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authorFrederick Muriuki Muriithi2024-07-25 11:07:33 -0500
committerFrederick Muriuki Muriithi2024-07-25 14:34:09 -0500
commit754e8f214b940e05298cb360ed829f5c685d55a5 (patch)
tree62c2c5b601746621f0949b38937ad232f006dee2 /uploader/templates/data_review.html
parentde9e1b9fe37928b864bea28b408de6c14d04526b (diff)
downloadgn-uploader-754e8f214b940e05298cb360ed829f5c685d55a5.tar.gz
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+{%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%}