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-rw-r--r--qc_app/templates/rqtl2/create-geno-dataset-success.html55
-rw-r--r--qc_app/templates/rqtl2/create-probe-dataset-success.html59
-rw-r--r--qc_app/templates/rqtl2/create-probe-study-success.html49
-rw-r--r--qc_app/templates/rqtl2/create-tissue-success.html106
-rw-r--r--qc_app/templates/rqtl2/index.html36
-rw-r--r--qc_app/templates/rqtl2/no-such-job.html13
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-error.html39
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-results.html24
-rw-r--r--qc_app/templates/rqtl2/rqtl2-job-status.html20
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-error.html120
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-results.html66
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-status.html41
-rw-r--r--qc_app/templates/rqtl2/rqtl2-qc-job-success.html37
-rw-r--r--qc_app/templates/rqtl2/select-geno-dataset.html144
-rw-r--r--qc_app/templates/rqtl2/select-population.html136
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html191
-rw-r--r--qc_app/templates/rqtl2/select-probeset-study-id.html143
-rw-r--r--qc_app/templates/rqtl2/select-tissue.html115
-rw-r--r--qc_app/templates/rqtl2/summary-info.html65
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html276
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html33
21 files changed, 0 insertions, 1768 deletions
diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html
deleted file mode 100644
index 1b50221..0000000
--- a/qc_app/templates/rqtl2/create-geno-dataset-success.html
+++ /dev/null
@@ -1,55 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<div class="explainer">
- <p>You successfully created the genotype dataset with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{geno_dataset.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{geno_dataset.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{geno_dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{geno_dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{geno_dataset.today}}</dd>
-
- <dt>Public?</dt>
- <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
- </dl>
- </p>
-</div>
-
-<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
deleted file mode 100644
index 790d174..0000000
--- a/qc_app/templates/rqtl2/create-probe-dataset-success.html
+++ /dev/null
@@ -1,59 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Dataset</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet dataset with the following
- information.
- <dl>
- <dt>Averaging Method</dt>
- <dd>{{avgmethod.Name}}</dd>
-
- <dt>ID</dt>
- <dd>{{dataset.datasetid}}</dd>
-
- <dt>Name</dt>
- <dd>{{dataset.name2}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{dataset.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{dataset.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{dataset.today}}</dd>
-
- <dt>DataScale</dt>
- <dd>{{dataset.datascale}}</dd>
- </dl>
- </p>
-</div>
-
-<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
deleted file mode 100644
index d0ee508..0000000
--- a/qc_app/templates/rqtl2/create-probe-study-success.html
+++ /dev/null
@@ -1,49 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Create ProbeSet Study</h2>
-
-<div class="row">
- <p>You successfully created the ProbeSet study with the following
- information.
- <dl>
- <dt>ID</dt>
- <dd>{{study.id}}</dd>
-
- <dt>Name</dt>
- <dd>{{study.name}}</dd>
-
- <dt>Full Name</dt>
- <dd>{{study.fname}}</dd>
-
- <dt>Short Name</dt>
- <dd>{{study.sname}}</dd>
-
- <dt>Created On</dt>
- <dd>{{study.today}}</dd>
- </dl>
- </p>
-
- <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
deleted file mode 100644
index 5f2c5a0..0000000
--- a/qc_app/templates/rqtl2/create-tissue-success.html
+++ /dev/null
@@ -1,106 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Tissue</h2>
-
-<div class="row">
- <p>You have successfully added a new tissue, organ or biological material with
- the following details:</p>
-</div>
-
-<div class="row">
- {{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}}" />
-
- <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',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- style="display: inline; width: 100%; grid-column: 3 / 4;
- 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}}" />
-
- <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
deleted file mode 100644
index f3329c2..0000000
--- a/qc_app/templates/rqtl2/index.html
+++ /dev/null
@@ -1,36 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 data upload</h1>
-
-<h2>R/qtl2 Upload</h2>
-
-<form method="POST" action="{{url_for('upload.rqtl2.select_species')}}"
- id="frm-rqtl2-upload">
- <legend class="heading">upload R/qtl2 bundle</legend>
- {{flash_messages("error-rqtl2")}}
-
- <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>
- <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.
