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-rw-r--r--qc_app/templates/base.html51
-rw-r--r--qc_app/templates/cli-output.html8
-rw-r--r--qc_app/templates/continue_from_create_dataset.html52
-rw-r--r--qc_app/templates/continue_from_create_study.html52
-rw-r--r--qc_app/templates/data_review.html85
-rw-r--r--qc_app/templates/dbupdate_error.html12
-rw-r--r--qc_app/templates/dbupdate_hidden_fields.html29
-rw-r--r--qc_app/templates/errors_display.html47
-rw-r--r--qc_app/templates/final_confirmation.html47
-rw-r--r--qc_app/templates/flash_messages.html25
-rw-r--r--qc_app/templates/http-error.html18
-rw-r--r--qc_app/templates/index.html81
-rw-r--r--qc_app/templates/insert_error.html32
-rw-r--r--qc_app/templates/insert_progress.html46
-rw-r--r--qc_app/templates/insert_success.html19
-rw-r--r--qc_app/templates/job_progress.html40
-rw-r--r--qc_app/templates/no_such_job.html14
-rw-r--r--qc_app/templates/parse_failure.html26
-rw-r--r--qc_app/templates/parse_results.html30
-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
-rw-r--r--qc_app/templates/samples/select-population.html99
-rw-r--r--qc_app/templates/samples/select-species.html30
-rw-r--r--qc_app/templates/samples/upload-failure.html27
-rw-r--r--qc_app/templates/samples/upload-progress.html22
-rw-r--r--qc_app/templates/samples/upload-samples.html139
-rw-r--r--qc_app/templates/samples/upload-success.html18
-rw-r--r--qc_app/templates/select_dataset.html161
-rw-r--r--qc_app/templates/select_platform.html82
-rw-r--r--qc_app/templates/select_species.html92
-rw-r--r--qc_app/templates/select_study.html108
-rw-r--r--qc_app/templates/stdout_output.html8
-rw-r--r--qc_app/templates/unhandled_exception.html21
-rw-r--r--qc_app/templates/upload_progress_indicator.html35
-rw-r--r--qc_app/templates/worker_failure.html24
54 files changed, 0 insertions, 3348 deletions
diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html
deleted file mode 100644
index eb5e6b7..0000000
--- a/qc_app/templates/base.html
+++ /dev/null
@@ -1,51 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="UTF-8" />
- <meta application-name="GeneNetwork Quality-Control Application" />
- <meta name="viewport" content="width=device-width, initial-scale=1.0" />
- {%block extrameta%}{%endblock%}
-
- <title>GN Uploader: {%block title%}{%endblock%}</title>
-
- <link rel="stylesheet" type="text/css"
- href="{{url_for('base.bootstrap',
- filename='css/bootstrap.min.css')}}" />
- <link rel="stylesheet" type="text/css"
- href="{{url_for('base.bootstrap',
- filename='css/bootstrap-theme.min.css')}}" />
-
-
- <link rel="shortcut icon" type="image/png" sizes="64x64"
- href="{{url_for('static', filename='images/CITGLogo.png')}}" />
-
- <link rel="stylesheet" type="text/css" href="/static/css/custom-bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
-
- {%block css%}{%endblock%}
- </head>
-
- <body>
- <div class="navbar navbar-inverse navbar-static-top pull-left"
- role="navigation"
- style="width: 100%;min-width: 850px;white-space: nowrap;">
- <div class="container-fluid" style="width: 100%">
- <ul class="nav navbar-nav">
- <li><a href="/" style="font-weight: bold">GN Uploader</a></li>
- <li>
- <a href="{{gnuri or 'https://genenetwork.org'}}">GeneNetwork</a>
- </li>
- </ul>
- </div>
- </div>
- <div class="container">
- {%block contents%}{%endblock%}
- </div>
-
- <script src="{{url_for('base.jquery',
- filename='jquery.min.js')}}"></script>
- <script src="{{url_for('base.bootstrap',
- filename='js/bootstrap.min.js')}}"></script>
- {%block javascript%}{%endblock%}
- </body>
-</html>
diff --git a/qc_app/templates/cli-output.html b/qc_app/templates/cli-output.html
deleted file mode 100644
index 33fb73b..0000000
--- a/qc_app/templates/cli-output.html
+++ /dev/null
@@ -1,8 +0,0 @@
-{%macro cli_output(job, stream)%}
-
-<h4>{{stream | upper}} Output</h4>
-<div class="cli-output">
- <pre>{{job.get(stream, "")}}</pre>
-</div>
-
-{%endmacro%}
diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html
deleted file mode 100644
index 03bb49c..0000000
--- a/qc_app/templates/continue_from_create_dataset.html
+++ /dev/null
@@ -1,52 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Create Study{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: create study</h2>
-
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend>continue with new dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, datasetid=datasetid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- <legend>Select from existing dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, datasetid=datasetid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">go back</button>
- </form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/continue_from_create_study.html b/qc_app/templates/continue_from_create_study.html
deleted file mode 100644
index 34e6e5e..0000000
--- a/qc_app/templates/continue_from_create_study.html
+++ /dev/null
@@ -1,52 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Create Study{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: create study</h2>
-
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend>continue with new study</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">continue</button>
- </form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- <legend>Select from existing study</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <button type="submit" class="btn btn-primary">go back</button>
- </form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/data_review.html b/qc_app/templates/data_review.html
deleted file mode 100644
index b7528fd..0000000
--- a/qc_app/templates/data_review.html
+++ /dev/null
@@ -1,85 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Review{%endblock%}
-
-{%block contents%}
-<h1 class="heading">data review</h1>
-
-<div class="row">
- <h2 id="data-concerns">Data Concerns</h2>
- <p>The following are some of the requirements that the data in your file
- <strong>MUST</strong> fulfil before it is considered valid for this system:
- </p>
-
- <ol>
- <li>File headings
- <ul>
- <li>The first row in the file should contains the headings. The number of
- headings in this first row determines the number of columns expected for
- all other lines in the file.</li>
- <li>Each heading value in the first row MUST appear in the first row
- <strong>ONE AND ONLY ONE</strong> time</li>
- <li>The sample/cases (previously 'strains') headers in your first row will be
- against those in the <a href="https://genenetwork.org"
- title="Link to the GeneNetwork service">
- GeneNetwork</a> database.<br />
- <small class="text-muted">
- If you encounter an error saying your sample(s)/case(s) do not exist
- in the GeneNetwork database, then you will have to use the
- <a href="{{url_for('samples.select_species')}}"
- title="Upload samples/cases feature">Upload Samples/Cases</a>
- option on this system to upload them.
