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diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html deleted file mode 100644 index 2bd5fab..0000000 --- a/uploader/templates/phenotypes/add-phenotypes.html +++ /dev/null @@ -1,231 +0,0 @@ -{%extends "phenotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block lvl4_breadcrumbs%} -<li {%if activelink=="add-phenotypes"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">Add Phenotypes</a> -</li> -{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - <form id="frm-add-phenotypes" - method="POST" - enctype="multipart/form-data" - action="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}"> - <legend>Add New Phenotypes</legend> - - <div class="form-text help-block"> - <p>Select the zip file bundle containing information on the phenotypes you - wish to upload, then click the "Upload Phenotypes" button below to - upload the data.</p> - <p>See the <a href="#section-file-formats">File Formats</a> section below - to get an understanding of what is expected of the bundle files you - upload.</p> - <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> - </div> - - <div class="form-group"> - <label for="finput-phenotypes-bundle" class="form-label"> - Phenotypes Bundle</label> - <input type="file" - id="finput-phenotypes-bundle" - name="phenotypes-bundle" - accept="application/zip, .zip" - required="required" - class="form-control" /> - </div> - - <div class="form-group"> - <input type="submit" - value="upload phenotypes" - class="btn btn-primary" /> - </div> - </form> -</div> - -<div class="row"> - <h2 class="heading" id="section-file-formats">File Formats</h2> - <p>We accept an extended form of the - <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files" - title="R/qtl2 software input file format documentation"> - input files' format used with the R/qtl2 software</a> as a single ZIP - file</p> - <p>The files that are used for this feature are: - <ul> - <li>the <em>control</em> file</li> - <li><em>pheno</em> file(s)</li> - <li><em>phenocovar</em> file(s)</li> - <li><em>phenose</em> files(s)</li> - </ul> - </p> - <p>Other files within the bundle will be ignored, for this feature.</p> - <p>The following section will detail the expectations for each of the - different file types within the uploaded ZIP file bundle for phenotypes:</p> - - <h3 class="subheading">Control File</h3> - <p>There <strong>MUST be <em>one, and only one</em></strong> file that acts - as the control file. This file can be: - <ul> - <li>a <em>JSON</em> file, or</li> - <li>a <em>YAML</em> file.</li> - </ul> - </p> - - <p>The control file is useful for defining things about the bundle such as:</p> - <ul> - <li>The field separator value (default: <code>sep: ','</code>). There can - only ever be one field separator and it <strong>MUST</strong> be the same - one for <strong>ALL</strong> files in the bundle.</li> - <li>The comment character (default: <code>comment.char: '#'</code>). Any - line that starts with this character will be considered a comment line and - be ignored in its entirety.</li> - <li>Code for missing values (default: <code>na.strings: 'NA'</code>). You - can specify more than one code to indicate missing values, e.g. - <code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li> - </ul> - - <h3 class="subheading"><em>pheno</em> File(s)</h3> - <p>These files are the main data files. You must have at least one of these - files in your bundle for it to be valid for this step.</p> - <p>The data is a matrix of <em>individuals × phenotypes</em> by default, as - below:<br /> - <code> - id,10001,10002,10003,10004,…<br /> - BXD1,61.400002,54.099998,483,49.799999,…<br /> - BXD2,49,50.099998,403,45.5,…<br /> - BXD5,62.5,53.299999,501,62.900002,…<br /> - BXD6,53.099998,55.099998,403,NA,…<br /> - ⋮<br /></code> - </p> - <p>If the <code>pheno_transposed</code> value is set to <code>True</code>, - then the data will be a <em>phenotypes × individuals</em> matrix as in the - example below:<br /> - <code> - id,BXD1,BXD2,BXD5,BXD6,…<br /> - 10001,61.400002,49,62.5,53.099998,…<br /> - 10002,54.099998,50.099998,53.299999,55.099998,…<br /> - 10003,483,403,501,403,…<br /> - 10004,49.799999,45.5,62.900002,NA,…<br /> - ⋮ - </code> - </p> - - - <h3 class="subheading"><em>phenocovar</em> File(s)</h3> - <p>At least one phenotypes metadata file with the metadata values such as - descriptions, PubMed Identifier, publication titles (if present), etc.</p> - <p>The data in this/these file(s) is a matrix of - <em>phenotypes × phenotypes-covariates</em>. The first column is always the - phenotype names/identifiers — same as in the R/qtl2 format.</p> - <p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p> - <p>This file <strong>MUST</strong> be present in the bundle, and have data for - the bundle to be considered valid by our system for this step.<br /> - In addition to that, the following are the fields that <strong>must be - present</strong>, and - have values, in the file before the file is considered valid: - <ul> - <li><em>description</em>: A description for each phenotype. Useful - for users to know what the phenotype is about.</li> - <li><em>units</em>: The units of measurement for the phenotype, - e.g. milligrams for brain weight, centimetres/millimetres for - tail-length, etc.</li> - </ul></p> - - <p>The following <em>optional</em> fields can also be provided: - <ul> - <li><em>pubmedid</em>: A PubMed Identifier for the publication where - the phenotype is published. If this field is not provided, the system will - assume your phenotype is not published.</li> - </ul> - </p> - <p>These files will be marked up in the control file with the - <code>phenocovar</code> key, as in the examples below: - <ol> - <li>JSON: single file<br /> - <code>{<br /> - ⋮,<br /> - "phenocovar": "your_covariates_file.csv",<br /> - ⋮<br /> - } - </code> - </li> - <li>JSON: multiple files<br /> - <code>{<br /> - ⋮,<br /> - "phenocovar": [<br /> - "covariates_file_01.csv",<br /> - "covariates_file_01.csv",<br /> - ⋮<br /> - ],<br /> - ⋮<br /> - } - </code> - </li> - <li>YAML: single file or<br /> - <code> - ⋮<br /> - phenocovar: your_covariates_file.csv<br /> - ⋮ - </code> - </li> - <li>YAML: multiple files<br /> - <code> - ⋮<br /> - phenocovar:<br /> - - covariates_file_01.csv<br /> - - covariates_file_02.csv<br /> - - covariates_file_03.csv<br /> - …<br /> - ⋮ - </code> - </li> - </ol> - </p> - - <h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3> - <p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are - not supported by the original R/qtl2 file format</p> - <p>We use these files to upload the standard errors (<em>phenose</em>) when - the data file (<em>pheno</em>) is average data. In that case, the - <em>phenonum</em> file(s) contains the number of individuals that were - involved when computing the averages.</p> - <p>Both types of files are matrices of <em>individuals × phenotypes</em> by - default. Like the related <em>pheno</em> files, if - <code>pheno_transposed: True</code>, then the file will be a matrix of - <em>phenotypes × individuals</em>.</p> -</div> - -<div class="row text-warning"> - <h3 class="subheading">Notes for Devs (well… Fred, really.)</h3> - <p>Use the following resources for automated retrieval of certain data</p> - <ul> - <li><a href="https://www.ncbi.nlm.nih.gov/pmc/tools/developers/" - title="NCBI APIs: Retrieve articles' metadata etc."> - NCBI APIS</a></li> - </ul> -</div> - -{%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} |