- </small>
- </div>
-
- <button type="submit" class="btn btn-primary" />submit</button>
-</form>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/no-such-job.html b/qc_app/templates/rqtl2/no-such-job.html
deleted file mode 100644
index b17004f..0000000
--- a/qc_app/templates/rqtl2/no-such-job.html
+++ /dev/null
@@ -1,13 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: No Such Job</h2>
-
-<p class="alert-danger">No job with ID {{jobid}} was found.</p>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-error.html b/qc_app/templates/rqtl2/rqtl2-job-error.html
deleted file mode 100644
index 9817518..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-error.html
+++ /dev/null
@@ -1,39 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<div class="explainer">
- <p>The processing of the R/qtl2 bundle you uploaded has failed. We have
- provided some information below to help you figure out what the problem
- could be.</p>
- <p>If you find that you cannot figure out what the problem is on your own,
- please contact the team running the system for assistance, providing the
- following details:
- <ul>
- <li>R/qtl2 bundle you uploaded</li>
- <li>This URL: <strong>{{request_url()}}</strong></li>
- <li>(maybe) a screenshot of this page</li>
- </ul>
- </p>
-</div>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-<h4>Log</h4>
-<div class="cli-output">
- {%for msg in messages%}
- {{msg}}<br />
- {%endfor%}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-results.html b/qc_app/templates/rqtl2/rqtl2-job-results.html
deleted file mode 100644
index 4ecd415..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-results.html
+++ /dev/null
@@ -1,24 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<div class="explainer">
- <p>The processing of the R/qtl2 bundle you uploaded has completed
- successfully.</p>
- <p>You should now be able to use GeneNetwork to run analyses on your data.</p>
-</div>
-
-<h4>Log</h4>
-<div class="cli-output">
- {%for msg in messages%}
- {{msg}}<br />
- {%endfor%}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-job-status.html b/qc_app/templates/rqtl2/rqtl2-job-status.html
deleted file mode 100644
index e896f88..0000000
--- a/qc_app/templates/rqtl2/rqtl2-job-status.html
+++ /dev/null
@@ -1,20 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="3">
-{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 job status</h1>
-
-<h2>R/qtl2 Upload: Job Status</h2>
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
deleted file mode 100644
index 90e8887..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ /dev/null
@@ -1,120 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
-
-{%macro errors_table(tableid, errors)%}
-<table id="{{tableid}}" class="table error-table">
- <caption>{{caption}}</caption>
- <thead>
- <tr>
- <th>Line</th>
- <th>Column</th>
- <th>Value</th>
- <th>Message</th>
- </tr>
- </thead>
- <tbody>
- {%for error in errors%}
- <tr>
- <td>{{error.line}}</td>
- <td>{{error.column}}</td>
- <td>{{error.value}}</td>
- <td>{{error.message}}</td>
- </tr>
- {%else%}
- <tr>
- <td colspan="4">No errors to display here.</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-{%endmacro%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job Error</h1>
-
-<div class="explainer">
- <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p>
- <p>We list below some of the errors that need to be fixed before the data can
- be uploaded onto GeneNetwork.</p>
-</div>
-
-{%if errorsgeneric | length > 0%}
-<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3>
-<div class="explainer">
- We found the following generic errors in your R/qtl2 bundle:
-</div>
-
-<h3>Missing Files</h3>
-<div class="explainer">
- <p>These files are listed in the bundle's control file, but do not actually
- exist in the bundle</p>
-</div>
-<table id="tbl-errors-missing-files" class="table error-table">
- <thead>
- <tr>
- <th>Control File Key</th>
- <th>Bundle File Name</th>
- <th>Message</th>
- </tr>
- </thead>
- <tbody>
- {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%}
- <tr>
- <td>{{error.controlfilekey}}</td>
- <td>{{error.filename}}</td>
- <td>{{error.message}}</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-
-<h3>Other Generic Errors</h3>
-{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}}
-{%endif%}
-
-{%if errorsgeno | length > 0%}
-<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'geno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
-{%endif%}
-
-{%if errorspheno | length > 0%}
-<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'pheno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
-{%endif%}
-
-{%if errorsphenose | length > 0%}
-<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'phenose' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
-{%endif%}
-
-{%if errorsphenocovar | length > 0%}
-<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
-<div class="explainer">
- We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
-</div>
-{{errorsphenocovar}}
-{%endif%}
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
deleted file mode 100644
index 59bc8cd..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
+++ /dev/null
@@ -1,66 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}R/qtl2 bundle: QC job results{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job results</h1>
-
-<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>
-
-<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-label">Name</span>
- <span class="form-text">{{species.Name | capitalize}}</span>
-
- <span class="form-label">Scientific</span>
- <span class="form-text">{{species.FullName | capitalize}}</span>
- </div>
-
- <div class="form-group">
- <legend>population</legend>
- <input type="hidden" name="population_id" value="{{population.Id}}" />
-
- <span class="form-label">Name</span>
- <span class="form-text">{{population.InbredSetName}}</span>
-
- <span class="form-label">Full Name</span>
- <span class="form-text">{{population.FullName}}</span>
-
- <span class="form-label">Genetic Type</span>
- <span class="form-text">{{population.GeneticType}}</span>
-
- <span class="form-label">Description</span>
- <span class="form-text">{{population.Description or "-"}}</span>
- </div>
-
- <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-label">Original Name</span>
- <span class="form-text">{{rqtl2bundleorig}}</span>
-
