diff options
Diffstat (limited to 'uploader/templates/phenotypes')
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes.html | 231 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/create-dataset.html | 106 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/list-datasets.html | 6 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/macro-display-pheno-dataset-card.html | 31 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 21 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-phenotype.html | 97 |
6 files changed, 475 insertions, 17 deletions
diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html new file mode 100644 index 0000000..196bc69 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes.html @@ -0,0 +1,231 @@ +{%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="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%} diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html new file mode 100644 index 0000000..93de92f --- /dev/null +++ b/uploader/templates/phenotypes/create-dataset.html @@ -0,0 +1,106 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="create-dataset"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}">Create Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>Create a new phenotype dataset.</p> +</div> + +<div class="row"> + <form id="frm-create-pheno-dataset" + action="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + method="POST"> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-name">Name</label> + {%if errors["dataset-name"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-name"]}}</p></small> + {%endif%} + <input type="text" + name="dataset-name" + id="txt-dataset-name" + value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}" + {%if errors["dataset-name"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A short representative name for the dataset.</p> + <p>Recommended: Use the population code and append "Publish" at the end. + <br />This field will only accept names composed of + letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p> + </small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-fullname">Full Name</label> + {%if errors["dataset-fullname"] is defined%} + <small class="form-text text-muted danger"> + <p>{{errors["dataset-fullname"]}}</p></small> + {%endif%} + <input id="txt-dataset-fullname" + name="dataset-fullname" + type="text" + value="{{original_formdata.get('dataset-fullname', '')}}" + {%if errors["dataset-fullname"] is defined%} + class="form-control danger" + {%else%} + class="form-control" + {%endif%} + required="required" /> + <small class="form-text text-muted"> + <p>A longer, descriptive name for the dataset — useful for humans. + </p></small> + </div> + + <div class="form-group"> + <label class="form-label" for="txt-dataset-shortname">Short Name</label> + <input id="txt-dataset-shortname" + name="dataset-shortname" + type="text" + class="form-control" + value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" /> + <small class="form-text text-muted"> + <p>An optional, short name for the dataset. <br /> + If this is not provided, it will default to the value provided for the + <strong>Name</strong> field above.</p></small> + </div> + + <div class="form-group"> + <input type="submit" + class="btn btn-primary" + value="create phenotype dataset" /> + </div> + + </form> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html index 360fd2c..2eaf43a 100644 --- a/uploader/templates/phenotypes/list-datasets.html +++ b/uploader/templates/phenotypes/list-datasets.html @@ -51,8 +51,10 @@ <p class="text-warning"> <span class="glyphicon glyphicon-exclamation-sign"></span> There is no dataset for this population!</p> - <p><a href="#" - class="not-implemented btn btn-primary" + <p><a href="{{url_for('species.populations.phenotypes.create_dataset', + species_id=species.SpeciesId, + population_id=population.Id)}}" + class="btn btn-primary" title="Create a new phenotype dataset.">create dataset</a></p> {%endif%} </div> 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..11b108b --- /dev/null +++ b/uploader/templates/phenotypes/macro-display-pheno-dataset-card.html @@ -0,0 +1,31 @@ +{%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"> + <table class="table"> + <tbody> + <tr> + <td>Name</td> + <td>{{dataset.Name}}</td> + </tr> + + <tr> + <td>Full Name</td> + <td>{{dataset.FullName}}</td> + </tr> + + <tr> + <td>Short Name</td> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> + </div> + </div> +</div> +{%endmacro%} diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 959b02a..b136bb6 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -1,5 +1,6 @@ {%extends "phenotypes/base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} {%from "populations/macro-display-population-card.html" import display_population_card%} {%block title%}Phenotypes{%endblock%} @@ -36,10 +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> @@ -48,13 +46,20 @@ </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> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - Limit access here, according to the authorisation privileges the user has on - this dataset!</p> + + {{table_pagination(start_from, count, phenotype_count, url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id), "phenotypes")}} <table class="table"> <thead> diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 5aef6c1..99bb8e5 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -24,18 +24,101 @@ {{flash_all_messages()}} <div class="row"> - {{resource}} -</div> + <div class="panel panel-default"> + <div class="panel-heading"><strong>Basic Phenotype Details</strong></div> -<div class="row"> - <h2>Dataset</h2> - {{dataset}} + <table class="table"> + <tbody> + <tr> + <td><strong>Phenotype</strong></td> + <td>{{phenotype.Post_publication_description or phenotype.Pre_publication_abbreviation or phenotype.Original_description}} + </tr> + <tr> + <td><strong>Cross-Reference ID</strong></td> + <td>{{phenotype.xref_id}}</td> + </tr> + <tr> + <td><strong>Collation</strong></td> + <td>{{dataset.FullName}}</td> + </tr> + <tr> + <td><strong>Units</strong></td> + <td>{{phenotype.Units}}</td> + </tr> + </tbody> + </table> + + <form action="#edit-delete-phenotype" + method="POST" + id="frm-delete-phenotype"> + + <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> + <input type="hidden" name="population_id" value="{{population.Id}}" /> + <input type="hidden" name="dataset_id" value="{{dataset.Id}}" /> + <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" /> + + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <input type="submit" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary not-implemented" + value="edit" /> + {%endif%} + </div> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <input type="submit" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + value="delete" /> + {%endif%} + </div> + </div> + </form> + </div> </div> <div class="row"> - <h2>Phenotype</h2> - {{phenotype}} + <div class="panel panel-default"> + <div class="panel-heading"><strong>Phenotype Data</strong></div> + {%if "group:resource:view-resource" in privileges%} + <table class="table"> + <thead> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + <th>Symbol</th> + <th>SE</th> + <th>N</th> + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td>{{item.value}}</td> + <td>{{item.Symbol or "-"}}</td> + <td>{{item.error or "-"}}</td> + <td>{{item.count or "-"}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + You do not currently have privileges to view this phenotype in greater + detail. + </p> + {%endif%} + </div> </div> + {%endblock%} {%block sidebarcontents%} |