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-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html323
1 files changed, 168 insertions, 155 deletions
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%}