diff options
Diffstat (limited to 'qc_app/templates/rqtl2')
| -rw-r--r-- | qc_app/templates/rqtl2/create-geno-dataset-success.html | 42 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/create-probe-dataset-success.html | 46 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/create-probe-study-success.html | 42 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/create-tissue-success.html | 116 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/index.html | 20 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/rqtl2-qc-job-results.html | 78 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/rqtl2-qc-job-success.html | 34 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-geno-dataset.html | 248 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-population.html | 148 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-probeset-dataset.html | 323 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-probeset-study-id.html | 242 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-tissue.html | 181 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/summary-info.html | 86 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html | 20 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html | 34 |
15 files changed, 847 insertions, 813 deletions
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 @@ </p> </div> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" - value="{{geno_dataset.id}}" /> - - <fieldset> - <input type="submit" - value="continue" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">select from existing genotype datasets</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" + value="{{geno_dataset.id}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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%} <h2 class="heading">Create ProbeSet Dataset</h2> -<div class="explainer"> +<div class="row"> <p>You successfully created the ProbeSet dataset with the following information. <dl> @@ -34,28 +34,26 @@ </p> </div> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.Id}}" /> - <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" /> - - <fieldset> - <input type="submit" - value="continue" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">Create ProbeSet dataset</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{study.Id}}" /> + <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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%} <h2 class="heading">Create ProbeSet Study</h2> -<div class="explainer"> +<div class="row"> <p>You successfully created the ProbeSet study with the following information. <dl> @@ -26,28 +26,24 @@ <dd>{{study.today}}</dd> </dl> </p> -</div> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet study</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{study.studyid}}" /> - - <fieldset> - <input type="submit" - value="continue" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">Create ProbeSet study</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{study.studyid}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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%} <h2 class="heading">Select Tissue</h2> -<div class="explainer"> +<div class="row"> <p>You have successfully added a new tissue, organ or biological material with the following details:</p> </div> -{{flash_all_messages()}} - -<form id="frm-create-tissue-display" - method="POST" - action="#"> - <legend class="heading">Create Tissue</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - - <fieldset> - <label>Name</label> - <label>{{tissue.TissueName}}</label> - </fieldset> - - <fieldset> - <label>Short Name</label> - <label>{{tissue.Short_Name}}</label> - </fieldset> - - {%if tissue.BIRN_lex_ID%} - <fieldset> - <label>BIRN Lex ID</label> - <label>{{tissue.BIRN_lex_ID}}</label> - </fieldset> - {%endif%} - - {%if tissue.BIRN_lex_Name%} - <fieldset> - <label>BIRN Lex Name</label> - <label>{{tissue.BIRN_lex_Name}}</label> - </fieldset> - {%endif%} -</form> - -<div id="action-buttons" - style="width:65ch;display:inline-grid;column-gap:5px;"> - - <form id="frm-create-tissue-success-continue" +<div class="row"> + {{flash_all_messages()}} + + <form id="frm-create-tissue-display" method="POST" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - style="display: inline; width: 100%; grid-column: 1 / 2; - padding-top: 0.5em; text-align: center; border: none; - background-color: inherit;"> + action="#"> + <legend class="heading">Create Tissue</legend> <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> <input type="hidden" name="population_id" @@ -69,16 +26,63 @@ <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="submit" - value="continue" - class="btn btn-primary form-col-2" /> + <div class="form-group"> + <label>Name</label> + <label>{{tissue.TissueName}}</label> + </div> + + <div class="form-group"> + <label>Short Name</label> + <label>{{tissue.Short_Name}}</label> + </div> + + {%if tissue.BIRN_lex_ID%} + <div class="form-group"> + <label>BIRN Lex ID</label> + <label>{{tissue.BIRN_lex_ID}}</label> + </div> + {%endif%} + + {%if tissue.BIRN_lex_Name%} + <div class="form-group"> + <label>BIRN Lex Name</label> + <label>{{tissue.BIRN_lex_Name}}</label> + </div> + {%endif%} </form> + <div id="action-buttons" + style="width:65ch;display:inline-grid;column-gap:5px;"> + + <form id="frm-create-tissue-success-continue" + method="POST" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + style="display: inline; width: 100%; grid-column: 1 / 2; + padding-top: 0.5em; text-align: center; border: none; + background-color: inherit;"> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <button type="submit" class="btn btn-primary">continue</button> + </form> + </div> +</div> + +<div class="row"> <p style="display:inline;width:100%;grid-column:2/3;text-align:center; color:#336699;font-weight:bold;"> OR </p> +</div> +<div class="row"> <form id="frm-create-tissue-success-select-existing" method="POST" action="{{url_for('upload.rqtl2.select_tissue', @@ -94,11 +98,9 @@ <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="submit" - value="select from existing