- </small>
- </ul>
- </li>
-
- <li>Data
- <ol>
- <li><strong>NONE</strong> of the data cells/fields is allowed to be empty.
- All fields/cells <strong>MUST</strong> contain a value.</li>
- <li>The first column of the data rows will be considered a textual field,
- holding the "identifier" for that row<li>
- <li>Except for the first column/field for each data row,
- <strong>NONE</strong> of the data columns/cells/fields should contain
- spurious characters like `eeeee`, `5.555iloveguix`, etc...<br />
- All of them should be decimal values</li>
- <li>decimal numbers must conform to the following criteria:
- <ul>
- <li>when checking an average file decimal numbers must have exactly three
- decimal places to the right of the decimal point.</li>
- <li>when checking a standard error file decimal numbers must have six or
- greater decimal places to the right of the decimal point.</li>
- <li>there must be a number to the left side of the decimal place
- (e.g. 0.55555 is allowed but .55555 is not).</li>
- </ul>
- </li>
- </ol>
- </li>
- </ol>
-</div>
-
-
-<div class="row">
- <h2 id="file-types">Supported File Types</h2>
- We support the following file types:
-
- <ul>
- <li>Tab-Separated value files (.tsv)
- <ul>
- <li>The <strong>TAB</strong> character is used to separate the fields of each
- column</li>
- <li>The values of each field <strong>ARE NOT</strong> quoted.</li>
- <li>Here is an
- <a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/tests/test_data/no_data_errors.tsv">
- example file</a> with a single data row.</li>
- </ul>
- </li>
- <li>.txt files: Content has the same format as .tsv file above</li>
- <li>.zip files: each zip file should contain
- <strong>ONE AND ONLY ONE</strong> file of the .tsv or .txt type above.
- <br />Any zip file with more than one file is invalid, and so is an empty
- zip file.</li>
- </ul>
-
-</div>
-{%endblock%}
diff --git a/qc_app/templates/dbupdate_error.html b/qc_app/templates/dbupdate_error.html
deleted file mode 100644
index e1359d2..0000000
--- a/qc_app/templates/dbupdate_error.html
+++ /dev/null
@@ -1,12 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}DB Update Error{%endblock%}
-
-{%block contents%}
-<h1 class="heading">database update error</h2>
-
-<p class="alert-danger">
- <strong>Database Update Error</strong>: {{error_message}}
-</p>
-
-{%endblock%}
diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/qc_app/templates/dbupdate_hidden_fields.html
deleted file mode 100644
index ccbc299..0000000
--- a/qc_app/templates/dbupdate_hidden_fields.html
+++ /dev/null
@@ -1,29 +0,0 @@
-{%macro hidden_fields(filename, filetype):%}
-
-<!-- {{kwargs}}: mostly for accessing the kwargs in macro -->
-
-<input type="hidden" name="filename" value="{{filename}}" />
-<input type="hidden" name="filetype" value="{{filetype}}" />
-{%if kwargs.get("totallines")%}
-<input type="hidden" name="totallines" value="{{kwargs['totallines']}}" />
-{%endif%}
-{%if kwargs.get("species"):%}
-<input type="hidden" name="species" value="{{kwargs['species']}}" />
-{%endif%}
-{%if kwargs.get("genechipid"):%}
-<input type="hidden" name="genechipid" value="{{kwargs['genechipid']}}" />
-{%endif%}
-{%if kwargs.get("inbredsetid"):%}
-<input type="hidden" name="inbredsetid" value="{{kwargs['inbredsetid']}}" />
-{%endif%}
-{%if kwargs.get("tissueid"):%}
-<input type="hidden" name="tissueid" value="{{kwargs['tissueid']}}" />
-{%endif%}
-{%if kwargs.get("studyid"):%}
-<input type="hidden" name="studyid" value="{{kwargs['studyid']}}" />
-{%endif%}
-{%if kwargs.get("datasetid"):%}
-<input type="hidden" name="datasetid" value="{{kwargs['datasetid']}}" />
-{%endif%}
-
-{%endmacro%}
diff --git a/qc_app/templates/errors_display.html b/qc_app/templates/errors_display.html
deleted file mode 100644
index 715cfcf..0000000
--- a/qc_app/templates/errors_display.html
+++ /dev/null
@@ -1,47 +0,0 @@
-{%macro errors_display(errors, no_error_msg, error_message, complete)%}
-
-{%if errors | length == 0 %}
-<span {%if complete%}class="alert-success"{%endif%}>{{no_error_msg}}</span>
-{%else %}
-<p class="alert-danger">{{error_message}}</p>
-
-<table class="table reports-table">
- <thead>
- <tr>
- <th>line number</th>
- <th>column(s)</th>
- <th>error</th>
- <th>error message</th>
- </tr>
- </thead>
-
- <tbody>
- {%for error in errors%}
- <tr>
- <td>{{error["line"]}}</td>
- <td>
- {%if isinvalidvalue(error):%}
- {{error.column}}
- {%elif isduplicateheading(error): %}
- {{error.columns}}
- {%else: %}
- -
- {%endif %}
- </td>
- <td>
- {%if isinvalidvalue(error):%}
- Invalid Value
- {%elif isduplicateheading(error): %}
- Duplicate Header
- {%else%}
- Inconsistent Columns
- {%endif %}
- </td>
- <td>{{error["message"]}}</td>
- </tr>
- {%endfor%}
- </tbody>
-</table>
-{%endif%}
-
-{%endmacro%}
diff --git a/qc_app/templates/final_confirmation.html b/qc_app/templates/final_confirmation.html
deleted file mode 100644
index 0727fc8..0000000
--- a/qc_app/templates/final_confirmation.html
+++ /dev/null
@@ -1,47 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Confirmation{%endblock%}
-
-{%macro display_item(item_name, item_data):%}
-<li>
- <strong>{{item_name}}</strong>
- {%if item_data%}
- <ul>
- {%for term,value in item_data.items():%}
- <li><strong>{{term}}:</strong> {{value}}</li>
- {%endfor%}
- </ul>
- {%endif%}
-</li>
-{%endmacro%}
-
-{%block contents%}
-<h2 class="heading">Final Confirmation</h2>
