ b/uploader/templates/populations/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)%} + + + + + + + + + + + + {%for error in errors%} + + + + + + + {%else%} + + + + {%endfor%} + +
{{caption}}
LineColumnValueMessage
{{error.line}}{{error.column}}{{error.value}}{{error.message}}
No errors to display here.
+{%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

+
+ + + + + + + + + + {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%} + + + + + + {%endfor%} + +
Control File KeyBundle File NameMessage
{{error.controlfilekey}}{{error.filename}}{{error.message}}
+ +

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/populations/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-results.html new file mode 100644 index 0000000..b3c3a8f --- /dev/null +++ b/uploader/templates/populations/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:

+
+ +
+
+
+ Species + + + Name + {{species.Name | capitalize}} + + Scientific + {{species.FullName | capitalize}} +
+ +
+ population + + + Name + {{population.InbredSetName}} + + Full Name + {{population.FullName}} + + Genetic Type + {{population.GeneticType}} + + Description + {{population.Description or "-"}} +
+ +
+ R/qtl2 Bundle File + + + + Original Name + {{rqtl2bundleorig}} + + Internal Name + {{rqtl2bundle[0:25]}}… +
+ + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-status.html new file mode 100644 index 0000000..f4a6266 --- /dev/null +++ b/uploader/templates/populations/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/populations/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/populations/rqtl2/rqtl2-qc-job-success.html new file mode 100644 index 0000000..f126835 --- /dev/null +++ b/uploader/templates/populations/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.

+
+ + +
+
+ {{flash_all_messages()}} + + + + + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-geno-dataset.html b/uploader/templates/populations/rqtl2/select-geno-dataset.html new file mode 100644 index 0000000..3233abc --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-geno-dataset.html @@ -0,0 +1,69 @@ +{%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 could contain 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.

+
+ +
+
+ select from existing genotype datasets + + + + + + {{flash_messages("error-rqtl2-select-geno-dataset")}} + +
+ Datasets + + + + Select from the existing genotype datasets for species + {{species.SpeciesName}} ({{species.FullName}}). + +
+ + +
+
+ +
+

If the genotype dataset you need does not currently exist for your dataset, + go the + genotypes page to create the genotype dataset

+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-population.html b/uploader/templates/populations/rqtl2/select-population.html new file mode 100644 index 0000000..ded425f --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-population.html @@ -0,0 +1,57 @@ +{%extends "expression-data/index.html"%} +{%from "flash_messages.html" import flash_messages%} +{%from "species/macro-display-species-card.html" import display_species_card%} + +{%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.

+
+ +
+
+ select grouping/population + {{flash_messages("error-select-population")}} + + + +
+ + + Select the population for your data from + the list below. +
+ + +
+
+ +{%endblock%} + +{%block sidebarcontents%} +{{display_species_card(species)}} +{%endblock%} + + +{%block javascript%} +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html new file mode 100644 index 0000000..74f8f69 --- /dev/null +++ b/uploader/templates/populations/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")}} + + + + + + + + +
+ + + + + Select from existing ProbeSet datasets. +
+ + +
+
+ +
+

OR

+
+{%endif%} + +
+

Create an entirely new ProbeSet dataset for your data.

+
+ +
+
+ Create a new ProbeSet dataset + {{flash_messages("error-rqtl2-create-probeset-dataset")}} + + + + + + + + +
+ + + + + Select the averaging method used for your data. + +
+ +
+ + + + + Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This + is mandatory MUST be provided. + +
+ +
+ + + + + Provide a longer, more descriptive name for the dataset e.g. + "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and + MUST be provided. + +
+ +
+ + + + + Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". + This is optional. + +
+ +
+ + + + + Check to specify that the dataset will be publicly available. Uncheck to + limit access to the dataset. + +
+ +
+ + + + + Select from a list of scaling methods. + +
+ + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-probeset-study-id.html b/uploader/templates/populations/rqtl2/select-probeset-study-id.html new file mode 100644 index 0000000..e3fd9cc --- /dev/null +++ b/uploader/templates/populations/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")}} + + + + + + + +
+ + + + Select from existing ProbeSet studies. + +
+ + +
+
+ +
+

