--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common.js	Wed Aug 30 14:21:18 2023 +0000
@@ -0,0 +1,304 @@
+
+this.ctx = () => context;
+var all_contexts = [] ;
+var inchidata = {} ;
+var all_mix_data = {} ;
+var already_sent_data = {} ;
+
+function no_success(tab_index, inchi, data) {
+  console.log(`inchikey ${inchi} not found...`) ;
+  console.log(`disabling ${data} ...`)
+  disable_tab(
+    tab_index,
+    "red",
+    "This compound has not been found on peakforest"
+  ) ;
+}
+
+function disable_tab(tab_index, color, title) {
+  var element = $(`#open_tab_${tab_index}`) ;
+  element.attr("disabled", "disabled").off("click");
+  element.attr("onclick", null) ;
+  element.attr("title", title) ;
+  element.attr("data-toggle", null) ;
+  element.attr("href", null) ;
+  element.css("color", color) ;
+  element.css("cursor", "not-allowed") ;
+}
+
+function successfull_send_to_pf(bundle, json, index) {
+  for (var i = 0 ; i < all_contexts.length ; i += 1) {
+    if (all_contexts[i] === null || all_contexts[i] === undefined) {
+      continue ;
+    }
+    if (all_contexts[i].inchikey == bundle["sample"]["inchikey"]) {
+      disable_tab(
+        all_contexts[i].tab_index,
+        "green",
+        "This compound has already been sent to peakforest"
+      )
+    }
+  }
+  if (already_sent_data[index] == null) {
+    already_sent_data[index] = [] ;
+  }
+  json.forEach((id) => {
+    already_sent_data[index].push(id)
+    $("#send_buttons_div").prepend(`
+    <div class="row">
+      <div class="col-lg-3">
+        <div class="alert alert-success alert-dismissible" role="alert">
+          <button type="button" class="close" data-dismiss="alert">
+            <span aria-hidden="true">×</span>
+            <span class="sr-only">
+              <spring:message code="alert.close" text="Close"></spring:message>
+            </span>
+          </button>
+          <strong>
+            <spring:message code="alert.strong.info" text="Success!"></spring:message>
+          </strong> Spectrum has been sent:
+          <a
+            href="${ctx().peakforest_url}/webapp/home?PFs=${id.slice(3)}"
+            target="_blank"
+          >${id}</a>
+        </div>
+      </div>
+    </div>`)
+  })
+}
+
+function failed_send_to_pf(err, bundle) {
+  console.log(err) ;
+  $("#send_buttons_div").prepend(`
+  <div class="row">
+    <div class="col-lg-3">
+      <div class="alert alert-error alert-dismissible" role="alert">
+        <button type="button" class="close" data-dismiss="alert">
+          <span aria-hidden="true">×</span>
+          <span class="sr-only">
+            <spring:message code="alert.close" text="Close"></spring:message>
+          </span>
+        </button>
+        <strong>
+          <spring:message code="alert.strong.info" text="Error!"></spring:message>
+        </strong> Spectrum has not been sent!
+      </div>
+    </div>
+  </div>`)
+}
+
+function already_sent(bundle, index) {
+  return already_sent_data[index] != null ;
+}
+
+function failed_already_sent(bundle, index) {
+  already_sent_data[index].forEach((id) => {
+    $("#send_buttons_div").prepend(`
+    <div class="row">
+      <div class="col-lg-3">
+        <div class="alert alert-warning alert-dismissible" role="alert">
+          <button type="button" class="close" data-dismiss="alert">
+            <span aria-hidden="true">×</span>
+            <span class="sr-only">
+              <spring:message code="alert.close" text="Close"></spring:message>
+            </span>
+          </button>
+          <strong>
+            <spring:message code="alert.strong.info" text="warning!"></spring:message>
+          </strong> Spectrum has already been sent:
+          <a
+            href="${ctx().peakforest_url}/webapp/home?PFs=${id.slice(3)}"
+            target="_blank"
+          >${id}</a>
+        </div>
+      </div>
+    </div>`)
+  }) ;
+}
+
+function send_everything_to_peakforest(url, token) {
+  var bundles ;
+  if (context.is_mix()) {
+    bundles = [all_mix_data] ;
+  } else {
+    bundles = create_dataset_bundles() ;
+  }
+  bundles.forEach((bundle, index) => {
+    if (already_sent(bundle, index)) {
+      return failed_already_sent(bundle, index) ;
+    }
+    console.log(bundle)
+    $.ajax({
+      type: "post",
+      url: `${url}/rest/v2/spectrum?token=${token}`,
+      data: JSON.stringify(bundle),
+      contentType: "application/json",
+      success: function(json) {
+        successfull_send_to_pf(bundle, json, index)
+      }, error: function(err) {
+        failed_send_to_pf(err, bundle)
+      }
+    })
+    $.ajax({
+      type: "post",
+      url: "/",
+      data: `{"index": ${index}, "object": ${JSON.stringify(bundle)}}`,
+      contentType: "application/json",
+      error: function(err) {
+        console.log(`Error: JSON will not be produced by the application.`)
+      }
+    })
+  })
+  // console.log(bundles)
+}
+
+function create_dataset_bundles() {
+  var bundles = [] ;
+  var data ;
+  all_contexts.forEach((context, index) => {
+    if ((data = context.sent_json) === null) {
+      return ;
+    }
+    if (bundles.length === 0) {
+      // console.log("First metadata!")