- <span class="form-label">Internal Name</span>
- <span class="form-text">{{rqtl2bundle[0:25]}}&hellip;</span>
- </div>
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html b/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
deleted file mode 100644
index f4a6266..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
+++ /dev/null
@@ -1,41 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="3">
-{%endblock%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job status</h1>
-
-{%if geno_percent%}
-<p>
- <h2>Checking 'geno' file:</h2>
- <progress id="prg-geno-checking" value="{{geno_percent}}" max="100">
- {{geno_percent}}%</progress>
- {{geno_percent}}%</p>
-{%endif%}
-
-{%if pheno_percent%}
-<p>
- <h2>Checking 'pheno' file:</h2>
- <progress id="prg-pheno-checking" value="{{pheno_percent}}" max="100">
- {{pheno_percent}}%</progress>
- {{pheno_percent}}%</p>
-{%endif%}
-
-{%if phenose_percent%}
-<p>
- <h2>Checking 'phenose' file:</h2>
- <progress id="prg-phenose-checking" value="{{phenose_percent}}" max="100">
- {{phenose_percent}}%</progress>
- {{phenose_percent}}%</p>
-{%endif%}
-
-<h4>Log</h4>
-<div class="cli-output">
- <pre>{{"\n".join(messages)}}</pre>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
deleted file mode 100644
index 2861a04..0000000
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
+++ /dev/null
@@ -1,37 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%}
-
-{%block contents%}
-<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2>
-
-<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>
-</div>
-
-<!--
- 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.
- -->
-<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}}" />
-
- <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
deleted file mode 100644
index 873f9c3..0000000
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ /dev/null
@@ -1,144 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Select Genotypes Dataset</h2>
-
-<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>
-
-<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
deleted file mode 100644
index 37731f0..0000000
--- a/qc_app/templates/rqtl2/select-population.html
+++ /dev/null
@@ -1,136 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div class="explainer">
- <p>The data is organised in a hierarchical form, beginning with
- <em>species</em> at the very top. Under <em>species</em> the data is
- organised by <em>population</em>, sometimes referred to as <em>grouping</em>.
- (In some really old documents/systems, you might see this referred to as
- <em>InbredSet</em>.)</p>
- <p>In this section, you get to define what population your data is to be
- organised by.</p>
-</div>
-
-<form method="POST"
- action="{{url_for('upload.rqtl2.select_population', species_id=species.SpeciesId)}}">
- <legend class="heading">select grouping/population</legend>
- {{flash_messages("error-select-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <label for="select:inbredset" class="form-label">population</label>
- <select id="select:inbredset"
- name="inbredset_id"
- required="required"
- 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-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>
- </div>
-
- <button type="submit" class="btn btn-primary" />select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST"
- action="{{url_for('upload.rqtl2.create_population', species_id=species.SpeciesId)}}">
- <legend class="heading">create new grouping/population</legend>
- {{flash_messages("error-create-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <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-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%}
-
-
-{%block javascript%}
-{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
deleted file mode 100644
index 26f52ed..0000000
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ /dev/null
@@ -1,191 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
-
-<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%}
-<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>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-{%endif%}
-
-<div class="row">
- <p>Create an entirely new ProbeSet dataset for your data.</p>
-</div>
-
-<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
deleted file mode 100644
index b9bf52e..0000000
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ /dev/null
@@ -1,143 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages %}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Phenotype(ProbeSet) Study</h2>
-
-<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>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-
-<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
deleted file mode 100644
index 34e1758..0000000
--- a/qc_app/templates/rqtl2/select-tissue.html
+++ /dev/null
@@ -1,115 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Tissue</h2>
-
-<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%}
-<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>
-
-<div class="row">
- <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-</div>
-{%endif%}
-
-<div class="row">
- <p>If you cannot find the biological material in the drop-down above, add it
- to the system below.</p>
-
- <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
deleted file mode 100644
index 1be87fa..0000000
--- a/qc_app/templates/rqtl2/summary-info.html
+++ /dev/null
@@ -1,65 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Summary</h2>
-
-<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>
-
-<div class="row">
- <dl>
- <dt>Species</dt>
- <dd>{{species.SpeciesName}} ({{species.FullName}})</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 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_dataset%}
- <dt>ProbeSet Dataset</dt>
- <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
- {%endif%}
- </dl>
-</div>
-
-<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}}" />
-
- <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
deleted file mode 100644
index 07c240f..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ /dev/null
@@ -1,276 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "upload_progress_indicator.html" import upload_progress_indicator%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-{%macro rqtl2_file_help()%}
-<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 data
- files in the zip bundle should be CSV files.