-
-<div class="two-col-sep-col1">
- <p><strong>Selected Data</strong></p>
- <ul>
- <li><strong>File</strong>
- <ul>
- <li><strong>Filename</strong>: {{filename}}</li>
- <li><strong>File Type</strong>: {{filetype}}</li>
- </ul>
- </li>
- {{display_item("Species", the_species)}}
- {{display_item("Platform", platform)}}
- {{display_item("Study", study)}}
- {{display_item("Dataset", dataset)}}
- </ul>
-</div>
-
-<form method="POST" action="{{url_for('dbinsert.insert_data')}}">
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid,datasetid=datasetid, totallines=totallines)}}
- <fieldset>
- <input type="submit" class="btn btn-primary" value="confirm" />
- </fieldset>
-</form>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/flash_messages.html b/qc_app/templates/flash_messages.html
deleted file mode 100644
index b7af178..0000000
--- a/qc_app/templates/flash_messages.html
+++ /dev/null
@@ -1,25 +0,0 @@
-{%macro flash_all_messages()%}
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-{%endmacro%}
-
-{%macro flash_messages(filter_class)%}
-{%with messages = get_flashed_messages(with_categories=true)%}
-{%if messages:%}
-<ul>
- {%for category, message in messages:%}
- {%if filter_class in category%}
- <li class="{{category}}">{{message}}</li>
- {%endif%}
- {%endfor%}
-</ul>
-{%endif%}
-{%endwith%}
-{%endmacro%}
diff --git a/qc_app/templates/http-error.html b/qc_app/templates/http-error.html
deleted file mode 100644
index 374fb86..0000000
--- a/qc_app/templates/http-error.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}HTTP Error: {{exc.code}}{%endblock%}
-
-{%block contents%}
-<h1>{{exc.code}}: {{exc.description}}</h1>
-
-<div class="row">
- <p>
- You attempted to access {{request_url}} which failed with the following
- error:
- </p>
-</div>
-
-<div class="row">
- <pre>{{"\n".join(trace)}}</pre>
-</div>
-{%endblock%}
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
deleted file mode 100644
index 89d2ae9..0000000
--- a/qc_app/templates/index.html
+++ /dev/null
@@ -1,81 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Upload{%endblock%}
-
-{%block contents%}
-<div class="row">
- <h1 class="heading">data upload</h1>
-
- <div class="explainer">
- <p>Each of the sections below gives you a different option for data upload.
- Please read the documentation for each section carefully to understand what
- each section is about.</p>
- </div>
-</div>
-
-<div class="row">
- <h2 class="heading">R/qtl2 Bundles</h2>
-
- <div class="explainer">
- <p>This feature combines and extends the two upload methods below. Instead of
- uploading one item at a time, the R/qtl2 bundle you upload can contain both
- the genotypes data (samples/individuals/cases and their data) and the
- expression data.</p>
- <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
- of the methods below can handle.</p>
-
- <a href="{{url_for('upload.rqtl2.select_species')}}"
- title="Upload a zip bundle of R/qtl2 files">
- <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
- </div>
-</div>
-
-
-<div class="row">
- <h2 class="heading">Expression Data</h2>
-
- <div class="explainer">
- <p>This feature enables you to upload expression data. It expects the data to
- be in <strong>tab-separated values (TSV)</strong> files. The data should be
- a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
- list of the <em>phenotypes</em> and the first row is a list of
- <em>samples/cases</em>.</p>
-
- <p>If you haven't done so please go to this page to learn the requirements for
- file formats and helpful suggestions to enter your data in a fast and easy
- way.</p>
-
- <ol>
- <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
- with our system requirements. (
- <a href="{{url_for('entry.data_review')}}#data-concerns"
- title="Details for the data expectations.">Help</a>
- )</li>
- <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
- <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
- files (<a href="{{url_for('entry.data_review')}}#file-types"
- title="Details for the data expectations.">Help</a>)</li>
- </ol>
- </div>
-
- <a href="{{url_for('entry.upload_file')}}"
- title="Upload your expression data"
- class="btn btn-primary">upload expression data</a>
-</div>
-
-<div class="row">
- <h2 class="heading">samples/cases</h2>
-
- <div class="explainer">
- <p>For the expression data above, you need the samples/cases in your file to
- already exist in the GeneNetwork database. If there are any samples that do
- not already exist the upload of the expression data will fail.</p>
- <p>This section gives you the opportunity to upload any missing samples</p>
- </div>
-
- <a href="{{url_for('samples.select_species')}}"
- title="Upload samples/cases/individuals for your data"
- class="btn btn-primary">upload Samples/Cases</a>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/insert_error.html b/qc_app/templates/insert_error.html
deleted file mode 100644
index 5301288..0000000
--- a/qc_app/templates/insert_error.html
+++ /dev/null
@@ -1,32 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Data Insertion Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Insertion Failure</h1>
-
-<div class="row">
- <p>
- There was an error inserting data into the database
- </p>
-
- <p>
- Please notify the developers of this issue when you encounter it,
- providing the information below.