tissues" - class="btn btn-primary form-col-2" /> + <button type="submit" class="btn btn-primary"> + select from existing tissues</button> </form> - </div> {%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"> <legend class="heading">upload R/qtl2 bundle</legend> {{flash_messages("error-rqtl2")}} - <fieldset> - <label for="select:species">Species</label> - <select id="select:species" name="species_id" required="required"> + + <div class="form-group"> + <label for="select:species" class="form-label">Species</label> + <select id="select:species" + name="species_id" + required="required" + class="form-control"> <option value="">Select species</option> {%for spec in species%} <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option> {%endfor%} </select> - <span class="form-input-help"> + <small class="form-text text-muted"> 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. - </span> - </fieldset> + </small> + </div> - <fieldset> - <input type="submit" value="submit" class="btn btn-primary form-col-2" /> - </fieldset> + <button type="submit" class="btn btn-primary" />submit</button> </form> {%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%} <h1 class="heading">R/qtl2 bundle: QC job results</h1> -<div class="explainer"> +<div class="row"> <p>The R/qtl2 bundle you uploaded has passed all automated quality-control checks successfully.</p> <p>You may now continue to load the data into GeneNetwork for the bundle, with the following details:</p> </div> -<form id="form-qc-job-results" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.Id)}}" - method="POST"> - <fieldset> - <legend>Species</legend> - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> +<div class="row"> + <form id="form-qc-job-results" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + <div class="form-group"> + <legend>Species</legend> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <span class="form-col-1">Name</span> - <span class="form-col-2">{{species.Name | capitalize}}</span> + <span class="form-label">Name</span> + <span class="form-text">{{species.Name | capitalize}}</span> - <span class="form-col-1">Scientific</span> - <span class="form-col-2">{{species.FullName | capitalize}}</span> - </fieldset> + <span class="form-label">Scientific</span> + <span class="form-text">{{species.FullName | capitalize}}</span> + </div> - <fieldset> - <legend>population</legend> - <input type="hidden" name="population_id" value="{{population.Id}}" /> + <div class="form-group"> + <legend>population</legend> + <input type="hidden" name="population_id" value="{{population.Id}}" /> - <span class="form-col-1">Name</span> - <span class="form-col-2">{{population.InbredSetName}}</span> + <span class="form-label">Name</span> + <span class="form-text">{{population.InbredSetName}}</span> - <span class="form-col-1">Full Name</span> - <span class="form-col-2">{{population.FullName}}</span> + <span class="form-label">Full Name</span> + <span class="form-text">{{population.FullName}}</span> - <span class="form-col-1">Genetic Type</span> - <span class="form-col-2">{{population.GeneticType}}</span> + <span class="form-label">Genetic Type</span> + <span class="form-text">{{population.GeneticType}}</span> - <span class="form-col-1">Description</span> - <span class="form-col-2">{{population.Description or "-"}}</span> - </fieldset> + <span class="form-label">Description</span> + <span class="form-text">{{population.Description or "-"}}</span> + </div> - <fieldset> - <legend>R/qtl2 Bundle File</legend> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" /> - <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" /> + <div class="form-group"> + <legend>R/qtl2 Bundle File</legend> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2bundle}}" /> + <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" /> - <span class="form-col-1">Original Name</span> - <span class="form-col-2">{{rqtl2bundleorig}}</span> + <span class="form-label">Original Name</span> + <span class="form-text">{{rqtl2bundleorig}}</span> - <span class="form-col-1">Internal Name</span> - <span class="form-col-2">{{rqtl2bundle[0:25]}}…</span> - </fieldset> + <span class="form-label">Internal Name</span> + <span class="form-text">{{rqtl2bundle[0:25]}}…</span> + </div> - <fieldset> - <input type="submit" value="continue" class="btn btn-primary form-col-2" /> - </fieldset> -</form> + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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%} <h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2> -<div class="explainer"> +<div class="row"> <p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control checks successfully, and is now ready for uploading into the database.</p> <p>Click "Continue" below to proceed.</p> @@ -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. --> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - {{flash_all_messages()}} - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + {{flash_all_messages()}} + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> - <fieldset> - <input type="submit" value="continue" class="btn btn-primary form-col-2" /> - </fieldset> -</form> + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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%} <h2 class="heading">Select Genotypes Dataset</h2> -<div class="explainer"> +<div class="row"> <p>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.</p> <p>This is the dataset where your data will be organised under.