OR

+
+ +
+ +

Create a new ProbeSet dataset below:

+ +
+ Create new ProbeSet study + + {{flash_messages("error-rqtl2-create-probeset-study")}} + + + + + + + +
+ + + + Select from a list of known genomics platforms. + +
+ +
+ + + + Provide a name for the study. +
+ +
+ + + + Provide a longer, more descriptive name for the study. This is optional + and you can leave it blank. + +
+ +
+ + + + Provide a shorter name for the study. This is optional and you can leave + it blank. + +
+ + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/select-tissue.html b/uploader/templates/populations/rqtl2/select-tissue.html new file mode 100644 index 0000000..fe3080a --- /dev/null +++ b/uploader/templates/populations/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")}} + + + + + + +
+ + + + + Select from existing biological material. +
+ + +
+
+ +
+

OR

+
+{%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")}} + + + + + + +
+ + + + + A name to identify the tissue, organ or biological material. + +
+ +
+ + + + + Provide a short name for the tissue, organ or biological material used in + the experiment. + +
+ + +
+
+ +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/summary-info.html b/uploader/templates/populations/rqtl2/summary-info.html new file mode 100644 index 0000000..0adba2e --- /dev/null +++ b/uploader/templates/populations/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 + + + + + + + + + +
+
+{%endblock%} diff --git a/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-01.html new file mode 100644 index 0000000..9d45c5f --- /dev/null +++ b/uploader/templates/populations/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

+ + + +
+ + + + {{flash_all_messages()}} + +
+ file upload + + + {{rqtl2_file_help()}} +
+ + +
+ +{%endblock%} + +{%block javascript%} + + + +{%endblock%} diff --git a/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/populations/rqtl2/upload-rqtl2-bundle-step-02.html new file mode 100644 index 0000000..8210ed0 --- /dev/null +++ b/uploader/templates/populations/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()}} + + + + + +
+
+ +{%endblock%} diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html deleted file mode 100644 index bb6d63d..0000000 --- a/uploader/templates/rqtl2/create-geno-dataset-success.html +++ /dev/null @@ -1,55 +0,0 @@ -{%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%}
-
-

-
- -
-
- select from existing genotype datasets - - - - - - - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html deleted file mode 100644 index 03b75c7..0000000 --- a/uploader/templates/rqtl2/create-probe-dataset-success.html +++ /dev/null @@ -1,59 +0,0 @@ -{%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}}
-
-

-
- -
-
- Create ProbeSet dataset - - - - - - - - - - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html deleted file mode 100644 index e293f6f..0000000 --- a/uploader/templates/rqtl2/create-probe-study-success.html +++ /dev/null @@ -1,49 +0,0 @@ -{%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}}
-
-

- -
- Create ProbeSet study - - - - - - - - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html deleted file mode 100644 index d6fe154..0000000 --- a/uploader/templates/rqtl2/create-tissue-success.html +++ /dev/null @@ -1,106 +0,0 @@ -{%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()}} - -
- Create Tissue - - - - - - - -
- - -
- -
- - -
- - {%if tissue.BIRN_lex_ID%} -
- - -
- {%endif%} - - {%if tissue.BIRN_lex_Name%} -
- - -
- {%endif%} -
- -
- -
- - - - - - - - -
-
-
- -
-

- OR -

-
- -
-
- - - - - - - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html deleted file mode 100644 index 8ce13bf..0000000 --- a/uploader/templates/rqtl2/index.html +++ /dev/null @@ -1,36 +0,0 @@ -{%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} - -{%block title%}Data Upload{%endblock%} - -{%block contents%} -