- </p>
-
- <h4>Debugging Information</h4>
-
- <ul>
- <li><strong>job id</strong>: {{job["jobid"]}}</li>
- </ul>
-</div>
-
-<div class="row">
- <h4>STDERR Output</h4>
- <pre class="cli-output">
- {{job["stderr"]}}
- </pre>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/insert_progress.html b/qc_app/templates/insert_progress.html
deleted file mode 100644
index 52177d6..0000000
--- a/qc_app/templates/insert_progress.html
+++ /dev/null
@@ -1,46 +0,0 @@
-{%extends "base.html"%}
-{%from "stdout_output.html" import stdout_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}</h1>
-
-<div class="row">
- <form>
- <div class="form-group">
- <label for="job_status" class="form-label">status:</label>
- <span class="form-text">{{job_status}}: {{message}}</span>
- </div>
-
-{%if job.get("stdout", "").split("\n\n") | length < 3 %}
-{%set lines = 0%}
-{%else%}
-{%set lines = (job.get("stdout", "").split("\n\n") | length / 3) %}
-{%endif%}
-{%set totallines = job.get("totallines", lines+3) | int %}
-{%if totallines > 1000 %}
-{%set fraction = ((lines*1000)/totallines) %}
-{%else%}
-{%set fraction = (lines/totallines)%}
-{%endif%}
-
- <div class="form-group">
- <label for="job_{{job_id}}" class="form-label">inserting: </label>
- <progress id="jobs_{{job_id}}"
- value="{{(fraction)}}"
- class="form-control">{{fraction*100}}</progress>
- <span class="form-text text-muted">
- {{"%.2f" | format(fraction * 100 | float)}}%</span>
- </div>
- </form>
-</div>
-
-
-{{stdout_output(job)}}
-
-{%endblock%}
diff --git a/qc_app/templates/insert_success.html b/qc_app/templates/insert_success.html
deleted file mode 100644
index 7e1fa8d..0000000
--- a/qc_app/templates/insert_success.html
+++ /dev/null
@@ -1,19 +0,0 @@
-{%extends "base.html"%}
-{%from "stdout_output.html" import stdout_output%}
-
-{%block title%}Insertion Success{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Insertion Success</h1>
-
-<div class="row">
-<p>Data inserted successfully!</p>
-
-<p>The following queries were run:</p>
-</div>
-
-<div class="row">
- {{stdout_output(job)}}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/job_progress.html b/qc_app/templates/job_progress.html
deleted file mode 100644
index 1af0763..0000000
--- a/qc_app/templates/job_progress.html
+++ /dev/null
@@ -1,40 +0,0 @@
-{%extends "base.html"%}
-{%from "errors_display.html" import errors_display%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}</h2>
-
-<div class="row">
- <form action="{{url_for('parse.abort')}}" method="POST">
- <legend class="heading">Status</legend>
- <div class="form-group">
- <label for="job_status" class="form-label">status:</label>
- <span class="form-text">{{job_status}}: {{message}}</span><br />
- </div>
-
- <div class="form-group">
- <label for="job_{{job_id}}" class="form-label">parsing: </label>
- <progress id="job_{{job_id}}"
- value="{{progress/100}}"
- class="form-control">
- {{progress}}</progress>
- <span class="form-text text-muted">{{"%.2f" | format(progress)}}%</span>
- </div>
-
- <input type="hidden" name="job_id" value="{{job_id}}" />
-
- <button type="submit" class="btn btn-danger">Abort</button>
- </form>
-</div>
-
-<div class="row">
- {{errors_display(errors, "No errors found so far", "We have found the following errors so far", False)}}
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/no_such_job.html b/qc_app/templates/no_such_job.html
deleted file mode 100644
index 42a2d48..0000000
--- a/qc_app/templates/no_such_job.html
+++ /dev/null
@@ -1,14 +0,0 @@
-{%extends "base.html"%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5;url={{url_for('entry.upload_file')}}">
-{%endblock%}
-
-{%block title%}No Such Job{%endblock%}
-
-{%block contents%}
-<h1 class="heading">No Such Job: {{job_id}}</h2>
-
-<p>No job, with the id '<em>{{job_id}}</em>' was found!</p>
-
-{%endblock%}
diff --git a/qc_app/templates/parse_failure.html b/qc_app/templates/parse_failure.html
deleted file mode 100644
index 31f6be8..0000000
--- a/qc_app/templates/parse_failure.html
+++ /dev/null
@@ -1,26 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Worker Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Worker Failure</h1>
-
-<p>
- There was an error while parsing your file.
-</p>
-
-<p>
- Please notify the developers of this issue when you encounter it,
- providing the information below.