</p> </div> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">select from existing genotype datasets</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-select-geno-dataset")}} - - <fieldset> - <legend>Datasets</legend> - <label for="select:geno-datasets">Dataset</label> - <select id="select:geno-datasets" - name="geno-dataset-id" - required="required" - {%if datasets | length == 0%} - disabled="disabled" - {%endif%}> - <option value="">Select dataset</option> - {%for dset in datasets%} - <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> - {%endfor%} - </select> - <span class="form-col-2"> - Select from the existing genotype datasets for species - {{species.SpeciesName}} ({{species.FullName}}). - </span> - </fieldset> - - <fieldset> - <input type="submit" - value="select dataset" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> - -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> - -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.create_geno_dataset', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">create a new genotype dataset</legend> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - - {{flash_messages("error-rqtl2-create-geno-dataset")}} - - <fieldset> - <label for="txt:dataset-name">Name</label> - <input type="text" - id="txt:dataset-name" - name="dataset-name" - maxlength="100" - required="required" /> - <span class="form-col-2"> - Provide the new name for the genotype dataset, e.g. "BXDGeno" - </span> - </fieldset> - - <fieldset> - <label for="txt:dataset-fullname">Full Name</label> - <input type="text" - id="txt:dataset-fullname" - name="dataset-fullname" - required="required" - maxlength="100" /> - - <span class="form-col-2"> - Provide a longer name that better describes the genotype dataset, e.g. - "BXD Genotypes" - </span> - </fieldset> - - <fieldset> - <label for="txt:dataset-shortname">Short Name</label> - <input type="text" - id="txt:dataset-shortname" - name="dataset-shortname" - maxlength="100" /> - - <span class="form-col-2"> - 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. - </span> - </fieldset> - - <fieldset> - <input type="checkbox" - id="chk:dataset-public" - name="dataset-public" - checked="checked" /> - <label for="chk:dataset-public">Public?</label> - - <span class="form-col-2"> - Specify whether the dataset will be available publicly. Check to make the - dataset publicly available and uncheck to limit who can access the dataset. - </span> - </fieldset> - - <fieldset> - <input type="submit" - value="create new dataset" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_geno_dataset', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">select from existing genotype datasets</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + {{flash_messages("error-rqtl2-select-geno-dataset")}} + + <div class="form-group"> + <legend>Datasets</legend> + <label for="select:geno-datasets" class="form-label">Dataset</label> + <select id="select:geno-datasets" + name="geno-dataset-id" + required="required" + {%if datasets | length == 0%} + disabled="disabled" + {%endif%} + class="form-control" + aria-describedby="help-geno-dataset-select-dataset"> + <option value="">Select dataset</option> + {%for dset in datasets%} + <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option> + {%endfor%} + </select> + <span id="help-geno-dataset-select-dataset" class="form-text text-muted"> + Select from the existing genotype datasets for species + {{species.SpeciesName}} ({{species.FullName}}). + </span> + </div> + + <button type="submit" class="btn btn-primary">select dataset</button> + </form> +</div> + +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> + +<div class="row"> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.create_geno_dataset', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">create a new genotype dataset</legend> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + + {{flash_messages("error-rqtl2-create-geno-dataset")}} + + <div class="form-group"> + <label for="txt:dataset-name" class="form-label">Name</label> + <input type="text" + id="txt:dataset-name" + name="dataset-name" + maxlength="100" + required="required" + class="form-control" + aria-describedby="help-geno-dataset-name" /> + <span id="help-geno-dataset-name" class="form-text text-muted"> + Provide the new name for the genotype dataset, e.g. "BXDGeno" + </span> + </div> + + <div class="form-group"> + <label for="txt:dataset-fullname" class="form-label">Full Name</label> + <input type="text" + id="txt:dataset-fullname" + name="dataset-fullname" + required="required" + maxlength="100" + class="form-control" + aria-describedby="help-geno-dataset-fullname" /> + + <span id="help-geno-dataset-fullname" class="form-text text-muted"> + Provide a longer name that better describes the genotype dataset, e.g. + "BXD Genotypes" + </span> + </div> + + <div class="form-group"> + <label for="txt:dataset-shortname" class="form-label">Short Name</label> + <input type="text" + id="txt:dataset-shortname" + name="dataset-shortname" + maxlength="100" + class="form-control" + aria-describedby="help-geno-dataset-shortname" /> + + <span id="help-geno-dataset-shortname" class="form-text text-muted"> + 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. + </span> + </div> + + <div class="form-group"> + <input type="checkbox" + id="chk:dataset-public" + name="dataset-public" + checked="checked" + class="form-check" + aria-describedby="help-geno-datasent-public" /> + <label for="chk:dataset-public" class="form-check-label">Public?</label> + + <span id="help-geno-dataset-public" class="form-text text-muted"> + Specify whether the dataset will be available publicly. Check to make the + dataset publicly available and uncheck to limit who can access the dataset. + </span> + </div> + + <button type="submit" class="btn btn-primary">create new dataset</button> + </form> +</div> {%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")}} <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <fieldset> - <label for="select:inbredset" class="form-col-1">population</label> + + <div class="form-group"> + <label for="select:inbredset" class="form-label">population</label> <select id="select:inbredset" name="inbredset_id" required="required" - class="form-col-2"> + class="form-control"> <option value="">Select a grouping/population</option> {%for pop in populations%} <option value="{{pop.InbredSetId}}"> {{pop.InbredSetName}} ({{pop.FullName}})</option> {%endfor%} </select> - <span class="form-input-help">If you are adding data to an already existing + <span class="form-text text-muted">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..