R/qtl2 data upload

- -

R/qtl2 Upload

- -
- upload R/qtl2 bundle - {{flash_messages("error-rqtl2")}} - -
- - - - Data that you upload to the system should belong to a know species. - Here you can select the species that you wish to upload data for. - -
- - -
- -{%endblock%} diff --git a/uploader/templates/rqtl2/no-such-job.html b/uploader/templates/rqtl2/no-such-job.html deleted file mode 100644 index b17004f..0000000 --- a/uploader/templates/rqtl2/no-such-job.html +++ /dev/null @@ -1,13 +0,0 @@ -{%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 deleted file mode 100644 index 9817518..0000000 --- a/uploader/templates/rqtl2/rqtl2-job-error.html +++ /dev/null @@ -1,39 +0,0 @@ -{%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: -

-

-
- -

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 deleted file mode 100644 index 4ecd415..0000000 --- a/uploader/templates/rqtl2/rqtl2-job-results.html +++ /dev/null @@ -1,24 +0,0 @@ -{%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 deleted file mode 100644 index e896f88..0000000 --- a/uploader/templates/rqtl2/rqtl2-job-status.html +++ /dev/null @@ -1,20 +0,0 @@ -{%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 deleted file mode 100644 index 90e8887..0000000 --- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html +++ /dev/null @@ -1,120 +0,0 @@ -{%extends "base.html"%} -{%from "cli-output.html" import cli_output%} - -{%block title%}R/qtl2 bundle: QC Job Error{%endblock%} - -{%macro errors_table(tableid, errors)%} - - - - - - - - - - - - {%for error in errors%} - - - - - - - {%else%} - - - - {%endfor%} - -
{{caption}}
LineColumnValueMessage
{{error.line}}{{error.column}}{{error.value}}{{error.message}}
No errors to display here.
-{%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

-
- - - - - - - - - - {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%} - - - - - - {%endfor%} - -
Control File KeyBundle File NameMessage
{{error.controlfilekey}}{{error.filename}}{{error.message}}
- -

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 deleted file mode 100644 index b3c3a8f..0000000 --- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html +++ /dev/null @@ -1,66 +0,0 @@ -{%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:

-
- -
-
-
- Species - - - Name - {{species.Name | capitalize}} - - Scientific - {{species.FullName | capitalize}} -
- -
- population - - - Name - {{population.InbredSetName}} - - Full Name - {{population.FullName}} - - Genetic Type - {{population.GeneticType}} - - Description - {{population.Description or "-"}} -
- -
- R/qtl2 Bundle File - - - - Original Name - {{rqtl2bundleorig}} - - Internal Name - {{rqtl2bundle[0:25]}}… -
- - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-status.html b/uploader/templates/rqtl2/rqtl2-qc-job-status.html deleted file mode 100644 index f4a6266..0000000 --- a/uploader/templates/rqtl2/rqtl2-qc-job-status.html +++ /dev/null @@ -1,41 +0,0 @@ -{%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 deleted file mode 100644 index f126835..0000000 --- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html +++ /dev/null @@ -1,37 +0,0 @@ -{%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.

-
- - -
-
- {{flash_all_messages()}} - - - - - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html deleted file mode 100644 index 1db51e0..0000000 --- a/uploader/templates/rqtl2/select-geno-dataset.html +++ /dev/null @@ -1,144 +0,0 @@ -{%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.

-
- -
-
- select from existing genotype datasets - - - - - - {{flash_messages("error-rqtl2-select-geno-dataset")}} - -
- Datasets - - - - Select from the existing genotype datasets for species - {{species.SpeciesName}} ({{species.FullName}}). - -
- - -
-
- -
-

OR

-
- -
-
- create a new genotype dataset - - - - - - {{flash_messages("error-rqtl2-create-geno-dataset")}} - -
- - - - Provide the new name for the genotype dataset, e.g. "BXDGeno" - -
- -
- - - - - Provide a longer name that better describes the genotype dataset, e.g. - "BXD Genotypes" - -
- -
- - - - - Provide a short name for the genotype dataset. This is optional. If not - provided, we'll default to the same value as the "Name" above. - -
- -
- - - - - Specify whether the dataset will be available publicly. Check to make the - dataset publicly available and uncheck to limit who can access the dataset. - -
- - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html deleted file mode 100644 index 7d27303..0000000 --- a/uploader/templates/rqtl2/select-population.html +++ /dev/null @@ -1,136 +0,0 @@ -{%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.

