diff options
Diffstat (limited to 'uploader/templates')
| -rw-r--r-- | uploader/templates/base.html | 4 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes-base.html | 351 | ||||
| -rw-r--r-- | uploader/templates/publications/create-publication.html | 191 | ||||
| -rw-r--r-- | uploader/templates/publications/index.html | 13 | ||||
| -rw-r--r-- | uploader/templates/publications/view-publication.html | 74 |
5 files changed, 368 insertions, 265 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html index de9c226..3c0d0d4 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -32,7 +32,7 @@ <a href="{{url_for('oauth2.logout')}}" title="Log out of the system"> <span class="glyphicon glyphicon-user"></span> - Sign Out</a> + {{user_email()}} Sign Out</a> {%else%} <a href="{{authserver_authorise_uri()}}" title="Log in to the system">Sign In</a> @@ -154,7 +154,7 @@ <!-- local dependencies --> - <script type="text/javascript" src="/static/js/misc.js"></script> + <script type="text/javascript" src="/static/js/utils.js"></script> <script type="text/javascript" src="/static/js/datatables.js"></script> {%block javascript%}{%endblock%} </body> diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html index a2d9484..a7aaeb0 100644 --- a/uploader/templates/phenotypes/add-phenotypes-base.html +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -42,110 +42,30 @@ {%block frm_add_phenotypes_elements%}{%endblock%} - <div class="checkbox"> - <label> - <input id="chk-published" type="checkbox" name="published?" /> - These phenotypes are published</label> - </div> - - <fieldset id="fldset-publication-info" class="visually-hidden"> + <fieldset id="fldset-publication-info"> <legend>Publication Information</legend> - <div class="form-group"> - <label for="txt-pubmed-id" class="form-label">Pubmed ID</label> - <div class="input-group"> - <input id="txt-pubmed-id" name="pubmed-id" type="text" - class="form-control" /> - <span class="input-group-btn"> - <button id="btn-search-pubmed-id" class="btn btn-info">Search</button> - </span> - </div> - <span id="search-pubmed-id-error" - class="form-text text-muted text-danger visually-hidden"> - </span><br /> - <span class="form-text text-muted"> - Enter your publication's PubMed ID above and click "Search" to search - for some (or all) of the publication details requested below. - </span> - </div> - - <div class="form-group"> - <label for="txt-publication-authors" class="form-label">Authors</label> - <input id="txt-publication-authors" name="publication-authors" - type="text" class="form-control" /> - <span class="form-text text-muted"> - Enter the authors in the following format …</span> - </div> - - <div class="form-group"> - <label for="txt-publication-title" class="form-label"> - Publication Title</label> - <input id="txt-publication-title" name="publication-title" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter your publication's title.</span> - </div> - - <div class="form-group"> - <label for="txt-publication-abstract" class="form-label"> - Publication Abstract</label> - <textarea id="txt-publication-abstract" name="publication-abstract" - class="form-control" rows="10"></textarea> - <span class="form-text text-muted"> - Enter the abstract for your publication.</span> - </div> - - <div class="form-group"> - <label for="txt-publication-journal" class="form-label">Journal</label> - <input id="txt-publication-journal" name="journal" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the name of the journal where your work was published.</span> - </div> - - <div class="form-group"> - <label for="txt-publication-volume" class="form-label">Volume</label> - <input id="txt-publication-volume" name="publication-volume" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the volume in the following format …</span> - </div> - - <div class="form-group"> - <label for="txt-publication-pages" class="form-label">Pages</label> - <input id="txt-publication-pages" name="publication-pages" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the journal volume where your work was published.</span> - </div> - - <div class="form-group"> - <label for="select-publication-month" class="form-label"> - Publication Month</label> - <select id="select-publication-month" name="publication-month" - class="form-control"> - {%for month in monthnames%} - <option value="{{month | lower}}" - {%if current_month | lower == month | lower%} - selected="selected" - {%endif%}>{{month | capitalize}}</option> - {%endfor%} - </select> - <span class="form-text text-muted"> - Select the month when the work was published. - <span class="text-danger"> - This cannot be before, say 1600 and cannot be in the future!