-</p>
-
-<h4>Debugging Information</h4>
-
-<ul>
- <li><strong>job id</strong>: {{job["job_id"]}}</li>
- <li><strong>filename</strong>: {{job["filename"]}}</li>
- <li><strong>line number</strong>: {{job["line_number"]}}</li>
- <li><strong>Progress</strong>: {{job["percent"]}} %</li>
-</ul>
-
-{%endblock%}
diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html
deleted file mode 100644
index e2bf7f0..0000000
--- a/qc_app/templates/parse_results.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "errors_display.html" import errors_display%}
-
-{%block title%}Parse Results{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job_name}}: parse results</h2>
-
-{%if user_aborted%}
-<span class="alert-warning">Job aborted by the user</span>
-{%endif%}
-
-{{errors_display(errors, "No errors found in the file", "We found the following errors", True)}}
-
-{%if errors | length == 0 and not user_aborted %}
-<form method="post" action="{{url_for('dbinsert.select_platform')}}">
- <input type="hidden" name="job_id" value="{{job_id}}" />
- <input type="submit" value="update database" class="btn btn-primary" />
-</form>
-{%endif%}
-
-{%if errors | length > 0 or user_aborted %}
-<br />
-<a href="{{url_for('entry.upload_file')}}" title="Back to index page."
- class="btn btn-primary">
- Go back
-</a>
-{%endif%}
-
-{%endblock%}
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%}
diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html
deleted file mode 100644
index da19ddc..0000000
--- a/qc_app/templates/samples/select-population.html
+++ /dev/null
@@ -1,99 +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>
- <p>We organise the samples/cases/strains in a hierarchichal form, starting
- with <strong>species</strong> at the very top. Under species, we have a
- grouping in terms of the relevant population
- (e.g. Inbred populations, cell tissue, etc.)</p>
-</div>
-
-<form method="POST" action="{{url_for('samples.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">grouping/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>
- </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('samples.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>mandatory</legend>
-
- <label for="txt:inbredset-name" class="form-label">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- placeholder="Enter grouping/population name"
- class="form-control" />
-
- <label for="txt:" class="form-label">full name</label>
- <input id="txt:inbredset-fullname"
- name="inbredset_fullname"
- type="text"
- required = "required"
- placeholder="Enter the grouping/population's full name"
- class="form-control" />
- </div>
- <div class="form-group">
- <legend>Optional</legend>
-
- <label for="num:public" class="form-label">public?</label>
- <input id="num:public"
- name="public"
- type="number"
- min="0" max="2" value="2"
- class="form-control" />
-
- <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" />
-
- <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>
- </div>
-
- <button type="submit" class="btn btn-primary">create grouping/population</button>
-</form>
-
-{%endblock%}
-
-
-{%block javascript%}
-{%endblock%}
diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html
deleted file mode 100644
index edadc61..0000000
--- a/qc_app/templates/samples/select-species.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h2 class="heading">upload samples/cases</h2>
-
-<p>We need to know what species your data belongs to.</p>
-
-{{flash_all_messages()}}
-
-<form method="POST" action="{{url_for('samples.select_species')}}">
- <legend class="heading">upload samples</legend>
- <div class="form-group">
- <label for="select_species02" class="form-label">Species</label>
- <select id="select_species02"
- 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>
- </div>
-
- <button type="submit" class="btn btn-primary">submit</button>
-</form>
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-failure.html b/qc_app/templates/samples/upload-failure.html
deleted file mode 100644
index 09e2ecf..0000000
--- a/qc_app/templates/samples/upload-failure.html
+++ /dev/null
@@ -1,27 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Samples Upload Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>There was a failure attempting to upload the samples.</p>
-
-<p>Here is some information to help with debugging the issue. Provide this
- information to the developer/maintainer.</p>
-
-<h3>Debugging Information</h3>
-<ul>
- <li><strong>job id</strong>: {{job.job_id}}</li>
- <li><strong>status</strong>: {{job.status}}</li>
- <li><strong>job type</strong>: {{job["job-type"]}}</li>
-</ul>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-progress.html b/qc_app/templates/samples/upload-progress.html
deleted file mode 100644
index 7bb02be..0000000
--- a/qc_app/templates/samples/upload-progress.html
+++ /dev/null
@@ -1,22 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>saving to database...</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html
deleted file mode 100644
index e62de57..0000000
--- a/qc_app/templates/samples/upload-samples.html
+++ /dev/null
@@ -1,139 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload Samples{%endblock%}
-
-{%block css%}{%endblock%}
-
-{%block contents%}
-<h1 class="heading">upload samples</h1>
-
-{{flash_messages("alert-success")}}
-
-<p>You can now upload a character-separated value (CSV) file that contains
- details about your samples. The CSV file should have the following fields:
- <dl>
- <dt>Name</dt>
- <dd>The primary name for the sample</dd>
-
- <dt>Name2</dt>
- <dd>A secondary name for the sample. This can simply be the same as
- <strong>Name</strong> above. This field <strong>MUST</strong> contain a
- value.</dd>
-
- <dt>Symbol</dt>
- <dd>A symbol for the sample. Can be an empty field.</dd>
-
- <dt>Alias</dt>
- <dd>An alias for the sample. Can be an empty field.</dd>
- </dl>
-</p>
-
-<form id="form-samples"
- method="POST"
- action="{{url_for('samples.upload_samples',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- enctype="multipart/form-data">
- <legend class="heading">upload samples</legend>
-
- <div class="form-group">
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <label class="form-label">species:</label>
- <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span>
- </div>
-
- <div class="form-group">
- <input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" />
- <label class="form-label">grouping/population:</label>
- <span class="form-text">{{population.Name}} [{{population.FullName}}]</span>
- </div>
-
- <div class="form-group">
- <label for="file-samples" class="form-label">select file</label>
- <input type="file" name="samples_file" id="file:samples"
- accept="text/csv, text/tab-separated-values"
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="select:separator" class="form-label">field separator</label>
- <select id="select:separator"
- name="separator"
- required="required"
- class="form-control">
- <option value="">Select separator for your file: (default is comma)</option>
- <option value="&#x0009;">TAB</option>
- <option value="&#x0020;">Space</option>
- <option value=",">Comma</option>
- <option value=";">Semicolon</option>
- <option value="other">Other</option>
- </select>
- <input id="txt:separator"
- type="text"
- name="other_separator"
- class="form-control" />
- <small class="form-text text-muted">
- If you select '<strong>Other</strong>' for the field separator value,
- enter the character that separates the fields in your CSV file in the form
- field below.
