From f726c71bf1636a838f45363d1613763a2926e34f Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 12 Jun 2024 16:38:54 -0500 Subject: Update html templates to use bootstrap for styling --- .../rqtl2/create-geno-dataset-success.html | 42 ++- .../rqtl2/create-probe-dataset-success.html | 46 ++- .../rqtl2/create-probe-study-success.html | 42 ++- qc_app/templates/rqtl2/create-tissue-success.html | 116 ++++---- qc_app/templates/rqtl2/index.html | 20 +- qc_app/templates/rqtl2/rqtl2-qc-job-results.html | 78 ++--- qc_app/templates/rqtl2/rqtl2-qc-job-success.html | 34 +-- qc_app/templates/rqtl2/select-geno-dataset.html | 248 ++++++++-------- qc_app/templates/rqtl2/select-population.html | 148 +++++----- .../templates/rqtl2/select-probeset-dataset.html | 323 +++++++++++---------- .../templates/rqtl2/select-probeset-study-id.html | 242 +++++++-------- qc_app/templates/rqtl2/select-tissue.html | 181 ++++++------ qc_app/templates/rqtl2/summary-info.html | 86 +++--- .../rqtl2/upload-rqtl2-bundle-step-01.html | 20 +- .../rqtl2/upload-rqtl2-bundle-step-02.html | 34 +-- 15 files changed, 847 insertions(+), 813 deletions(-) (limited to 'qc_app/templates/rqtl2') diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html index 4333612..1b50221 100644 --- a/qc_app/templates/rqtl2/create-geno-dataset-success.html +++ b/qc_app/templates/rqtl2/create-geno-dataset-success.html @@ -31,27 +31,25 @@

-
- select from existing genotype datasets - - - - - - -
- -
-
+
+
+ select from existing genotype datasets + + + + + + + +
+
{%endblock%} diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html index 57df449..790d174 100644 --- a/qc_app/templates/rqtl2/create-probe-dataset-success.html +++ b/qc_app/templates/rqtl2/create-probe-dataset-success.html @@ -6,7 +6,7 @@ {%block contents%}

Create ProbeSet Dataset

-
+

You successfully created the ProbeSet dataset with the following information.

@@ -34,28 +34,26 @@

-
- Create ProbeSet dataset - - - - - - - - - -
- -
-
+
+
+ Create ProbeSet dataset + + + + + + + + + + +
+
{%endblock%} diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html index 5d3d123..d0ee508 100644 --- a/qc_app/templates/rqtl2/create-probe-study-success.html +++ b/qc_app/templates/rqtl2/create-probe-study-success.html @@ -6,7 +6,7 @@ {%block contents%}

Create ProbeSet Study

-
+

You successfully created the ProbeSet study with the following information.

@@ -26,28 +26,24 @@
{{study.today}}

-
-
- Create ProbeSet study - - - - - - - -
- -
-
+
+ Create ProbeSet study + + + + + + + + +
+
{%endblock%} diff --git a/qc_app/templates/rqtl2/create-tissue-success.html b/qc_app/templates/rqtl2/create-tissue-success.html index 7ea0c65..5f2c5a0 100644 --- a/qc_app/templates/rqtl2/create-tissue-success.html +++ b/qc_app/templates/rqtl2/create-tissue-success.html @@ -6,61 +6,18 @@ {%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%} -
- -
- -
+ {{flash_all_messages()}} + + + action="#"> + Create Tissue - +
+ + +
+ +
+ + +
+ + {%if tissue.BIRN_lex_ID%} +
+ + +
+ {%endif%} + + {%if tissue.BIRN_lex_Name%} +
+ + +
+ {%endif%}
+
+ +
+ + + + + + + + +
+
+
+ +

OR

+
+
- +
-
{%endblock%} diff --git a/qc_app/templates/rqtl2/index.html b/qc_app/templates/rqtl2/index.html index 45018e7..f3329c2 100644 --- a/qc_app/templates/rqtl2/index.html +++ b/qc_app/templates/rqtl2/index.html @@ -12,23 +12,25 @@ id="frm-rqtl2-upload"> upload R/qtl2 bundle {{flash_messages("error-rqtl2")}} -
- - {%for spec in species%} {%endfor%} - + 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/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html index 35dc95a..59bc8cd 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html +++ b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html @@ -6,61 +6,61 @@ {%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 - +
+ +
+ Species + - Name - {{species.Name | capitalize}} + Name + {{species.Name | capitalize}} - Scientific - {{species.FullName | capitalize}} -
+ Scientific + {{species.FullName | capitalize}} +
-
- population - +
+ population + - Name - {{population.InbredSetName}} + Name + {{population.InbredSetName}} - Full Name - {{population.FullName}} + Full Name + {{population.FullName}} - Genetic Type - {{population.GeneticType}} + Genetic Type + {{population.GeneticType}} - Description - {{population.Description or "-"}} -
+ Description + {{population.Description or "-"}} +
-
- R/qtl2 Bundle File - - +
+ R/qtl2 Bundle File + + - Original Name - {{rqtl2bundleorig}} + Original Name + {{rqtl2bundleorig}} - Internal Name - {{rqtl2bundle[0:25]}}… -
+ Internal Name + {{rqtl2bundle[0:25]}}… + -
- -
- + + + {%endblock%} diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html index d492898..2861a04 100644 --- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html +++ b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html @@ -6,7 +6,7 @@ {%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.