</span></span> - </div> - - <div class="form-group"> - <label for="txt-publication-year" class="form-label">Publication Year</label> - <input id="txt-publication-year" name="publication-year" type="text" - class="form-control" value="{{current_year}}" /> - <span class="form-text text-muted"> - Enter the year your work was published. - <span class="text-danger"> - This cannot be before, say 1600 and cannot be in the future!</span> - </span> - </div> + <input type="hidden" name="publication-id" id="txt-publication-id" /> + <span class="form-text text-muted"> + Select a publication for your data. <br /> + Can't find a publication you can use? Go ahead and + <a href="{{url_for( + 'publications.create_publication', + return_to='species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">create a new publication</a>.</span> + <table id="tbl-select-publication" class="table compact stripe"> + <thead> + <tr> + <th>#</th> + <th>PubMed ID</th> + <th>Title</th> + <th>Authors</th> + </tr> + </thead> + + <tbody></tbody> + </table> </fieldset> <div class="form-group"> @@ -165,165 +85,74 @@ {%block javascript%} <script type="text/javascript"> - var remove_class = (element, classvalue) => { - new_classes = (element.attr("class") || "").split(" ").map((val) => { - return val.trim(); - }).filter((val) => { - return ((val !== classvalue) && - (val !== "")) - }).join(" "); - - if(new_classes === "") { - element.removeAttr("class"); - } else { - element.attr("class", new_classes); - } - }; - - var add_class = (element, classvalue) => { - remove_class(element, classvalue); - element.attr("class", (element.attr("class") || "") + " " + classvalue); - }; - - $("#chk-published").on("click", (event) => { - pub_details = $("#fldset-publication-info") - if(event.target.checked) { - // display the publication details - remove_class(pub_details, "visually-hidden"); - } else { - // hide the publication details - add_class(pub_details, "visually-hidden"); - } - }); - - var extract_details = (pubmed_id, details) => { - var months = { - "jan": "January", - "feb": "February", - "mar": "March", - "apr": "April", - "may": "May", - "jun": "June", - "jul": "July", - "aug": "August", - "sep": "September", - "oct": "October", - "nov": "November", - "dec": "December" - }; - var _date = details[pubmed_id].pubdate.split(" "); - return { - "authors": details[pubmed_id].authors.map((authobj) => { - return authobj.name; - }), - "title": details[pubmed_id].title, - "journal": details[pubmed_id].fulljournalname, - "volume": details[pubmed_id].volume, - "pages": details[pubmed_id].pages, - "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan", - "year": _date[0], - }; - }; - - var update_publication_details = (details) => { - Object.entries(details).forEach((entry) => {; - switch(entry[0]) { - case "authors": - $("#txt-publication-authors").val(entry[1].join(", ")); - break; - case "month": - $("#select-publication-month") - .children("option") - .each((index, child) => { - child.selected = child.value == entry[1].toLowerCase(); - }); - default: - $("#txt-publication-" + entry[0]).val(entry[1]); - break; - } + $(function() { + var publicationsDataTable = buildDataTable( + "#tbl-select-publication", + [], + [ + {data: "index"}, + { + data: (pub) => { + if(pub.PubMed_ID) { + return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + + `${pub.PubMed_ID}</a>`; + } + return ""; + } + }, + { + data: (pub) => { + var title = "⸻"; + if(pub.Title) { + title = pub.Title + } + return `<a href="/publications/view/${pub.Id}" ` + + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; + } + }, + { + data: (pub) => { + authors = pub.Authors.split(",").map( + (item) => {return item.trim();}); + if(authors.length > 1) { + return authors[0] + ", et. al."; + } + return authors[0]; + } + } + ], + { + ajax: { + url: "/publications/list", + dataSrc: "publications" + }, + select: "single", + scrollY: 700, + paging: false, + deferRender: true, + layout: { + topStart: "info", + topEnd: "search" + } + }); + publicationsDataTable.on("select", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + console.debug(datatable.row(element).data()); + $("#frm-add-phenotypes #txt-publication-id").val( + datatable.row(element).data().Id); + }); + }); + publicationsDataTable.on("deselect", (event, datatable, type, indexes) => { + indexes.forEach((element, index, thearray) => { + let row = datatable.row(element).node(); + $("#frm-add-phenotypes #txt-publication-id").val(null); + }); }); - }; - - var fetch_publication_abstract = (pubmed_id, pub_details) => { - $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", - { - "method": "GET", - "data": { - "db": "pubmed", - "id": pubmed_id, - "rettype": "abstract", - "retmode": "xml" - }, - "success": (data, textStatus, jqXHR) => { - update_publication_details({ - ...pub_details, - ...