- </p>
- <p>See the
- <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
- target="_blank">
- R/qtl2 file format specifications
- </a>
- for more details.
- </p>
-</span>
-{%endmacro%}
-{{upload_progress_indicator()}}
-
-<div id="resumable-file-display-template"
- class="panel panel-info"
- style="display: none">
- <div class="panel-heading"></div>
- <div class="panel-body"></div>
-</div>
-
-
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<div id="resumable-drop-area"
- style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;">
- <p>
- <a id="resumable-browse-button" href="#"
- class="btn btn-info">Browse</a>
- </p>
- <p class="form-text text-muted">
- You can drag and drop your file here, or click the browse button.
- Click on the file to remove it.
- </p>
- {{rqtl2_file_help()}}
- <div id="resumable-selected-files"
- style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div>
- <div id="resumable-class-buttons" style="text-align: right;">
- <button id="resumable-upload-button"
- class="btn btn-primary"
- style="display: none">start upload</button>
- <button id="resumable-cancel-upload-button"
- class="btn btn-danger"
- style="display: none">cancel upload</button>
- </div>
- <div id="resumable-progress-bar" class="progress" style="display: none">
- <div class="progress-bar"
- role="progress-bar"
- aria-valuenow="60"
- aria-valuemin="0"
- aria-valuemax="100"
- style="width: 0%;">
- Uploading: 60%
- </div>
- </div>
-</div>
-
-<form id="frm-upload-rqtl2-bundle"
- action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- method="POST"
- enctype="multipart/form-data"
- data-resumable-target="{{url_for(
- 'upload.rqtl2.upload_rqtl2_bundle_chunked_post',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}">
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <input type="hidden" name="population_id"
- value="{{population.InbredSetId}}" />
-
- {{flash_all_messages()}}
-
- <div class="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"
- class="form-control" />
- {{rqtl2_file_help()}}
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- data-toggle="modal"
- data-target="#upload-progress-indicator">upload R/qtl2 bundle</button>
-</form>
-
-{%endblock%}
-
-{%block javascript%}
-<script src="{{url_for('base.node_modules',
- filename='resumablejs/resumable.js')}}"></script>
-<script type="text/javascript" src="/static/js/upload_progress.js"></script>
-<script type="text/javascript">
- function readBinaryFile(file) {
- return new Promise((resolve, reject) => {
- var _reader = new FileReader();
- _reader.onload = (event) => {resolve(_reader.result);};
- _reader.readAsArrayBuffer(file);
- });
- }
-
- function computeFileChecksum(file) {
- return readBinaryFile(file)
- .then((content) => {
- return window.crypto.subtle.digest(
- "SHA-256", new Uint8Array(content));
- }).then((digest) => {
- return Uint8ArrayToHex(new Uint8Array(digest))
- });
- }
-
- function Uint8ArrayToHex(arr) {
- var toHex = (val) => {
- _hex = val.toString(16);
- if(_hex.length < 2) {
- return "0" + val;
- }
- return _hex;
- };
- _hexstr = ""
- arr.forEach((val) => {_hexstr += toHex(val)});
- return _hexstr
- }
-
- var r = Resumable({
- target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"),
- fileType: ["zip"],
- maxFiles: 1,
- forceChunkSize: true,
- generateUniqueIdentifier: (file, event) => {
- return computeFileChecksum(file).then((checksum) => {
- var _relativePath = (file.webkitRelativePath
- || file.relativePath
- || file.fileName
- || file.name);
- return checksum + "-" + _relativePath.replace(
- /[^a-zA-Z0-9_-]/img, "");
- });
- }
- });
-
- if(r.support) {
- //Hide form and display drag&drop UI
