diff options
Diffstat (limited to 'uploader/templates/phenotypes/add-phenotypes-base.html')
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes-base.html | 129 |
1 files changed, 72 insertions, 57 deletions
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html index b3a53b0..97b55f2 100644 --- a/uploader/templates/phenotypes/add-phenotypes-base.html +++ b/uploader/templates/phenotypes/add-phenotypes-base.html @@ -30,7 +30,9 @@ action="{{url_for('species.populations.phenotypes.add_phenotypes', species_id=species.SpeciesId, population_id=population.Id, - dataset_id=dataset.Id)}}"> + dataset_id=dataset.Id, + use_bundle=use_bundle)}}" + data-resumable-target="{{url_for('files.resumable_upload_post')}}"> <legend>Add New Phenotypes</legend> <div class="form-text help-block"> @@ -57,6 +59,9 @@ <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 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. @@ -114,7 +119,7 @@ </div> <div class="form-group"> - <label for="txt-publication-month" class="form-label"> + <label for="select-publication-month" class="form-label"> Publication Month</label> <select id="select-publication-month" name="publication-month" class="form-control"> @@ -157,10 +162,6 @@ {%endblock%} -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} - {%block javascript%} <script type="text/javascript"> @@ -219,13 +220,12 @@ "journal": details[pubmed_id].fulljournalname, "volume": details[pubmed_id].volume, "pages": details[pubmed_id].pages, - "month": months[_date[1].toLowerCase()], + "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan", "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": @@ -244,41 +244,7 @@ }); }; - 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 + var fetch_publication_abstract = (pubmed_id, pub_details) => { $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", { "method": "GET", @@ -289,25 +255,74 @@ "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") - }); + ...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) => { - flag_pub_abstract = true; - enable_button(); - }, + "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, "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, "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> |