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| author | Frederick Muriuki Muriithi | 2024-07-25 11:07:33 -0500 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-07-25 14:34:09 -0500 |
| commit | 754e8f214b940e05298cb360ed829f5c685d55a5 (patch) | |
| tree | 62c2c5b601746621f0949b38937ad232f006dee2 /qc_app/templates | |
| parent | de9e1b9fe37928b864bea28b408de6c14d04526b (diff) | |
| download | gn-uploader-754e8f214b940e05298cb360ed829f5c685d55a5.tar.gz | |
Rename module: qc_app --> uploader
Diffstat (limited to 'qc_app/templates')
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]}}…</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="	">TAB</option> - <option value=" ">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%} |