@@ -16,22 +16,22 @@ The "action" on this form takes us to the next step, where we can select all the other data necessary to enter the data into the database. --> -
- {{flash_all_messages()}} - - - +
+ + {{flash_all_messages()}} + + + -
- -
- + + +
{%endblock%} diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html index f092dbc..873f9c3 100644 --- a/qc_app/templates/rqtl2/select-geno-dataset.html +++ b/qc_app/templates/rqtl2/select-geno-dataset.html @@ -6,131 +6,139 @@ {%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. - -
- -
- -
-
+
+
+ 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/qc_app/templates/rqtl2/select-population.html b/qc_app/templates/rqtl2/select-population.html index 1102805..37731f0 100644 --- a/qc_app/templates/rqtl2/select-population.html +++ b/qc_app/templates/rqtl2/select-population.html @@ -22,29 +22,26 @@ {{flash_messages("error-select-population")}} -
- + +
+ - If you are adding data to an already existing + 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

@@ -55,70 +52,81 @@ {{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. - - + +
+ 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. -
- -
- -
+ class="form-control"> + + A long-form description of what the population consists of. Useful for + humans. +
+
+ + {%endblock%} diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html index c5acb72..26f52ed 100644 --- a/qc_app/templates/rqtl2/select-probeset-dataset.html +++ b/qc_app/templates/rqtl2/select-probeset-dataset.html @@ -6,173 +6,186 @@ {%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. -
- -
- -
+
+ + Select from existing ProbeSet datasets + {{flash_messages("error-rqtl2")}} + + + + + + + + +
+ + + + + Select from existing ProbeSet datasets. +
+ + +
-

OR

+
+

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. - -
- -
- -
-
+
+
+ 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/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html index c387514..b9bf52e 100644 --- a/qc_app/templates/rqtl2/select-probeset-study-id.html +++ b/qc_app/templates/rqtl2/select-probeset-study-id.html @@ -6,128 +6,138 @@ {%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. + +
+ + +
-
- Select from existing ProbeSet studies - {{flash_messages("error-rqtl2-select-probeset-study")}} - - - - - - - -
- - - Select from existing ProbeSet studies. -
- -
- -
-
- -

OR

- -
-

Create a new ProbeSet dataset below:

+
+

OR

-
- 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. - -
- -
- -
-
+
+ +

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/qc_app/templates/rqtl2/select-tissue.html b/qc_app/templates/rqtl2/select-tissue.html index 78d5afe..34e1758 100644 --- a/qc_app/templates/rqtl2/select-tissue.html +++ b/qc_app/templates/rqtl2/select-tissue.html @@ -6,107 +6,110 @@ {%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. -
- -
- -
-
+
+
+ Select from existing ProbeSet datasets + {{flash_messages("error-select-tissue")}} + + + + + + +
+ + + + + Select from existing biological material. +
+ + +
+
-

OR

+
+

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. - -
- -
- -
+ + 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/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html index 8b05578..1be87fa 100644 --- a/qc_app/templates/rqtl2/summary-info.html +++ b/qc_app/templates/rqtl2/summary-info.html @@ -6,60 +6,60 @@ {%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}})
+
+
+
Species
+
{{species.SpeciesName}} ({{species.FullName}})
-
Population
-
{{population.InbredSetName}}
+
Population
+
{{population.InbredSetName}}
- {%if geno_dataset%} -
Genotype Dataset
-
{{geno_dataset.Name}} ({{geno_dataset.FullName}})
- {%endif%} + {%if geno_dataset%} +
Genotype Dataset
+
{{geno_dataset.Name}} ({{geno_dataset.FullName}})
+ {%endif%} - {%if tissue%} -
Tissue
-
{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})
- {%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_study%} +
ProbeSet Study
+
{{probe_study.Name}} ({{probe_study.FullName}})
+ {%endif%} - {%if probe_dataset%} -
ProbeSet Dataset
-
{{probe_dataset.Name2}} ({{probe_dataset.FullName}})
- {%endif%} -
+ {%if probe_dataset%} +
ProbeSet Dataset
+
{{probe_dataset.Name2}} ({{probe_dataset.FullName}})
+ {%endif%} +
+
-
- Create ProbeSet dataset +
+ + Create ProbeSet dataset - - - - - - + + + + + + -
- -
- + + +
{%endblock%} diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html index cc7c92e..5cf9dfd 100644 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html +++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html @@ -21,13 +21,14 @@ {{flash_all_messages()}} -
- file upload - +
+ file upload + -

Provide a valid R/qtl2 zip file here. In + required="required" + class="form-control" /> +

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 @@ -36,12 +37,9 @@ R/qtl2 file format specifications for more details.

 -
-
- -
+
+ + {%endblock%} diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html index 75f4a96..93b1dc9 100644 --- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html +++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html @@ -6,30 +6,28 @@ {%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()}} - - - + + {{flash_all_messages()}} + + + -
- -
-
+ + +
{%endblock%} -- cgit v1.2.3