-
- -
- select grouping/population - {{flash_messages("error-select-population")}} - - - -
- - - If you are adding data to an already existing - population, simply pick the population from this drop-down selector. If - you cannot find your population from this list, try the form below to - create a new one.. -
- - -
- -

OR

- -
- create new grouping/population - {{flash_messages("error-create-population")}} - - - -
- mandatory - -
- - - This is a short name that identifies the - population. Useful for menus, and quick scanning. -
- -
- - - This can be the same as the name above, or can - be longer. Useful for documentation, and human communication. -
-
- -
- optional - -
- - - This determines whether the - population/grouping will appear on the menus for users. -
- -
- - - I do not currently know what this is about. - This is a failure on my part to figure out what this is and provide a - useful description. Please feel free to remind me. -
- -
- - - - A long-form description of what the population consists of. Useful for - humans. -
-
- - -
- -{%endblock%} - - -{%block javascript%} -{%endblock%} diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html deleted file mode 100644 index 74f8f69..0000000 --- a/uploader/templates/rqtl2/select-probeset-dataset.html +++ /dev/null @@ -1,191 +0,0 @@ -{%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")}} - - - - - - - - -
- - - - - Select from existing ProbeSet datasets. -
- - -
-
- -
-

OR

-
-{%endif%} - -
-

Create an entirely new ProbeSet dataset for your data.

-
- -
-
- Create a new ProbeSet dataset - {{flash_messages("error-rqtl2-create-probeset-dataset")}} - - - - - - - - -
- - - - - Select the averaging method used for your data. - -
- -
- - - - - Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This - is mandatory MUST be provided. - -
- -
- - - - - Provide a longer, more descriptive name for the dataset e.g. - "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and - MUST be provided. - -
- -
- - - - - Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". - This is optional. - -
- -
- - - - - Check to specify that the dataset will be publicly available. Uncheck to - limit access to the dataset. - -
- -
- - - - - Select from a list of scaling methods. - -
- - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html deleted file mode 100644 index e3fd9cc..0000000 --- a/uploader/templates/rqtl2/select-probeset-study-id.html +++ /dev/null @@ -1,143 +0,0 @@ -{%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")}} - - - - - - - -
- - - - Select from existing ProbeSet studies. - -
- - -
-
- -
-

OR

-
- -
- -

Create a new ProbeSet dataset below:

- -
- Create new ProbeSet study - - {{flash_messages("error-rqtl2-create-probeset-study")}} - - - - - - - -
- - - - Select from a list of known genomics platforms. - -
- -
- - - - Provide a name for the study. -
- -
- - - - Provide a longer, more descriptive name for the study. This is optional - and you can leave it blank. - -
- -
- - - - Provide a shorter name for the study. This is optional and you can leave - it blank. - -
- - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html deleted file mode 100644 index fe3080a..0000000 --- a/uploader/templates/rqtl2/select-tissue.html +++ /dev/null @@ -1,115 +0,0 @@ -{%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")}} - - - - - - -
- - - - - Select from existing biological material. -
- - -
-
- -
-

OR

-
-{%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")}} - - - - - - -
- - - - - A name to identify the tissue, organ or biological material. - -
- -
- - - - - Provide a short name for the tissue, organ or biological material used in - the experiment. - -
- - -
-
- -{%endblock%} diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html deleted file mode 100644 index 0adba2e..0000000 --- a/uploader/templates/rqtl2/summary-info.html +++ /dev/null @@ -1,65 +0,0 @@ -{%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 - - - - - - - - - -
-
-{%endblock%} diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html deleted file mode 100644 index 9d45c5f..0000000 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ /dev/null @@ -1,276 +0,0 @@ -{%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

- - - -
- - - - {{flash_all_messages()}} - -
- file upload - - - {{rqtl2_file_help()}} -
- - -
- -{%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 deleted file mode 100644 index 8210ed0..0000000 --- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ /dev/null @@ -1,33 +0,0 @@ -{%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()}} - - - - - -
-
- -{%endblock%} -- cgit v1.2.3