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 --- qc_app/static/css/custom-bootstrap.css | 4 + qc_app/static/css/styles.css | 7 + qc_app/templates/base.html | 3 + qc_app/templates/continue_from_create_dataset.html | 18 +- qc_app/templates/continue_from_create_study.html | 18 +- qc_app/templates/errors_display.html | 2 +- qc_app/templates/index.html | 214 +++++++------- qc_app/templates/insert_error.html | 32 +- qc_app/templates/insert_progress.html | 21 +- qc_app/templates/insert_success.html | 6 +- qc_app/templates/job_progress.html | 29 +- .../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 +-- qc_app/templates/samples/select-population.html | 54 ++-- qc_app/templates/samples/select-species.html | 15 +- qc_app/templates/samples/upload-samples.html | 132 ++++----- qc_app/templates/select_dataset.html | 102 +++---- qc_app/templates/select_platform.html | 96 +++--- qc_app/templates/select_study.html | 61 ++-- qc_app/templates/stdout_output.html | 4 +- 33 files changed, 1268 insertions(+), 1210 deletions(-) create mode 100644 qc_app/static/css/custom-bootstrap.css create mode 100644 qc_app/static/css/styles.css diff --git a/qc_app/static/css/custom-bootstrap.css b/qc_app/static/css/custom-bootstrap.css new file mode 100644 index 0000000..e5f6594 --- /dev/null +++ b/qc_app/static/css/custom-bootstrap.css @@ -0,0 +1,4 @@ +/** Customize some bootstrap selectors **/ +.btn { + text-transform: capitalize; +} diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css new file mode 100644 index 0000000..a88c229 --- /dev/null +++ b/qc_app/static/css/styles.css @@ -0,0 +1,7 @@ +.heading { + text-transform: capitalize; +} + +label { + text-transform: capitalize; +} diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html index 00ff2d7..91faee8 100644 --- a/qc_app/templates/base.html +++ b/qc_app/templates/base.html @@ -14,6 +14,9 @@ + + + {%block css%}{%endblock%} diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html index f95f96f..03bb49c 100644 --- a/qc_app/templates/continue_from_create_dataset.html +++ b/qc_app/templates/continue_from_create_dataset.html @@ -20,7 +20,7 @@ {%endif%} {%endwith%} -
+
@@ -29,15 +29,15 @@ filename, filetype, species=species, genechipid=genechipid, studyid=studyid, datasetid=datasetid, totallines=totallines)}} -
- -
+
+
+

OR

+
+
@@ -46,11 +46,7 @@ filename, filetype, species=species, genechipid=genechipid, studyid=studyid, datasetid=datasetid, totallines=totallines)}} -
- -
+
{%endblock%} diff --git a/qc_app/templates/continue_from_create_study.html b/qc_app/templates/continue_from_create_study.html index 7455fbc..34e6e5e 100644 --- a/qc_app/templates/continue_from_create_study.html +++ b/qc_app/templates/continue_from_create_study.html @@ -20,7 +20,7 @@ {%endif%} {%endwith%} -
+
@@ -29,15 +29,15 @@ filename, filetype, species=species, genechipid=genechipid, studyid=studyid, totallines=totallines)}} -
- -
+
+
+

OR

+
+
@@ -46,11 +46,7 @@ filename, filetype, species=species, genechipid=genechipid, studyid=studyid, totallines=totallines)}} -
- -
+
{%endblock%} diff --git a/qc_app/templates/errors_display.html b/qc_app/templates/errors_display.html index 0ee5e85..715cfcf 100644 --- a/qc_app/templates/errors_display.html +++ b/qc_app/templates/errors_display.html @@ -5,7 +5,7 @@ {%else %}

{{error_message}}

- +
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html index 06d1e87..0d301f5 100644 --- a/qc_app/templates/index.html +++ b/qc_app/templates/index.html @@ -5,118 +5,130 @@ {%block title%}Data Upload{%endblock%} {%block contents%} -

data upload

- -
-

Each of the sections below gives you a different option for data upload. - Please read the documentation for each section carefully to understand what - each section is about.