</span> - </fieldset> + </div> - <fieldset> - <input type="submit" - value="select population" - class="btn btn-primary form-col-2" /> - </fieldset> + <button type="submit" class="btn btn-primary" />select population</button> </form> <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> @@ -55,70 +52,81 @@ {{flash_messages("error-create-population")}} <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <fieldset> - <legend>mandatory</legend> - <label for="txt:inbredset-name" class="form-col-1">name</label> - <input id="txt:inbredset-name" - name="inbredset_name" - type="text" - required="required" - maxlength="30" - placeholder="Enter grouping/population name" - class="form-col-2" /> - <span class="form-input-help">This is a short name that identifies the - population. Useful for menus, and quick scanning.</span> - - <label for="txt:" class="form-col-1">full name</label> - <input id="txt:inbredset-fullname" - name="inbredset_fullname" - type="text" - required="required" - maxlength="100" - placeholder="Enter the grouping/population's full name" - class="form-col-2" /> - <span class="form-input-help">This can be the same as the name above, or can - be longer. Useful for documentation, and human communication.</span> - </fieldset> - <fieldset> - <legend>Optional</legend> - - <label for="num:public" class="form-col-1">public?</label> - <select id="num:public" - name="public" - class="form-col-2"> - <option value="0">0 - Only accessible to authorised users</option> - <option value="1">1 - Publicly accessible to all users</option> - <option value="2" selected> - 2 - Publicly accessible to all users</option> - </select> - <span class="form-input-help">This determines whether the - population/grouping will appear on the menus for users.</span> - - <label for="txt:inbredset-family" class="form-col-1">family</label> - <input id="txt:inbredset-family" - name="inbredset_family" - type="text" - placeholder="I am not sure what this is about." - class="form-col-2" /> - <span class="form-input-help">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.</span> - - <label for="txtarea:" class="form-col-1">Description</label> + + <div class="form-group"> + <legend class="heading">mandatory</legend> + + <div class="form-group"> + <label for="txt:inbredset-name" class="form-label">name</label> + <input id="txt:inbredset-name" + name="inbredset_name" + type="text" + required="required" + maxlength="30" + placeholder="Enter grouping/population name" + class="form-control" /> + <span class="form-text text-muted">This is a short name that identifies the + population. Useful for menus, and quick scanning.</span> + </div> + + <div class="form-group"> + <label for="txt:" class="form-label">full name</label> + <input id="txt:inbredset-fullname" + name="inbredset_fullname" + type="text" + required="required" + maxlength="100" + placeholder="Enter the grouping/population's full name" + class="form-control" /> + <span class="form-text text-muted">This can be the same as the name above, or can + be longer. Useful for documentation, and human communication.</span> + </div> + </div> + + <div class="form-group"> + <legend class="heading">optional</legend> + + <div class="form-group"> + <label for="num:public" class="form-label">public?</label> + <select id="num:public" + name="public" + class="form-control"> + <option value="0">0 - Only accessible to authorised users</option> + <option value="1">1 - Publicly accessible to all users</option> + <option value="2" selected> + 2 - Publicly accessible to all users</option> + </select> + <span class="form-text text-muted">This determines whether the + population/grouping will appear on the menus for users.</span> + </div> + + <div class="form-group"> + <label for="txt:inbredset-family" class="form-label">family</label> + <input id="txt:inbredset-family" + name="inbredset_family" + type="text" + placeholder="I am not sure what this is about." + class="form-control" /> + <span class="form-text text-muted">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.</span> + </div> + + <div class="form-group"> + <label for="txtarea:" class="form-label">Description</label> <textarea id="txtarea:description" name="description" rows="5" placeholder="Enter a description of this grouping/population" - class="form-col-2"></textarea> - <span class="form-input-help">A long-form description of what the population - consists of. Useful for humans.</span> - </fieldset> - - <fieldset> - <input type="submit" - value="create grouping/population" - class="btn btn-primary form-col-2" /> - </fieldset> + class="form-control"></textarea> + <span class="form-text text-muted"> + A long-form description of what the population consists of. Useful for + humans.</span> + </div> + </div> + + <button type="submit" class="btn btn-primary" /> + create grouping/population</button> </form> {%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%} <h2 class="heading">Phenotype(ProbeSet) Dataset</h2> -<div class="explainer"> +<div class="row"> <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>" file(s). This data needs to be organised under a dataset.</p> <p>This page gives you the ability to do that.</p> </div> {%if datasets | length > 0%} -<form method="POST" - action="{{url_for('upload.rqtl2.select_probeset_dataset', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:select-probeset-dataset"> - <legend class="heading">Select from existing ProbeSet datasets</legend> - {{flash_messages("error-rqtl2")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> - - <fieldset> - <label for="select:probe-dataset">Dataset</label> - <select id="select:probe-dataset" - name="probe-dataset-id" - required="required" - {%if datasets | length == 0%}disabled="disabled"{%endif%}> - <option value="">Select a dataset</option> - {%for dataset in datasets%} - <option value={{dataset.Id}}> - {{dataset.Name}} - {%if dataset.FullName%} - -- ({{dataset.FullName}}) - {%endif%} - </option> - {%endfor%} - </select> - - <span class="form-col-2">Select from existing ProbeSet datasets.