diff options
| -rw-r--r-- | qc_app/entry.py | 5 | ||||
| -rw-r--r-- | qc_app/static/css/styles.css | 29 | ||||
| -rw-r--r-- | qc_app/templates/data_review.html | 77 | ||||
| -rw-r--r-- | qc_app/templates/index.html | 20 |
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"> |