{ - "abstract": Array.from(data - .getElementsByTagName( - "Abstract")[0] - .children) - .map((elt) => {return elt.textContent.trim();}) - .join("\r\n") - }}); - }, - "error": (jqXHR, textStatus, errorThrown) => {}, - "complete": (jqXHR, textStatus) => {}, - "dataType": "xml" - }); - }; - - var fetch_publication_details = (pubmed_id, complete_thunks) => { - error_display = $("#search-pubmed-id-error"); - error_display.text(""); - add_class(error_display, "visually-hidden"); - $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", - { - "method": "GET", - "data": {"db": "pubmed", "id": pubmed_id, "format": "json"}, - "success": (data, textStatus, jqXHR) => { - // process and update publication details - hasError = ( - Object.hasOwn(data, "error") || - Object.hasOwn(data.result[pubmed_id], "error")); - if(hasError) { - error_display.text( - "There was an error fetching a publication with " + - "the given PubMed ID! The error received " + - "was: '" + ( - data.error || - data.result[pubmed_id].error) + - "'. Please check ID you provided and try " + - "again."); - remove_class(error_display, "visually-hidden"); - } else { - fetch_publication_abstract( - pubmed_id, - extract_details(pubmed_id, data.result)); - } - }, - "error": (jqXHR, textStatus, errorThrown) => {}, - "complete": () => { - complete_thunks.forEach((thunk) => {thunk()}); - }, - "dataType": "json" - }); - }; - - $("#btn-search-pubmed-id").on("click", (event) => { - event.preventDefault(); - var search_button = event.target; - var pubmed_id = $("#txt-pubmed-id").val().trim(); - remove_class($("#txt-pubmed-id").parent(), "has-error"); - if(pubmed_id == "") { - add_class($("#txt-pubmed-id").parent(), "has-error"); - return false; - } - - search_button.disabled = true; - // Fetch publication details - fetch_publication_details(pubmed_id, - [() => {search_button.disabled = false;}]); - return false; }); </script> diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html new file mode 100644 index 0000000..3f828a9 --- /dev/null +++ b/uploader/templates/publications/create-publication.html @@ -0,0 +1,191 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <form id="frm-create-publication" + method="POST" + action="{{url_for('publications.create_publication', **request.args)}}" + class="form-horizontal"> + + <div class="row mb-3"> + <label for="txt-pubmed-id" class="col-sm-2 col-form-label"> + PubMed ID</label> + <div class="col-sm-10"> + <div class="input-group"> + <input type="text" + id="txt-pubmed-id" + name="pubmed-id" + class="form-control"/> + <div class="input-group-text"> + <button class="btn btn-outline-primary" + id="btn-search-pubmed-id">search</button> + </div> + </div> + <span id="search-pubmed-id-error" + class="form-text text-muted text-danger visually-hidden"> + </span> + <span class="form-text text-muted">This is the publication's ID on + <a href="https://pubmed.ncbi.nlm.nih.gov/" + title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a> + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-title" class="col-sm-2 col-form-label"> + Title</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-title" + name="publication-title" + class="form-control" /> + <span class="form-text text-muted">Provide the publication's title here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-authors" class="col-sm-2 col-form-label"> + Authors</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-authors" + name="publication-authors" + required="required" + class="form-control" /> + <span class="form-text text-muted"> + A publication <strong>MUST</strong> have an author. You <em>must</em> + provide a value for the authors field. + </span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-journal" class="col-sm-2 col-form-label"> + Journal</label> + <div class="col-sm-10"> + <input type="text" + id="txt-publication-journal" + name="publication-journal" + class="form-control" /> + <span class="form-text text-muted">Provide the name journal where the + publication was done, here.</span> + </div> + </div> + + <div class="row mb-3"> + <label for="select-publication-month" + class="col-sm-2 col-form-label"> + Month</label> + <div class="col-sm-4"> + <select class="form-control" + id="select-publication-month" + name="publication-month"> + <option value="">Select a month</option> + <option value="january">January</option> + <option value="february">February</option> + <option value="march">March</option> + <option value="april">April</option> + <option value="may">May</option> + <option value="june">June</option> + <option value="july">July</option> + <option value="august">August</option> + <option value="september">September</option> + <option value="october">October</option> + <option value="november">November</option> + <option value="december">December</option> + </select> + <span class="form-text text-muted">Month