</span> - </fieldset> - - <fieldset> - <input type="submit" - value="select dataset" - class="btn btn-primary form-col-2" /> - </fieldset> +<div class="row"> + <form method="POST" + action="{{url_for('upload.rqtl2.select_probeset_dataset', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-dataset"> + <legend class="heading">Select from existing ProbeSet datasets</legend> + {{flash_messages("error-rqtl2")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select:probe-dataset">Dataset</label> + <select id="select:probe-dataset" + name="probe-dataset-id" + required="required" + {%if datasets | length == 0%}disabled="disabled"{%endif%} + class="form-control" + aria-describedby="help-probe-dataset"> + <option value="">Select a dataset</option> + {%for dataset in datasets%} + <option value={{dataset.Id}}> + {{dataset.Name}} + {%if dataset.FullName%} + -- ({{dataset.FullName}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-probe-dataset" class="form-text text-muted"> + Select from existing ProbeSet datasets.</span> + </div> + + <button type="submit" class="btn btn-primary" />select dataset</button> </form> +</div> -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> {%endif%} -<div class="explainer"> +<div class="row"> <p>Create an entirely new ProbeSet dataset for your data.</p> </div> -<form method="POST" - action="{{url_for('upload.rqtl2.create_probeset_dataset', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:create-probeset-dataset"> - <legend class="heading">Create a new ProbeSet dataset</legend> - {{flash_messages("error-rqtl2-create-probeset-dataset")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> - - <fieldset> - <label for="select:average">averaging method</label> - <select id="select:average" - name="averageid" - required="required"> - <option value="">Select averaging method</option> - {%for avgmethod in avgmethods%} - <option value="{{avgmethod.Id}}"> - {{avgmethod.Name}} - {%if avgmethod.Normalization%} - ({{avgmethod.Normalization}}) - {%endif%} - </option> - {%endfor%} - </select> - - <span class="form-col-2"> - Select the averaging method used for your data. - </span> - </fieldset> - - <fieldset> - <label for="txt:datasetname">Name</label> - <input type="text" id="txt:datasetname" name="datasetname" - required="required" - maxlength="40" - title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" /> - - <span class="form-col-2"> - Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This - is mandatory <strong>MUST</strong> be provided. - </span> - </fieldset> - - <fieldset> - <label for="txt:datasetfullname">Full Name</label> - <input type="text" id="txt:datasetfullname" name="datasetfullname" - required="required" - maxlength="100" - title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" /> - - <span class="form-col-2"> - Provide a longer, more descriptive name for the dataset e.g. - "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and - <strong>MUST</strong> be provided. - </span> - </fieldset> - - <fieldset> - <label for="txt:datasetshortname">Short Name</label> - <input type="text" id="txt:datasetshortname" name="datasetshortname" - maxlength="100" - title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" /> - - <span class="form-col-2"> - Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". - This is optional. - </span> - </fieldset> - - <fieldset> - <input type="checkbox" id="chk:public" name="datasetpublic" - checked="checked" - title="Whether or not the dataset is accessible by the general public." /> - <label for="chk:datasetpublic">Public?</label> - - <span class="form-col-2"> - Check to specify that the dataset will be publicly available. Uncheck to - limit access to the dataset. - </span> - </fieldset> - - <fieldset> - <label for="select:datasetdatascale">Data Scale</label> - <select id="select:datasetdatascale" - name="datasetdatascale" - required="required"> - <option value="log2" selected="selected">log2</option> - <option value="z_score">z_score</option> - <option value="log2_ratio">log2_ratio</option> - <option value="linear">linear</option> - <option value="linear_positive">linear_positive</option> - </select> - - <span class="form-col-2"> - Select from a list of scaling methods. - </span> - </fieldset> - - <fieldset> - <input type="submit" - value="create dataset" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + <form method="POST" + action="{{url_for('upload.rqtl2.create_probeset_dataset', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-dataset"> + <legend class="heading">Create a new ProbeSet dataset</legend> + {{flash_messages("error-rqtl2-create-probeset-dataset")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select:average">averaging method</label> + <select id="select:average" + name="averageid" + required="required" + class="form-control" + aria-describedby="help-average"> + <option value="">Select averaging method</option> + {%for avgmethod in avgmethods%} + <option value="{{avgmethod.Id}}"> + {{avgmethod.Name}} + {%if avgmethod.Normalization%} + ({{avgmethod.Normalization}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-average" class="form-text text-muted"> + Select the averaging method used for your data. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetname">Name</label> + <input type="text" id="txt:datasetname" name="datasetname" + required="required" + maxlength="40" + title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" + class="form-control" + aria-describedby="help-dataset-name" /> + + <span id="help-dataset-name" class="form-text text-muted"> + Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This + is mandatory <strong>MUST</strong> be provided. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetfullname">Full Name</label> + <input type="text" id="txt:datasetfullname" name="datasetfullname" + required="required" + maxlength="100" + title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" + class="form-control" + aria-describedby="help-dataset-fullname" /> + + <span id="help-dataset-fullname" class="form-text text-muted"> + Provide a longer, more descriptive name for the dataset e.g. + "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and + <strong>MUST</strong> be provided. