Move functions to fetch pubmed data out into a separate js file.

1 files changed, 113 insertions, 0 deletions

diff --git a/uploader/static/js/pubmed.js b/uploader/static/js/pubmed.js
new file mode 100644
index 0000000..9afd4c3
--- /dev/null
+++ b/uploader/static/js/pubmed.js
@@ -0,0 +1,113 @@
+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) => {
+                                                            console.debug(entry[1].toLowerCase());
+                                                            child.selected = child.value == entry[1].toLowerCase();
+                                                        });
+                                                default:
+                                                    $("#txt-publication-" + entry[0]).val(entry[1]);
+                                                    break;
+                                                }
+                                               });
+};
+
+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"
+           });
+};