+      return bundles.push(data) ;
+    }
+    if (merge_in_bundle(bundles, data)) {
+      // console.log("Merged!")
+    } else {
+      // console.log("New metadata!")
+    }
+  }) ;
+  return bundles ;
+}
+
+function merge_in_bundle(bundles, data) {
+  for(var i = 0 ; i < bundles.length ; i += 1) {
+    if (
+      identical(bundles[i]["sample"], data["sample"])
+      && identical(bundles[i]["chromatography"], data["chromatography"])
+      && identical(bundles[i]["analyzer"], data["analyzer"])
+      && identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
+      && identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
+      && identical(bundles[i]["other_metadata"], data["other_metadata"])
+    ) {
+      bundles[i]["peaklists"].push(data["peaklists"][0]) ;
+      return true ;
+    } else {
+      continue ;
+      console.log(
+        "sample: "
+        + identical(bundles[i]["sample"], data["sample"])
+      )
+      console.log(
+        "chromatography: "
+        + identical(bundles[i]["chromatography"], data["chromatography"])
+      )
+      console.log(
+        "analyzer: "
+        + identical(bundles[i]["analyzer"], data["analyzer"])
+      )
+      console.log(
+        "ionization_mode_positive: "
+        + identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
+      )
+      console.log(
+        "ionization_mode_negative: "
+        + identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
+      )
+      console.log(
+        "other_metadata: "
+        + identical(bundles[i]["other_metadata"], data["other_metadata"])
+      )
+    }
+  }
+  bundles.push(data) ;
+  return false ;
+}
+
+function identical(left, right) {
+  if (typeof left !== typeof right) {
+    return false ;
+  }
+  if (left === null) {
+    return right === null ;
+  }
+  if (right === null) {
+    return left === null ;
+  }
+  switch (typeof left) {
+    case "array":
+      return identical_array(left, right) ;
+      break ;
+    case "object":
+      return identical_object(left, right) ;
+      break ;
+    default:
+      break ;
+  }
+  return (left === right)
+}
+
+function identical_array(left, right) {
+  if (right.length !== left.length) {
+    return false ;
+  }
+  for(var i = 0 ; i < left.length ; i += 1) {
+    if (!identical(left[i], right[i])) {
+      return false ;
+    }
+  }
+  return true ;
+}
+
+function identical_object(left, right) {
+  var left_keys ;
+
+  if (!(
+    share_keys(left, right)
+    && share_keys(right, left)
+  )) {
+    return true ;
+  }
+  left_keys = Object.keys(left) ;
+  for (var i = 0 ; i < left_keys.length ; i += 1){
+    if (!identical(left[left_keys[i]], right[left_keys[i]])) {
+      return false ;
+    }
+  }
+  return true ;
+}
+
+function share_keys(left, right) {
+  var left_keys ;
+  var right_keys ;
+
+  left_keys = Object.keys(left) ;
+  right_keys = Object.keys(right) ;
+  for(var i = 0 ; i < left_keys.length ; i += 1) {
+    if (!right_keys.includes(left_keys[i])) {
+      return false ;
+    }
+  }
+  return true ;
+}
+
+var set_inchi_data = function(data, tab_index) {
+  inchidata[data.inchikey] = data ;
+  $(`#add1spectrum-sample-inchi-${tab_index}`).val(data.inchi);
+  $(`#add1spectrum-sample-inchi-${tab_index}`).change();
+  $(`#add1spectrum-sample-commonName-${tab_index}`).val(data.name);
+  $(`#add1spectrum-sample-commonName-${tab_index}`).change();
+  $(`#sample-bonus-display-${tab_index}`).html(
+    `<img
+      class=""
+      src="{{ PF_URL_PLACEHOLDER }}/webapp/image/${data.type}/${data.inchikey}"
+      alt="${data.name}"
+    >`
+  );
+}
+
+var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) {
+  Handsontable.renderers.TextRenderer.apply(this, arguments);
+  td.style.backgroundColor = "#EEE";
+}