diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 22 | ||||
| -rw-r--r-- | uploader/static/css/styles.css | 20 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes.html | 222 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/macro-display-pheno-dataset-card.html | 23 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 14 |
5 files changed, 297 insertions, 4 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ddf6908..eb0b460 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -286,3 +286,25 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= return redirect(url_for("species.populations.phenotypes.list_datasets", species_id=species["SpeciesId"], population_id=population["Id"])) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/add-phenotypes", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def add_phenotypes(species: dict, population: dict, dataset: dict, **kwargs): + """Add one or more phenotypes to the dataset.""" + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + if request.method == "GET": + return render_template("phenotypes/add-phenotypes.html", + species=species, + population=population, + dataset=dataset, + activelink="add-phenotypes") + raise NotImplementedError("Please implement this...") diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css index 0e9a029..5161169 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -131,3 +131,23 @@ input[type="submit"], .btn { border-color: #DCA7A7; background-color: #F2DEDE; } + +.heading { + border-bottom: solid #EEBB88; +} + +.subheading { + padding: 1em 0 0.1em 0.5em; + border-bottom: solid #88BBEE; +} + +form { + margin-top: 0.3em; + background: #E5E5FF; + padding: 0.5em; + border-radius:0.5em; +} + +form .form-control { + background-color: #EAEAFF; +} diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html new file mode 100644 index 0000000..20f8087 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes.html @@ -0,0 +1,222 @@ +{%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)}}">View Datasets</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>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="not-implemented 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 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%} diff --git a/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html new file mode 100644 index 0000000..1121443 --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -0,0 +1,23 @@ +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%macro display_pheno_dataset_card(species, population, dataset)%} +{{display_population_card(species, population)}} + +<div class="card"> + <div class="card-body"> + <h5 class="card-title">Phenotypes' Dataset</h5> + <div class="card-text"> + <dl> + <dt>Name</dt> + <dd>{{dataset.Name}}</dd> + + <dt>Full Name</dt> + <dd>{{dataset.FullName}}</dd> + + <dt>Short Name</dt> + <dd>{{dataset.ShortName}}</dd> + </dl> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 5a17755..b136bb6 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -37,10 +37,7 @@ <tbody> <tr> - <td><a href="{{url_for('species.populations.phenotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td> + <td>{{dataset.Name}}</td> <td>{{dataset.FullName}}</td> <td>{{dataset.ShortName}}</td> </tr> @@ -49,6 +46,15 @@ </div> <div class="row"> + <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a></p> +</div> + +<div class="row"> <h2>Phenotype Data</h2> <p>This dataset has a total of {{phenotype_count}} phenotypes.</p> |