- </small>
- </div>
-
- <div class="form-group form-check">
- <input id="chk:heading"
- type="checkbox"
- name="first_line_heading"
- class="form-check-input" />
- <label for="chk:heading" class="form-check-label">
- first line is a heading?</label>
- <small class="form-text text-muted">
- Select this if the first line in your file contains headings for the
- columns.
- </small>
- </div>
-
- <div class="form-group">
- <label for="txt:delimiter" class="form-label">field delimiter</label>
- <input id="txt:delimiter"
- type="text"
- name="field_delimiter"
- maxlength="1"
- class="form-control" />
- <small class="form-text text-muted">
- If there is a character delimiting the string texts within particular
- fields in your CSV, provide the character here. This can be left blank if
- no such delimiters exist in your file.
- </small>
- </div>
-
- <button type="submit"
- class="btn btn-primary">upload samples file</button>
-</form>
-
-<table id="tbl:samples-preview" class="table">
- <caption class="heading">preview content</caption>
-
- <thead>
- <tr>
- <th>Name</th>
- <th>Name2</th>
- <th>Symbol</th>
- <th>Alias</th>
- </tr>
- </thead>
-
- <tbody>
- <tr id="default-row">
- <td colspan="4">
- Please make some selections to preview the data.</td>
- </tr>
- </tbody>
-</table>
-
-{%endblock%}
-
-
-{%block javascript%}
-<script src="/static/js/upload_samples.js" type="text/javascript"></script>
-{%endblock%}
diff --git a/qc_app/templates/samples/upload-success.html b/qc_app/templates/samples/upload-success.html
deleted file mode 100644
index cb745c3..0000000
--- a/qc_app/templates/samples/upload-success.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>Successfully uploaded the samples.</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
deleted file mode 100644
index 2f07de8..0000000
--- a/qc_app/templates/select_dataset.html
+++ /dev/null
@@ -1,161 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select dataset</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.final_confirmation')}}"
- id="select-dataset-form" class="two-col-sep-col1">
- <legend class="heading">choose existing dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- <div class="form-group">
- <label for="datasetid" class="form-label">dataset:</label>
- <select id="datasetid" name="datasetid" class="form-control"
- {%if datasets | length == 0:%}
- disabled="disabled"
- {%endif%}>
- {%for dataset in datasets:%}
- <option value="{{dataset['Id']}}">
- [{{dataset["Name"]}}] - {{dataset["FullName"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary"
- {%if datasets | length == 0:%}
- disabled="disabled"
- {%endif%} />update database</button>
-</form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" id="create-dataset-form"
- action="{{url_for('dbinsert.create_dataset')}}"
- class="two-col-sep-col2">
- <legend class="heading">create new dataset</legend>
- {{hidden_fields(
- filename, filetype, species=species, genechipid=genechipid,
- studyid=studyid, totallines=totallines)}}
-
- {%with messages = get_flashed_messages(with_categories=true)%}
- {%if messages:%}
- <ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
- </ul>
- {%endif%}
- {%endwith%}
-
- <div class="form-group">
- <label for="avgid" class="form-label">average:</label>
- <select id="avgid" name="avgid" required="required" class="form-control">
- <option value="">Select averaging method</option>
- {%for method in avgmethods:%}
- <option value="{{method['AvgMethodId']}}"
- {%if avgid is defined and method['AvgMethodId'] | int == avgid | int%}
- selected="selected"
- {%endif%}>
- {{method["Name"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <label for="datasetname" class="form-label">name:</label>
- <input id="datasetname" name="datasetname" type="text"
- class="form-control"
- {%if datasetname is defined %}
- value="{{datasetname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetname2" class="form-label">name 2:</label>
- <input id="datasetname2" name="datasetname2" type="text"
- required="required" class="form-control"
- {%if datasetname2 is defined %}
- value="{{datasetname2}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetfullname" class="form-label">full name:</label>
- <input id="datasetfullname" name="datasetfullname" type="text"
- required="required" class="form-control"
- {%if datasetfullname is defined %}
- value="{{datasetfullname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetshortname" class="form-label">short name:</label>
- <input id="datasetshortname" name="datasetshortname" type="text"
- required="required" class="form-control"
- {%if datasetshortname is defined %}
- value="{{datasetshortname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label for="datasetpublic" class="form-label">public:</label>
- <input id="datasetpublic" name="datasetpublic" type="number"
- required="required" min="0" max="2"
- {%if datasetpublic is defined %}
- value="{{datasetpublic | int}}"
- {%else%}
- value="0"
- {%endif%}
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="datasetconfidentiality">confidentiality:</label>
- <input id="datasetconfidentiality" name="datasetconfidentiality"
- type="number" required="required" min="0" max="2"
- {%if datasetconfidentiality is defined %}
- value="{{datasetconfidentiality | int}}"
- {%else%}
- value="0"
- {%endif%}
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="datasetdatascale" class="form-label">data scale:</label>
- <select id="datasetdatascale" name="datasetdatascale" class="form-control">
- <option value="">None</option>
- {%for dscale in datascales:%}
- <option value="{{dscale}}"
