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-rw-r--r--qc_app/entry.py5
-rw-r--r--qc_app/static/css/styles.css29
-rw-r--r--qc_app/templates/data_review.html77
-rw-r--r--qc_app/templates/index.html20
4 files changed, 129 insertions, 2 deletions
diff --git a/qc_app/entry.py b/qc_app/entry.py
index 2c4600d..abea5ed 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -101,3 +101,8 @@ def upload_file():
return redirect(url_for(
"parse.parse", filename=filename,
filetype=request.form["filetype"]))
+
+@entrybp.route("/data-review", methods=["GET"])
+def data_review():
+ """Provide some help on data expectations to the user."""
+ return render_template("data_review.html")
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index d2071e6..c9f6737 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -10,12 +10,20 @@ label, legend {
text-transform: capitalize;
}
+#explainer {
+ font-family: Georgia, Garamond, serif;
+ font-style: normal;
+ font-size: 1.275em;
+}
+
.heading {
color: #FEFEFE;
background-color: #336699;
text-transform: capitalize;
- border-radius: 5px;
+ border-radius: 5px 5px 0 0;
padding-left: 0.5em;
+ font-weight: bold;
+ line-height: 1.5em;
}
fieldset {
@@ -108,6 +116,23 @@ table th,td {
border-radius: 1em;
}
+form {
+ border-radius: 5px;
+ border-width: 1px;
+ border-style: solid;
+ border-color: #336699;
+}
+
+@media(min-width: 1250px) {
+ form {
+ width: 40%;
+ }
+
+ #explainer {
+ width: 65ch;
+ }
+}
+
fieldset {
border-style: none;
display: grid;
@@ -132,7 +157,7 @@ input[disabled="true"],input[disabled="disabled"] {
background-color: #F8D7DA;
}
-form legend {
+form fieldset legend {
padding-left: 3em;
text-transform: capitalize;
font-weight: bolder;
diff --git a/qc_app/templates/data_review.html b/qc_app/templates/data_review.html
new file mode 100644
index 0000000..7ac01ba
--- /dev/null
+++ b/qc_app/templates/data_review.html
@@ -0,0 +1,77 @@
+{%extends "base.html"%}
+
+{%block title%}Data Review{%endblock%}
+
+{%block contents%}
+<h1 class="heading">data review</h1>
+
+<div id="explainer">
+ <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 strain headers in your first row will be against a source of truth
+ (<a href="https://gitlab.com/fredmanglis/gnqc_py/-/blob/main/etc/strains.csv"
+ title="list of expected strains">see strains.csv [1.7M]</a>).<br />
+ Pick the strain names from the <strong>'Name'</strong> and
+ <strong>'Name2'</strong> fields.</li>
+ </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>
+
+
+ <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/index.html b/qc_app/templates/index.html
index 9111af0..9ee3af6 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -5,8 +5,28 @@
{%block contents%}
<h1 class="heading">upload file</h1>
+<div id="explainer">
+ <p>This application assumes that you are familiar with the basics of data
+ verification formats and uploading procedures. 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>
+
<form action="{{url_for('entry.upload_file')}}"
method="POST" enctype="multipart/form-data">
+ <legend class="heading">upload file</legend>
{%with messages = get_flashed_messages(with_categories=True) %}
{%if messages %}
<div class="alerts">