+
+

data upload

+ +
+

Each of the sections below gives you a different option for data upload. + Please read the documentation for each section carefully to understand what + each section is about.

+
-

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.

- - - +
+

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.

+ + + +
-

Expression Data

- -
-

This feature enables you to upload expression data. It expects the data to - be in tab-separated values (TSV) files. The data should be - a simple matrix of phenotype × sample, i.e. The first column is a - list of the phenotypes and the first row is a list of - samples/cases.

- -

If you haven't done so please go to this page to learn the requirements for - file formats and helpful suggestions to enter your data in a fast and easy - way.

- -
    -
  1. PLEASE REVIEW YOUR DATA.Make sure your data complies - with our system requirements. ( - Help - )
    2. -
  2. UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept - .csv, .txt and .zip - files (Help)
    3. -
-
-
- upload expression data - {{flash_messages("error-expr-data")}} - -
- - -
- -
- file type - - - - - - -
- -
- - - -
- -
- -
+
+

Expression Data

+ +
+

This feature enables you to upload expression data. It expects the data to + be in tab-separated values (TSV) files. The data should be + a simple matrix of phenotype × sample, i.e. The first column is a + list of the phenotypes and the first row is a list of + samples/cases.

+ +

If you haven't done so please go to this page to learn the requirements for + file formats and helpful suggestions to enter your data in a fast and easy + way.

+ +
    +
  1. PLEASE REVIEW YOUR DATA.Make sure your data complies + with our system requirements. ( + Help + )
    2. +
  2. UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept + .csv, .txt and .zip + files (Help)
    3. +
+
+ + + upload expression data + {{flash_messages("error-expr-data")}} + +
+ + +
+ +
+ file type + +
+ + +
+ +
+ + +
+
+ +
+ + + +
+ + {{upload_progress_indicator()}} +
-

samples/cases

+
+

samples/cases

-
-

For the expression data above, you need the samples/cases in your file to - already exist in the GeneNetwork database. If there are any samples that do - not already exist the upload of the expression data will fail.

-

This section gives you the opportunity to upload any missing samples

-
+
+

For the expression data above, you need the samples/cases in your file to + already exist in the GeneNetwork database. If there are any samples that do + not already exist the upload of the expression data will fail.

+

This section gives you the opportunity to upload any missing samples

+
- - upload Samples/Cases + upload Samples/Cases +
{%endblock%} diff --git a/qc_app/templates/insert_error.html b/qc_app/templates/insert_error.html index 56dd195..5301288 100644 --- a/qc_app/templates/insert_error.html +++ b/qc_app/templates/insert_error.html @@ -5,24 +5,28 @@ {%block contents%}

Insertion Failure

-

- There was an error inserting data into the database -

+
+

+ There was an error inserting data into the database +

-

- Please notify the developers of this issue when you encounter it, - providing the information below. -

+

+ Please notify the developers of this issue when you encounter it, + providing the information below. +

-

Debugging Information

+

Debugging Information

-
    -
  • job id: {{job["job_id"]}}
    • -
+
    +
  • job id: {{job["jobid"]}}
    • +
+
-

STDERR Output

-
- {{job["stderr"]}} +
+

STDERR Output

+ 
+    {{job["stderr"]}}
+
{%endblock%} diff --git a/qc_app/templates/insert_progress.html b/qc_app/templates/insert_progress.html index 0e1a9e0..52177d6 100644 --- a/qc_app/templates/insert_progress.html +++ b/qc_app/templates/insert_progress.html @@ -10,8 +10,12 @@ {%block contents%}

