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-rw-r--r--uploader/templates/expression-data/base.html13
-rw-r--r--uploader/templates/expression-data/data-review.html85
-rw-r--r--uploader/templates/expression-data/index.html33
-rw-r--r--uploader/templates/expression-data/job-progress.html47
-rw-r--r--uploader/templates/expression-data/no-such-job.html15
-rw-r--r--uploader/templates/expression-data/parse-failure.html26
-rw-r--r--uploader/templates/expression-data/parse-results.html39
-rw-r--r--uploader/templates/expression-data/select-file.html115
-rw-r--r--uploader/templates/expression-data/select-population.html29
9 files changed, 402 insertions, 0 deletions
diff --git a/uploader/templates/expression-data/base.html b/uploader/templates/expression-data/base.html
new file mode 100644
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--- /dev/null
+++ b/uploader/templates/expression-data/base.html
@@ -0,0 +1,13 @@
+{%extends "populations/base.html"%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="expression-data"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.expression-data.index')}}">
+ Expression Data</a>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/expression-data/data-review.html b/uploader/templates/expression-data/data-review.html
new file mode 100644
index 0000000..c985b03
--- /dev/null
+++ b/uploader/templates/expression-data/data-review.html
@@ -0,0 +1,85 @@
+{%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('species.populations.samples.index')}}"
+ 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"
+ target="_blank">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/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html
new file mode 100644
index 0000000..9ba3582
--- /dev/null
+++ b/uploader/templates/expression-data/index.html
@@ -0,0 +1,33 @@
+{%extends "expression-data/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Expression Data{%endblock%}
+
+{%block pagetitle%}Expression Data{%endblock%}
+
+{%block breadcrumb%}
+<li class="breadcrumb-item">
+ <a href="{{url_for('base.index')}}">Home</a>
+</li>
+<li class="breadcrumb-item active">
+ <a href="{{url_for('species.populations.expression-data.index')}}"
+ title="Upload expression data.">
+ Expression Data</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+ <h2 class="heading">Expression Data</h2>
+ {{flash_all_messages()}}
+
+ <p>This section allows you to enter the expression data for your experiment.
+ You will need to select the species that your data concerns below.</p>
+</div>
+
+<div class="row">
+ {{select_species_form(url_for("species.populations.expression-data.index"),
+ species)}}
+</div>
+{%endblock%}
diff --git a/uploader/templates/expression-data/job-progress.html b/uploader/templates/expression-data/job-progress.html
new file mode 100644
index 0000000..ef264e1
--- /dev/null
+++ b/uploader/templates/expression-data/job-progress.html
@@ -0,0 +1,47 @@
+{%extends "base.html"%}
+{%from "errors_display.html" import errors_display%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%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('species.populations.expression-data.abort',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}" 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%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
diff --git a/uploader/templates/expression-data/no-such-job.html b/uploader/templates/expression-data/no-such-job.html
new file mode 100644
index 0000000..d22c429
--- /dev/null
+++ b/uploader/templates/expression-data/no-such-job.html
@@ -0,0 +1,15 @@
+{%extends "base.html"%}
+
+{%block extrameta%}
+<meta http-equiv="refresh"
+ content="5;url={{url_for('species.populations.expression-data.index.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/uploader/templates/expression-data/parse-failure.html b/uploader/templates/expression-data/parse-failure.html
new file mode 100644
index 0000000..31f6be8
--- /dev/null
+++ b/uploader/templates/expression-data/parse-failure.html
@@ -0,0 +1,26 @@
+{%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/uploader/templates/expression-data/parse-results.html b/uploader/templates/expression-data/parse-results.html
new file mode 100644
index 0000000..03a23e2
--- /dev/null
+++ b/uploader/templates/expression-data/parse-results.html
@@ -0,0 +1,39 @@
+{%extends "base.html"%}
+{%from "errors_display.html" import errors_display%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Parse Results{%endblock%}
+
+{%block contents%}
+
+<div class="row">
+ <h2 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('species.populations.expression-data.upload_file',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ title="Back to index page."
+ class="btn btn-primary">Go back</a>
+
+ {%endif%}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
diff --git a/uploader/templates/expression-data/select-file.html b/uploader/templates/expression-data/select-file.html
new file mode 100644
index 0000000..4ca461e
--- /dev/null
+++ b/uploader/templates/expression-data/select-file.html
@@ -0,0 +1,115 @@
+{%extends "expression-data/base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+{%from "upload_progress_indicator.html" import upload_progress_indicator%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Expression Data &mdash; Upload Data{%endblock%}
+
+{%block pagetitle%}Expression Data &mdash; Upload Data{%endblock%}
+
+{%block contents%}
+{{upload_progress_indicator()}}
+
+<div class="row">
+ <h2 class="heading">Upload Expression Data</h2>
+
+ <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('species.populations.expression-data.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('species.populations.expression-data.data_review')}}#file-types"
+ title="Details for the data expectations.">Help</a>)</li>
+ </ol>
+</div>
+
+<div class="row">
+ <form action="{{url_for(
+ 'species.populations.expression-data.upload_file',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ method="POST"
+ enctype="multipart/form-data"
+ id="frm-upload-expression-data">
+ {{flash_messages("error-expr-data")}}
+
+ <div class="form-group">
+ <legend class="heading">File Type</legend>
+
+ <div class="radio">
+ <label for="filetype_average" class="form-check-label">
+ <input type="radio" name="filetype" value="average" id="filetype_average"
+ required="required" class="form-check-input" />
+ Average</label>
+ <p class="form-text text-muted">
+ <small>The averages data …</small></p>
+ </div>
+
+ <div class="radio">
+ <label for="filetype_standard_error" class="form-check-label">
+ <input type="radio" name="filetype" value="standard-error"
+ id="filetype_standard_error" required="required"
+ class="form-check-input" />
+ Standard Error
+ </label>
+ <p class="form-text text-muted">
+ <small>The standard errors computed from the averages …</small></p>
+ </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"/>
+ <p class="form-text text-muted">
+ <small>Select the file to upload.</small></p>
+ </div>
+
+ <button type="submit"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#upload-progress-indicator">upload file</button>
+ </form>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%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(
+ "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/uploader/templates/expression-data/select-population.html b/uploader/templates/expression-data/select-population.html
new file mode 100644
index 0000000..8555e27
--- /dev/null
+++ b/uploader/templates/expression-data/select-population.html
@@ -0,0 +1,29 @@
+{%extends "expression-data/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
+{%from "populations/macro-select-population.html" import select_population_form%}
+
+{%block title%}Expression Data{%endblock%}
+
+{%block pagetitle%}Expression Data{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <p>You have selected the species. Now you need to select the population that
+ the expression data belongs to.</p>
+</div>
+
+<div class="row">
+ {{select_population_form(url_for(
+ "species.populations.expression-data.select_population",
+ species_id=species.SpeciesId),
+ populations)}}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}