- {%if datasetdatascale is defined and dscale == datasetdatascale%}
- selected="selected"
- {%elif dscale == "log2":%}
- selected="selected"
- {%endif%}>
- {{dscale}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">create new dataset</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html
deleted file mode 100644
index d9bc68f..0000000
--- a/qc_app/templates/select_platform.html
+++ /dev/null
@@ -1,82 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select platform</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}">
- <input type="hidden" name="filename" value="{{filename}}" />
- <input type="hidden" name="filetype" value="{{filetype}}" />
- <input type="hidden" name="totallines" value="{{totallines}}" />
-
- <div class="form-group">
- <label for="species" class="form-label">species</label>
- <select id="species" name="species" class="form-control">
- {%for row in species:%}
- <option value="{{row['SpeciesId']}}"
- {%if row["Name"] == default_species:%}
- selected="selected"
- {%endif%}>
- {{row["MenuName"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <table id="genechips-table" class="table">
- <caption>select platform</caption>
- <thead>
- <tr>
- <th>Select</th>
- <th>GeneChip ID</th>
- <th>GeneChip Name</th>
- </tr>
- </thead>
-
- <tbody>
- {%for chip in genechips:%}
- <tr>
- <td>
- <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
- required="required" />
- </td>
- <td>{{chip["GeneChipId"]}}</td>
- <td>{{chip["GeneChipName"]}}</td>
- </tr>
- {%else%}
- <tr>
- <td colspan="5">No chips found for selected species</td>
- </tr>
- {%endfor%}
- </tbody>
- </table>
-
- <button type="submit" class="btn btn-primary">submit platform</button>
- </form>
-</div>
-{%endblock%}
-
-{%block javascript%}
-<script type="text/javascript" src="/static/js/utils.js"></script>
-<script type="text/javascript" src="/static/js/select_platform.js"></script>
-<script type="text/javascript">
- document.getElementById(
- "species").addEventListener("change", update_genechips);
- document.getElementById(
- "genechips-table").getElementsByTagName(
- "tbody")[0].addEventListener(
- "click",
- function(event) {
- if(event.target.tagName.toLowerCase() == "td") {
- return select_row_radio(event.target.parentElement);
- }
- if(event.target.tagName.toLowerCase() == "td") {
- return select_row_radio(event.target);
- }
- return false;
- });
-</script>
-{%endblock%}
diff --git a/qc_app/templates/select_species.html b/qc_app/templates/select_species.html
deleted file mode 100644
index 3b1a8a9..0000000
--- a/qc_app/templates/select_species.html
+++ /dev/null
@@ -1,92 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-{%from "upload_progress_indicator.html" import upload_progress_indicator%}
-
-{%block title%}expression data: select species{%endblock%}
-
-{%block contents%}
-{{upload_progress_indicator()}}
-
-<h2 class="heading">expression data: select species</h2>
-
-<div class="row">
- <form action="{{url_for('entry.upload_file')}}"
- method="POST"
- enctype="multipart/form-data"
- id="frm-upload-expression-data">
- <legend class="heading">upload expression data</legend>
- {{flash_messages("error-expr-data")}}
-
- <div class="form-group">
- <label for="select_species01" class="form-label">Species</label>
- <select id="select_species01"
- name="speciesid"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for aspecies in species%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <legend class="heading">file type</legend>
-
- <div class="form-check">
- <input type="radio" name="filetype" value="average" id="filetype_average"
- required="required" class="form-check-input" />
- <label for="filetype_average" class="form-check-label">average</label>
- </div>
-
- <div class="form-check">
- <input type="radio" name="filetype" value="standard-error"
- id="filetype_standard_error" required="required"
- class="form-check-input" />
- <label for="filetype_standard_error" class="form-check-label">
- standard error
- </label>
- </div>
- </div>
-
- <div class="form-group">
- <span id="no-file-error" class="alert-danger" style="display: none;">
- No file selected
- </span>
- <label for="file_upload" class="form-label">select file</label>
- <input type="file" name="qc_text_file" id="file_upload"
- accept="text/plain, text/tab-separated-values, application/zip"
- class="form-control"/>
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- data-toggle="modal"
- data-target="#upload-progress-indicator">upload file</button>
- </form>
-</div>
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript" src="static/js/upload_progress.js"></script>
-<script type="text/javascript">
- function setup_formdata(form) {
- var formdata = new FormData();
- formdata.append(
- "speciesid",
- form.querySelector("#select_species01").value)
- formdata.append(
- "qc_text_file",
- form.querySelector("input[type='file']").files[0]);
- formdata.append(
- "filetype",
- selected_filetype(
- Array.from(form.querySelectorAll("input[type='radio']"))));
- return formdata;
- }
-
- setup_upload_handlers(
- "frm-upload-expression-data", make_data_uploader(setup_formdata));
-</script>
-{%endblock%}
diff --git a/qc_app/templates/select_study.html b/qc_app/templates/select_study.html
deleted file mode 100644
index 648ad4c..0000000
--- a/qc_app/templates/select_study.html
+++ /dev/null
@@ -1,108 +0,0 @@
-{%extends "base.html"%}
-{%from "dbupdate_hidden_fields.html" import hidden_fields%}
-
-{%block title%}Select Dataset{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<h2 class="heading">{{filename}}: select study</h2>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.select_dataset')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col1">