{{job_name}}

- -{{job_status}}: {{message}}
+
+
+
+ + {{job_status}}: {{message}} +
{%if job.get("stdout", "").split("\n\n") | length < 3 %} {%set lines = 0%} @@ -25,9 +29,16 @@ {%set fraction = (lines/totallines)%} {%endif%} - -{{fraction*100}} -{{"%.2f" | format(fraction * 100 | float)}}%
+
+ + {{fraction*100}} + + {{"%.2f" | format(fraction * 100 | float)}}% +
+ +
{{stdout_output(job)}} diff --git a/qc_app/templates/insert_success.html b/qc_app/templates/insert_success.html index 4406c66..7e1fa8d 100644 --- a/qc_app/templates/insert_success.html +++ b/qc_app/templates/insert_success.html @@ -6,10 +6,14 @@ {%block contents%}

Insertion Success

+

Data inserted successfully!

The following queries were run:

+
-{{stdout_output(job)}} +
+ {{stdout_output(job)}} +
{%endblock%} diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html index 1b08814..1af0763 100644 --- a/qc_app/templates/job_progress.html +++ b/qc_app/templates/job_progress.html @@ -10,21 +10,30 @@ {%block contents%}

{{job_name}}

- -{{job_status}}: {{message}}
- - -{{progress}} -{{"%.2f" | format(progress)}}% - -
+
+ Status +
+ + {{job_status}}: {{message}}
+
+ +
+ + + {{progress}} + {{"%.2f" | format(progress)}}% +
+ - + +
-
+
{{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}}
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%} diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html index 5d78826..da19ddc 100644 --- a/qc_app/templates/samples/select-population.html +++ b/qc_app/templates/samples/select-population.html @@ -13,33 +13,28 @@ (e.g. Inbred populations, cell tissue, etc.)

-
-
select grouping/population {{flash_messages("error-select-population")}} -
- + +
+ -
+
-
- -
+

OR

@@ -50,54 +45,51 @@ {{flash_messages("error-create-population")}} -
+
mandatory - + + + class="form-control" /> - + -
-
+ class="form-control" /> +
+
Optional - + + class="form-control" /> - + + class="form-control" /> - + - - -
- -
+ class="form-control"> +
+ + {%endblock%} diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html index 44c0d4f..edadc61 100644 --- a/qc_app/templates/samples/select-species.html +++ b/qc_app/templates/samples/select-species.html @@ -12,18 +12,19 @@
upload samples -
- - {%for spec in species%} {%endfor%} -
+
-
- -
+ {%endblock%} diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html index 29b08f6..e62de57 100644 --- a/qc_app/templates/samples/upload-samples.html +++ b/qc_app/templates/samples/upload-samples.html @@ -3,16 +3,7 @@ {%block title%}Upload Samples{%endblock%} -{%block css%} - -{%endblock%} +{%block css%}{%endblock%} {%block contents%}

upload samples

@@ -20,23 +11,23 @@ {{flash_messages("alert-success")}}

You can now upload a character-separated value (CSV) file that contains - details about your samples. The CSV file should have the following fields: -

-
Name
-
The primary name for the sample
+ details about your samples. The CSV file should have the following fields: +
+
Name
+
The primary name for the sample
-
Name2
-
A secondary name for the sample. This can simply be the same as - Name above. This field MUST contain a - value.
+
Name2
+
A secondary name for the sample. This can simply be the same as + Name above. This field MUST contain a + value.
-
Symbol
-
A symbol for the sample. Can be an empty field.
+
Symbol
+
A symbol for the sample. Can be an empty field.
-
Alias
-
An alias for the sample. Can be an empty field.
-
-