- $("#frm-upload-rqtl2-bundle").css("display", "none");
- $("#resumable-drop-area").css("display", "block");
-
- // Define UI elements for browse and drag&drop
- r.assignDrop(document.getElementById("resumable-drop-area"));
- r.assignBrowse(document.getElementById("resumable-browse-button"));
-
- // Event handlers
-
- function display_files(files) {
- displayArea = $("#resumable-selected-files")
- displayArea.empty();
- files.forEach((file) => {
- var displayElement = $(
- "#resumable-file-display-template").clone();
- displayElement.removeAttr("id");
- displayElement.css("display", "");
- displayElement.find(".panel-heading").text(file.fileName);
- list = $("<ul></ul>");
- list.append($("<li><strong>Name</strong>: "
- + (file.name
- || file.fileName
- || file.relativePath
- || file.webkitRelativePath)
- + "</li>"));
- list.append($("<li><strong>Size</strong>: "
- + (file.size / (1024*1024)).toFixed(2)
- + " MB</li>"));
- list.append($("<li><strong>Unique Identifier</strong>: "
- + file.uniqueIdentifier + "</li>"));
- list.append($("<li><strong>Mime</strong>: "
- + file.file.type
- + "</li>"));
- displayElement.find(".panel-body").append(list);
- displayElement.appendTo("#resumable-selected-files");
- });
- }
-
- r.on("filesAdded", function(files) {
- display_files(files);
- $("#resumable-upload-button").css("display", "");
- $("#resumable-upload-button").on("click", (event) => {
- r.upload();
- });
- });
-
- r.on("uploadStart", (event) => {
- $("#resumable-upload-button").css("display", "none");
- $("#resumable-cancel-upload-button").css("display", "");
- $("#resumable-cancel-upload-button").on("click", (event) => {
- r.files.forEach((file) => {
- if(file.isUploading()) {
- file.abort();
- }
- });
- $("#resumable-cancel-upload-button").css("display", "none");
- $("#resumable-upload-button").on("click", (event) => {
- r.files.forEach((file) => {file.retry();});
- });
- $("#resumable-upload-button").css("display", "");
- });
- });
-
- r.on("progress", () => {
- var progress = (r.progress() * 100).toFixed(2);
- var pbar = $("#resumable-progress-bar > .progress-bar");
- $("#resumable-progress-bar").css("display", "");
- pbar.css("width", progress+"%");
- pbar.attr("aria-valuenow", progress);
- pbar.text("Uploading: " + progress + "%");
- })
-
- r.on("fileSuccess", (file, message) => {
- if(message != "OK") {
- var uri = (window.location.protocol
- + "//"
- + window.location.host
- + message);
- window.location.replace(uri);
- }
- });
-
- r.on("error", (message, file) => {
- filename = (file.webkitRelativePath
- || file.relativePath
- || file.fileName
- || file.name);
- jsonmsg = JSON.parse(message);
- alert("There was an error while uploading your file '"
- + filename
- + "'. The error message was:\n\n\t"
- + jsonmsg.error
- + " ("
- + jsonmsg.statuscode
- + "): " + jsonmsg.message);
- })
- } else {
- setup_upload_handlers(
- "frm-upload-rqtl2-bundle", make_data_uploader(
- function (form) {
- var formdata = new FormData();
- formdata.append(
- "species_id",
- form.querySelector('input[name="species_id"]').value);
- formdata.append(
- "population_id",
- form.querySelector('input[name="population_id"]').value);
- formdata.append(
- "rqtl2_bundle_file",
- form.querySelector("#file-rqtl2-bundle").files[0]);
- return formdata;
- }));
- }
-</script>
-{%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
deleted file mode 100644
index 93b1dc9..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ /dev/null
@@ -1,33 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<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>
-
- <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}}" />
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-{%endblock%}