- <legend class="heading">Select from existing study</legend>
- {{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
- totallines=totallines)}}
-
- <div class="form-group">
- <label class="form-label" for="study">study:</label>
- <select id="study" name="studyid" class="form-control">
- {%for study in studies:%}
- <option value="{{study['Id']}}">{{study["Name"]}}</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit"
- class="btn btn-primary"
- {%if studies | length == 0:%}
- disabled="disabled"
- {%endif%} />submit selected study</button>
-</form>
-</div>
-
-<div class="row">
- <p class="two-col-sep-separator">OR</p>
-</div>
-
-<div class="row">
- <form method="POST" action="{{url_for('dbinsert.create_study')}}"
- id="select-platform-form" data-genechips="{{genechips_data}}"
- class="two-col-sep-col2">
- {%with messages = get_flashed_messages(with_categories=true)%}
- {%if messages:%}
- <ul>
- {%for category, message in messages:%}
- <li class="{{category}}">{{message}}</li>
- {%endfor%}
- </ul>
- {%endif%}
- {%endwith%}
- <legend class="heading">Create new study</legend>
- {{hidden_fields(filename, filetype, species=species, genechipid=genechipid,
- totallines=totallines)}}
-
- <div class="form-group">
- <label class="form-label" for="studyname">name:</label>
- <input type="text" id="studyname" name="studyname" class="form-control"
- required="required"
- {%if studyname:%}
- value="{{studyname}}"
- {%endif%} />
- </div>
-
- <div class="form-group">
- <label class="form-label" for="group">group:</label>
- <select id="group" name="inbredsetid" class="form-control"
- required="required">
- <option value="">Select group</option>
- {%for family in groups:%}
- <optgroup label="{{family}}">
- {%for group in groups[family]:%}
- <option value="{{group['InbredSetId']}}"
- {%if group["InbredSetId"] == selected_group:%}
- selected="selected"
- {%endif%}>
- {{group["FullName"]}}
- </option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
- </div>
-
- <div class="form-group">
- <label class="form-label" for="tissue">tissue:</label>
- <select id="tissue" name="tissueid" class="form-control"
- required="required">
- <option value="">Select type</option>
- {%for tissue in tissues:%}
- <option value="{{tissue['TissueId']}}"
- {%if tissue["TissueId"] == selected_tissue:%}
- selected="selected"
- {%endif%}>
- {{tissue["Name"]}}
- </option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">create study</button>
- </form>
-</div>
-
-{%endblock%}
diff --git a/qc_app/templates/stdout_output.html b/qc_app/templates/stdout_output.html
deleted file mode 100644
index 85345a9..0000000
--- a/qc_app/templates/stdout_output.html
+++ /dev/null
@@ -1,8 +0,0 @@
-{%macro stdout_output(job)%}
-
-<h4>STDOUT Output</h4>
-<div class="cli-output">
- <pre>{{job.get("stdout", "")}}</pre>
-</div>
-
-{%endmacro%}
diff --git a/qc_app/templates/unhandled_exception.html b/qc_app/templates/unhandled_exception.html
deleted file mode 100644
index 6e6a051..0000000
--- a/qc_app/templates/unhandled_exception.html
+++ /dev/null
@@ -1,21 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}System Error{%endblock%}
-
-{%block css%}
-<link rel="stylesheet" href="/static/css/two-column-with-separator.css" />
-{%endblock%}
-
-{%block contents%}
-<p>
- An error has occured, and your request has been aborted. Please notify the
- administrator to try and get this sorted.
-</p>
-<p>
- Provide the following information to help the administrator figure out and fix
- the issue:<br />
- <hr /><br />
- {{trace}}
- <hr /><br />
-</p>
-{%endblock%}
diff --git a/qc_app/templates/upload_progress_indicator.html b/qc_app/templates/upload_progress_indicator.html
deleted file mode 100644
index e274e83..0000000
--- a/qc_app/templates/upload_progress_indicator.html
+++ /dev/null
@@ -1,35 +0,0 @@
-{%macro upload_progress_indicator()%}
-<div id="upload-progress-indicator" class="modal fade" tabindex="-1" role="dialog">
- <div class="modal-dialog" role="document">
- <div class="modal-content">
- <div class="modal-header">
- <h3 class="modal-title">Uploading file</h3>
- </div>
-
- <div class="modal-body">
- <form id="frm-cancel-upload" style="border-style: none;">
- <div class="form-group">
- <span id="progress-filename" class="form-text">No file selected!</span>
- <progress id="progress-bar" value="0" max="100" class="form-control">
- 0</progress>
- </div>
-
- <div class="form-group">
- <span class="form-text text-muted" id="progress-text">
- Uploading 0%</span>
- <span class="form-text text-muted" id="progress-extra-text">
- Processing</span>
- </div>
- </form>
- </div>
-
- <div class="modal-footer">
- <button id="btn-cancel-upload"
- type="button"
- class="btn btn-danger"
- data-dismiss="modal">Cancel</button>
- </div>
- </div>
- </div>
-</div>
-{%endmacro%}
diff --git a/qc_app/templates/worker_failure.html b/qc_app/templates/worker_failure.html
deleted file mode 100644
index b65b140..0000000
--- a/qc_app/templates/worker_failure.html
+++ /dev/null
@@ -1,24 +0,0 @@
-{%extends "base.html"%}
-
-{%block title%}Worker Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">Worker Failure</h1>
-
-<p>
- There was a critical failure launching the job to parse your file.
- This is our fault and (probably) has nothing to do with the file you uploaded.
-</p>
-
-<p>
- Please notify the developers of this issue when you encounter it,
- providing the link to this page, or the information below.
-</p>
-
-<h4>Debugging Information</h4>
-
-<ul>
- <li><strong>job id</strong>: {{job_id}}</li>
-</ul>
-
-{%endblock%}