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="txt:datasetshortname">Short Name</label> + <input type="text" id="txt:datasetshortname" name="datasetshortname" + maxlength="100" + title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" + class="form-control" + aria-describedby="help-dataset-shortname" /> + + <span id="help-dataset-shortname" class="form-text text-muted"> + Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". + This is optional. + </span> + </div> + + <div class="form-check"> + <input type="checkbox" id="chk:public" name="datasetpublic" + checked="checked" + title="Whether or not the dataset is accessible by the general public." + class="form-check-input" + aria-describedby="help-public" /> + <label class="form-check-label" for="chk:datasetpublic">Public?</label> + + <span id="help-public" class="form-text text-muted"> + Check to specify that the dataset will be publicly available. Uncheck to + limit access to the dataset. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="select:datasetdatascale">Data Scale</label> + <select id="select:datasetdatascale" + name="datasetdatascale" + required="required" + class="form-control" + aria-describedby="help-dataset-datascale"> + <option value="log2" selected="selected">log2</option> + <option value="z_score">z_score</option> + <option value="log2_ratio">log2_ratio</option> + <option value="linear">linear</option> + <option value="linear_positive">linear_positive</option> + </select> + + <span id="help-dataset-datascale" class="form-text text-muted"> + Select from a list of scaling methods. + </span> + </div> + + <button type="submit" class="btn btn-primary">create dataset</button> + </form> +</div> {%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%} <h2 class="heading">Phenotype(ProbeSet) Study</h2> -<div class="explainer"> +<div class="row"> <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>" file(s). This data needs to be organised under a study.</p> <p>In this page, you can either select from a existing dataset:</p> + + <form method="POST" + action="{{url_for('upload.rqtl2.select_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-study"> + <legend class="heading">Select from existing ProbeSet studies</legend> + {{flash_messages("error-rqtl2-select-probeset-study")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <div> + <label for="select:probe-study" class="form-label">Study</label> + <select id="select:probe-study" + name="probe-study-id" + required="required" + aria-describedby="help-select-probeset-study" + {%if studies | length == 0%}disabled="disabled"{%endif%} + class="form-control"> + <option value="">Select a study</option> + {%for study in studies%} + <option value={{study.Id}}> + {{study.Name}} + {%if study.FullName%} + -- ({{study.FullName}}) + {%endif%} + </option> + {%endfor%} + </select> + <small id="help-select-probeset-study" class="form-text text-muted"> + Select from existing ProbeSet studies. + </small> + </div> + + <button type="submit" class="btn btn-primary">select study</button> + </form> </div> -<form method="POST" - action="{{url_for('upload.rqtl2.select_probeset_study', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:select-probeset-study"> - <legend class="heading">Select from existing ProbeSet studies</legend> - {{flash_messages("error-rqtl2-select-probeset-study")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - - <fieldset> - <label for="select:probe-study">Study</label> - <select id="select:probe-study" - name="probe-study-id" - required="required" - {%if studies | length == 0%}disabled="disabled"{%endif%}> - <option value="">Select a study</option> - {%for study in studies%} - <option value={{study.Id}}> - {{study.Name}} - {%if study.FullName%} - -- ({{study.FullName}}) - {%endif%} - </option> - {%endfor%} - </select> - <span class="form-col-2">Select from existing ProbeSet studies.</span> - </fieldset> - - <fieldset> - <input type="submit" - value="select study" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> - -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> - -<div class="explainer"> - <p>Create a new ProbeSet dataset below:</p> +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> </div> -<form method="POST" - action="{{url_for('upload.rqtl2.create_probeset_study', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:create-probeset-study"> - <legend class="heading">Create new ProbeSet study</legend> - - {{flash_messages("error-rqtl2-create-probeset-study")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> - - <fieldset> - <label for="select:platform">Platform</label> - <select id="select:platform" - name="platformid" - required="required" - {%if platforms | length == 0%}disabled="disabled"{%endif%}> - <option value="">Select a platform</option> - {%for platform in platforms%} - <option value="{{platform.GeneChipId}}"> - {{platform.GeneChipName}} ({{platform.Name}}) - </option> - {%endfor%} - </select> - <span class="form-col-2">Select from a list of known genomics platforms. - </span> - </fieldset> - - <fieldset> - <label for="txt:studyname">Study name</label> - <input type="text" id="txt:studyname" name="studyname" - placeholder="Name of the study. (Required)" - required="required" - maxlength="100" /> - <span class="form-col-2">Provide a name for the study.