+
Alias
+
An alias for the sample. Can be an empty field.
+
+

upload samples -
+ +
- - {{species.SpeciesName}} [{{species.MenuName}}] -
+ + {{species.SpeciesName}} [{{species.MenuName}}] +
-
+
- - {{population.Name}} [{{population.FullName}}] -
+ + {{population.Name}} [{{population.FullName}}] +
-
- - -
+
+ + +
-
- +
+ - - This is the character that separates the fields in your CSV file. If you - select "Other", then you must provide the separator in - the text field provided. - -
- -
- + class="form-control" /> + + If you select 'Other' for the field separator value, + enter the character that separates the fields in your CSV file in the form + field below. + + + +
+ + + + Select this if the first line in your file contains headings for the + columns. + +
+ +
+ - + class="form-control" /> + If there is a character delimiting the string texts within particular fields in your CSV, provide the character here. This can be left blank if no such delimiters exist in your file. - -
+ + -
- - -
- -
- -
+ -
line number
+
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html index 3c9bd6b..2f07de8 100644 --- a/qc_app/templates/select_dataset.html +++ b/qc_app/templates/select_dataset.html @@ -10,17 +10,17 @@ {%block contents%}

{{filename}}: select dataset

-
+
- choose existing dataset + choose existing dataset {{hidden_fields( filename, filetype, species=species, genechipid=genechipid, studyid=studyid, totallines=totallines)}} -
- - @@ -30,23 +30,24 @@ {%endfor%} -
+
-
- -
- + + +
+

OR

+
+
- create new dataset + create new dataset {{hidden_fields( filename, filetype, species=species, genechipid=genechipid, studyid=studyid, totallines=totallines)}} @@ -61,9 +62,9 @@ {%endif%} {%endwith%} -
- - {%for method in avgmethods:%}
+
-
- +
+ -
+ -
- +
+ -
+ -
- +
+ -
+ -
- +
+ -
+ -
- +
+ -
+ class="form-control" /> + -
+
-
+ class="form-control" /> + -
- - {%for dscale in datascales:%}
+ -
- -
+ - {%endblock%} - -{%block javascript%} -{%endblock%} diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html index d69a970..d9bc68f 100644 --- a/qc_app/templates/select_platform.html +++ b/qc_app/templates/select_platform.html @@ -5,58 +5,58 @@ {%block contents%}

{{filename}}: select platform

- - - - +
+ + + + -
- - -
+
+ + +
-
preview content
- - - - - - - +
SelectGeneChip IDGeneChip Name
+ + + + + + + + - - {%for chip in genechips:%} - - - - - - {%else%} - - - - {%endfor%} - -
select platform
SelectGeneChip IDGeneChip Name
- - {{chip["GeneChipId"]}}{{chip["GeneChipName"]}}
No chips found for selected species
+ + {%for chip in genechips:%} + + + + + {{chip["GeneChipId"]}} + {{chip["GeneChipName"]}} + + {%else%} + + No chips found for selected species + + {%endfor%} + + -
- -
- + + +
{%endblock%} {%block javascript%} diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html index e474c50..648ad4c 100644 --- a/qc_app/templates/select_study.html +++ b/qc_app/templates/select_study.html @@ -10,34 +10,36 @@ {%block contents%}

{{filename}}: select study

-
+
- Select from existing study + Select from existing study {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, totallines=totallines)}} -
- - {%for study in studies:%} {%endfor%} -
+
-
- -
- + + +
+

OR

+
+
@@ -50,22 +52,22 @@ {%endif%} {%endwith%} - Create new study + Create new study {{hidden_fields(filename, filetype, species=species, genechipid=genechipid, totallines=totallines)}} -
- - + + -
+
-
- - {%for family in groups:%} @@ -81,11 +83,11 @@ {%endfor%} -
+
-
- - {%for tissue in tissues:%} @@ -97,12 +99,9 @@ {%endfor%} -
+ -
- -
+ diff --git a/qc_app/templates/stdout_output.html b/qc_app/templates/stdout_output.html index f3fcde5..85345a9 100644 --- a/qc_app/templates/stdout_output.html +++ b/qc_app/templates/stdout_output.html @@ -2,9 +2,7 @@

STDOUT Output

- {%for line in job.get("stdout", "").split("\n\n"):%} -

{{line}}

- {%endfor%} + 
{{job.get("stdout", "")}}
{%endmacro%} -- cgit v1.2.3