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| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes-base.html | 314 |
1 files changed, 314 insertions, 0 deletions
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html new file mode 100644 index 0000000..7de3fc8 --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -0,0 +1,314 @@ +{%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"> + {%block frm_add_phenotypes_documentation%}{%endblock%} + <p><strong class="text-warning">This will not update any existing phenotypes!</strong></p> + </div> + + {%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="hidden"> + <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 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="txt-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> + </fieldset> + + <div class="form-group"> + <input type="submit" + value="upload phenotypes" + class="btn btn-primary" /> + </div> + </form> +</div> + +<div class="row"> + {%block page_documentation%}{%endblock%} +</div> + +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} + + +{%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, "hidden"); + } else { + // hide the publication details + add_class(pub_details, "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": months[_date[1].toLowerCase()], + "year": _date[0], + }; + }; + + var update_publication_details = (details) => { + console.log("Updating with the following 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; + } + }); + }; + + var freds_variable = undefined; + $("#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; + } + + var flag_pub_details = false; + var flag_pub_abstract = false; + var enable_button = () => { + search_button.disabled = !(flag_pub_details && flag_pub_abstract); + }; + search_button.disabled = true; + // Fetch publication details + $.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 + update_publication_details(extract_details( + pubmed_id, data.result)); + }, + "error": (jqXHR, textStatus, errorThrown) => {}, + "complete": () => { + flag_pub_details = true; + enable_button(); + }, + "dataType": "json" + }); + // Fetch the abstract + $.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) => { + // process and update the abstract... + freds_variable = data; + console.log("ABSTRACT DETAILS:", data); + update_publication_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) => { + flag_pub_abstract = true; + enable_button(); + }, + "dataType": "xml" + }); + return false; + }); +</script> +{%endblock%} |