</span> - </fieldset> - - <fieldset> - <label for="txt:studyfullname">Full Study Name</label> - <input type="text" id="txt:studyfullname" name="studyfullname" - placeholder="Longer name of the study. (Optional)" - maxlength="100" /> - <span class="form-col-2"> - Provide a longer, more descriptive name for the study. This is optional - and you can leave it blank. - </span> - </fieldset> - - <fieldset> - <label for="txt:studyshortname">Short Study Name</label> - <input type="text" id="txt:studyshortname" name="studyshortname" - placeholder="Shorter name of the study. (Optional)" - maxlength="100" /> - <span class="form-col-2"> - Provide a shorter name for the study. This is optional and you can leave - it blank. - </span> - </fieldset> - - <fieldset> - <input type="submit" - value="create study" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + + <p>Create a new ProbeSet dataset below:</p> + + <form method="POST" + action="{{url_for('upload.rqtl2.create_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-study"> + <legend class="heading">Create new ProbeSet study</legend> + + {{flash_messages("error-rqtl2-create-probeset-study")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="tissueid" value="{{tissue.Id}}" /> + + <div> + <label for="select:platform" class="form-label">Platform</label> + <select id="select:platform" + name="platformid" + required="required" + aria-describedby="help-select-platform" + {%if platforms | length == 0%}disabled="disabled"{%endif%} + class="form-control"> + <option value="">Select a platform</option> + {%for platform in platforms%} + <option value="{{platform.GeneChipId}}"> + {{platform.GeneChipName}} ({{platform.Name}}) + </option> + {%endfor%} + </select> + <small id="help-select-platform" class="form-text text-muted"> + Select from a list of known genomics platforms. + </small> + </div> + + <div class="form-group"> + <label for="txt:studyname" class="form-label">Study name</label> + <input type="text" id="txt:studyname" name="studyname" + placeholder="Name of the study. (Required)" + required="required" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-name"> + Provide a name for the study.</span> + </div> + + <div class="form-group"> + <label for="txt:studyfullname" class="form-label">Full Study Name</label> + <input type="text" + id="txt:studyfullname" + name="studyfullname" + placeholder="Longer name of the study. (Optional)" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-full-name"> + Provide a longer, more descriptive name for the study. This is optional + and you can leave it blank. + </span> + </div> + + <div class="form-group"> + <label for="txt:studyshortname" class="form-label">Short Study Name</label> + <input type="text" + id="txt:studyshortname" + name="studyshortname" + placeholder="Shorter name of the study. (Optional)" + maxlength="100" + class="form-control" /> + <span class="form-text text-muted" id="help-study-short-name"> + Provide a shorter name for the study. This is optional and you can leave + it blank. + </span> + </div> + + <button type="submit" class="btn btn-primary">create study</button> + </form> +</div> {%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%} <h2 class="heading">Tissue</h2> -<div class="explainer"> +<div class="row"> <p>The data you are uploading concerns a tissue, cell, organ, or other biological material used in an experiment.</p> <p>Select the appropriate biological material below</p> </div> {%if tissues | length > 0%} -<form method="POST" - action="{{url_for('upload.rqtl2.select_tissue', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:select-probeset-dataset"> - <legend class="heading">Select from existing ProbeSet datasets</legend> - {{flash_messages("error-select-tissue")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - - <fieldset> - <label for="select-tissue">Tissue</label> - <select id="select-tissue" - name="tissueid" - required="required" - {%if tissues | length == 0%}disabled="disabled"{%endif%}> - <option value="">Select a tissue</option> - {%for tissue in tissues%} - <option value={{tissue.Id}}> - {{tissue.Name}} - {%if tissue.Short_Name%} - -- ({{tissue.Short_Name}}) - {%endif%} - </option> - {%endfor%} - </select> - - <span class="form-col-2">Select from existing biological material.</span> - </fieldset> - - <fieldset> - <input type="submit" - value="use selected" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> +<div class="row"> + <form method="POST" + action="{{url_for('upload.rqtl2.select_tissue', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-dataset"> + <legend class="heading">Select from existing ProbeSet datasets</legend> + {{flash_messages("error-select-tissue")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select-tissue">Tissue</label> + <select id="select-tissue" + name="tissueid" + required="required" + {%if tissues | length == 0%}disabled="disabled"{%endif%} + class="form-control" + aria-describedby="help-select-tissue"> + <option value="">Select a tissue</option> + {%for tissue in tissues%} + <option value={{tissue.Id}}> + {{tissue.Name}} + {%if tissue.Short_Name%} + -- ({{tissue.Short_Name}}) + {%endif%} + </option> + {%endfor%} + </select> + + <span id="help-select-tissue" class="form-text text-muted"> + Select from existing biological material.</span> + </div> + + <button type="submit" class="btn btn-primary">use selected</button> + </form> +</div> -<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> {%endif%} -<div class="explainer"> +<div class="row"> <p>If you cannot find the biological material in the drop-down above, add it to the system below.</p> -</div> -<form method="POST" - action="{{url_for('upload.rqtl2.create_tissue', - species_id=species.SpeciesId, population_id=population.Id)}}" - id="frm:create-probeset-dataset"> - <legend class="heading">Add new tissue, organ or biological material</legend> - {{flash_messages("error-create-tissue")}} - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - - <fieldset> - <label for="tissue-name">name</label> - <input type="text" - id="txt-tissuename" - name="tissuename" - required="required" - title = "A name to identify the tissue, organ or biological material." /> - - <span class="form-col-2"> - A name to identify the tissue, organ or biological material. - </span> - </fieldset> - - <fieldset> - <label for="txt-shortname">short name</label> - <input type="text" id="txt-tissueshortname" name="tissueshortname" - required="required" - maxlength="7" - title="A short name (e.g. 