of publication</span> + </div> + + <label for="txt-publication-year" + class="col-sm-2 col-form-label"> + Year</label> + <div class="col-sm-4"> + <input type="number" + id="txt-publication-year" + name="publication-year" + class="form-control" + min="1960" /> + <span class="form-text text-muted">Year of publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-publication-volume" + class="col-sm-2 col-form-label"> + Volume</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-volume" + name="publication-volume" + class="form-control"> + <span class="form-text text-muted">Journal volume</span> + </div> + + <label for="txt-publication-pages" + class="col-sm-2 col-form-label"> + Pages</label> + <div class="col-sm-4"> + <input type="text" + id="txt-publication-pages" + name="publication-pages" + class="form-control" /> + <span class="form-text text-muted">Journal pages for the publication</span> + </div> + </div> + + <div class="row mb-3"> + <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" + name="publication-abstract" + class="form-control" + rows="7"></textarea> + </div> + </div> + + <div class="row mb-3"> + <div class="col-sm-2"></div> + <div class="col-sm-8"> + <input type="submit" class="btn btn-primary" value="Add" /> + <input type="reset" class="btn btn-danger" /> + </div> + </div> + +</form> +</div> + +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/pubmed.js"></script> +<script type="text/javascript"> + $(function() { + $("#btn-search-pubmed-id").on("click", (event) => { + event.preventDefault(); + var search_button = event.target; + var pubmed_id = $("#txt-pubmed-id").val().trim(); + remove_class($("#txt-pubmed-id").parent(), "has-error"); + if(pubmed_id == "") { + add_class($("#txt-pubmed-id").parent(), "has-error"); + return false; + } + + search_button.disabled = true; + // Fetch publication details + fetch_publication_details(pubmed_id, + [() => {search_button.disabled = false;}]); + return false; + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/publications/index.html b/uploader/templates/publications/index.html index f6f6fa0..f846d54 100644 --- a/uploader/templates/publications/index.html +++ b/uploader/templates/publications/index.html @@ -9,6 +9,12 @@ {%block contents%} {{flash_all_messages()}} +<div class="row" style="padding-bottom: 1em;"> + <a href="{{url_for('publications.create_publication')}}" + class="btn btn-primary"> + add new publication</a> +</div> + <div class="row"> <table id="tbl-list-publications" class="table compact stripe"> <thead> @@ -38,7 +44,8 @@ data: (pub) => { if(pub.PubMed_ID) { return `<a href="https://pubmed.ncbi.nlm.nih.gov/` + - `${pub.PubMed_ID}/" target="_blank">` + + `${pub.PubMed_ID}/" target="_blank" ` + + `title="Link to publication on NCBI.">` + `${pub.PubMed_ID}</a>`; } return ""; @@ -51,7 +58,9 @@ title = pub.Title } return `<a href="/publications/view/${pub.Id}" ` + - `target="_blank">${title}</a>`; + `target="_blank" ` + + `title="Link to view publication details">` + + `${title}</a>`; } }, { diff --git a/uploader/templates/publications/view-publication.html b/uploader/templates/publications/view-publication.html new file mode 100644 index 0000000..5b93434 --- /dev/null +++ b/uploader/templates/publications/view-publication.html @@ -0,0 +1,74 @@ +{%extends "publications/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}View Publication{%endblock%} + +{%block pagetitle%}View Publication{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <table class="table"> + <tr> + <th>PubMed</th> + <td> + {%if publication.PubMed_ID%} + <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/" + target="_blank">{{publication.PubMed_ID}}</a> + {%else%} + — + {%endif%} + </td> + </tr> + <tr> + <th>Title</th> + <td>{{publication.Title or "—"}}</td> + </tr> + <tr> + <th>Authors</th> + <td>{{publication.Authors or "—"}}</td> + </tr> + <tr> + <th>Journal</th> + <td>{{publication.Journal or "—"}}</td> + </tr> + <tr> + <th>Published</th> + <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td> + </tr> + <tr> + <th>Volume</th> + <td>{{publication.Volume or "—"}}</td> + </tr> + <tr> + <th>Pages</th> + <td>{{publication.Pages or "—"}}</td> + </tr> + <tr> + <th>Abstract</th> + <td>{{publication.Abstract or "—"}}</td> + </tr> + </table> +</div> + +<div class="row"> + <form id="frm-edit-delete-publication" method="POST" action="#"> + <input type="hidden" name="publication_id" value="{{publication.Id}}" /> + <div class="form-group"> + <input type="submit" value="edit" class="btn btn-primary not-implemented" /> + {%if linked_phenotypes | length == 0%} + <input type="submit" value="delete" class="btn btn-danger not-implemented" /> + {%endif%} + </div> + </form> +</div> +{%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() {}); +</script> +{%endblock%} |