'Mam') for the biological material." /> - - <span class="form-col-2"> - Provide a short name for the tissue, organ or biological material used in - the experiment. - </span> - </fieldset> - - <fieldset> - <input type="submit" - value="add new material" - class="btn btn-primary form-col-2" /> - </fieldset> + <form method="POST" + action="{{url_for('upload.rqtl2.create_tissue', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-dataset"> + <legend class="heading">Add new tissue, organ or biological material</legend> + {{flash_messages("error-create-tissue")}} + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="tissue-name">name</label> + <input type="text" + id="txt-tissuename" + name="tissuename" + required="required" + title = "A name to identify the tissue, organ or biological material." + class="form-control" + aria-describedby="help-tissue-name" /> + + <span class="form-text text-muted" id="help-tissue-name"> + A name to identify the tissue, organ or biological material. + </span> + </div> + + <div class="form-group"> + <label for="txt-shortname" class="form-label">short name</label> + <input type="text" id="txt-tissueshortname" name="tissueshortname" + required="required" + maxlength="7" + title="A short name (e.g. 'Mam') for the biological material." + class="form-control" + aria-describedby="help-tissue-short-name" /> + + <span class="form-text text-muted" id="help-tissue-short-name"> + Provide a short name for the tissue, organ or biological material used in + the experiment. + </span> + </div> + + <button type="submit" class="btn btn-primary" />add new material</button> </form> +</div> {%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%} <h2 class="heading">Summary</h2> -<div class="explainer"> +<div class="row"> <p>This is the information you have provided to accompany the R/qtl2 bundle you have uploaded. Please verify the information is correct before proceeding.</p> </div> -<dl> - <dt>Species</dt> - <dd>{{species.SpeciesName}} ({{species.FullName}})</dd> +<div class="row"> + <dl> + <dt>Species</dt> + <dd>{{species.SpeciesName}} ({{species.FullName}})</dd> - <dt>Population</dt> - <dd>{{population.InbredSetName}}</dd> + <dt>Population</dt> + <dd>{{population.InbredSetName}}</dd> - {%if geno_dataset%} - <dt>Genotype Dataset</dt> - <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd> - {%endif%} + {%if geno_dataset%} + <dt>Genotype Dataset</dt> + <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd> + {%endif%} - {%if tissue%} - <dt>Tissue</dt> - <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd> - {%endif%} + {%if tissue%} + <dt>Tissue</dt> + <dd>{{tissue.TissueName}} ({{tissue.Name}}, {{tissue.Short_Name}})</dd> + {%endif%} - {%if probe_study%} - <dt>ProbeSet Study</dt> - <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd> - {%endif%} + {%if probe_study%} + <dt>ProbeSet Study</dt> + <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd> + {%endif%} - {%if probe_dataset%} - <dt>ProbeSet Dataset</dt> - <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd> - {%endif%} -</dl> + {%if probe_dataset%} + <dt>ProbeSet Dataset</dt> + <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd> + {%endif%} + </dl> +</div> -<form id="frm:confirm-rqtl2bundle-details" - action="{{url_for('upload.rqtl2.confirm_bundle_details', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - <legend class="heading">Create ProbeSet dataset</legend> +<div class="row"> + <form id="frm:confirm-rqtl2bundle-details" + action="{{url_for('upload.rqtl2.confirm_bundle_details', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + <legend class="heading">Create ProbeSet dataset</legend> - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> - <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> - <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" /> + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> + <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" /> - <fieldset> - <input type="submit" - value="continue" - class="btn btn-primary form-col-2" /> - </fieldset> -</form> + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%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()}} - <fieldset> - <legend>file upload</legend> - <label for="file-rqtl2-bundle">R/qtl2 bundle</label> + <div form-group> + <legend class="heading">file upload</legend> + <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label> <input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file" accept="application/zip, .zip" - required="required" /> - <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In + required="required" + class="form-control" /> + <span class="form-text text-muted"><p>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.</p> <p>The control file can be either a YAML or JSON file. <em>ALL</em> other @@ -36,12 +37,9 @@ <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html" target="_blank"> R/qtl2 file format specifications</a> for more details.</p></span> - </fieldset> - <fieldset> - <input type="submit" - value="upload R/qtl2 bundle" - class="btn btn-primary form-col-2" /> - </fieldset> + </div> + + <button type="submit" class="btn btn-primary">upload R/qtl2 bundle</button> </form> {%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%} <h2 class="heading">Upload R/qtl2 Bundle</h2> -<div class="explainer"> +<div class="row"> <p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p> <p>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.</p> <p>Click "Continue" below to proceed.</p> -</div> -<form id="frm-upload-rqtl2-bundle" - action="{{url_for('upload.rqtl2.select_dataset_info', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}" - method="POST" - enctype="multipart/form-data"> - {{flash_all_messages()}} - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" - value="{{population.InbredSetId}}" /> - <input type="hidden" name="rqtl2_bundle_file" - value="{{rqtl2_bundle_file}}" /> + <form id="frm-upload-rqtl2-bundle" + action="{{url_for('upload.rqtl2.select_dataset_info', + species_id=species.SpeciesId, + population_id=population.InbredSetId)}}" + method="POST" + enctype="multipart/form-data"> + {{flash_all_messages()}} + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" + value="{{population.InbredSetId}}" /> + <input type="hidden" name="rqtl2_bundle_file" + value="{{rqtl2_bundle_file}}" /> - <fieldset> - <input type="submit" value="continue" class="btn btn-primary form-col-2" /> - </fieldset> -</form> + <button type="submit" class="btn btn-primary">continue</button> + </form> +</div> {%endblock%} |