705420e703b067fbcad43ab67ed3e131552e7ac8
angie
  Wed Apr 24 14:23:03 2024 -0700
Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type.
Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files.
nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen.
SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups.
Presentation is still kinda rough, just a loop on the original results output.
The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).

diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c
index ec9739c..4f96671 100644
--- src/hg/hgPhyloPlace/hgPhyloPlace.c
+++ src/hg/hgPhyloPlace/hgPhyloPlace.c
@@ -1,53 +1,53 @@
 /* hgPhyloPlace - Upload SARS-CoV-2 or MPXV sequence for placement in phylo tree. */
 
-/* Copyright (C) 2020-2022 The Regents of the University of California */
+/* Copyright (C) 2020-2024 The Regents of the University of California */
 
 #include "common.h"
 #include "botDelay.h"
 #include "cart.h"
 #include "cgiApoptosis.h"
 #include "cheapcgi.h"
 #include "hCommon.h"
 #include "hash.h"
 #include "hgConfig.h"
 #include "htmshell.h"
 #include "hui.h"
 #include "jsHelper.h"
 #include "knetUdc.h"
 #include "linefile.h"
 #include "md5.h"
 #include "net.h"
 #include "options.h"
 #include "phyloPlace.h"
 #include "portable.h"
 #include "trackLayout.h"
 #include "udc.h"
 #include "web.h"
 #include "wikiLink.h"
 
 /* Global Variables */
 struct cart *cart = NULL;      // CGI and other variables
 struct hash *oldVars = NULL;   // Old contents of cart before it was updated by CGI
 boolean measureTiming = FALSE; // Print out how long things take
-char *leftLabelWidthForLongNames = "55";// Leave plenty of room for tree and long virus strain names
 
 /* for botDelay call, 10 second for warning, 20 second for immediate exit */
 #define delayFraction   0.25
 static boolean issueBotWarning = FALSE;
 static long enteredMainTime = 0;
 
+#define orgVar "hgpp_org"
 #define seqFileVar "sarsCoV2File"
 #define pastedIdVar "namesOrIds"
 #define remoteFileVar "remoteFile"
 #define serverCommandVar "hgpp_serverCommand"
 #define serverCommentVar "hgpp_serverComment"
 #define serverPlainVar "hgpp_serverPlain"
 #define serverSaltyVar "hgpp_serverSalty"
 
 static struct lineFile *lineFileFromFileInput(struct cart *cart, char *fileVar)
 /* Return a lineFile on data from an uploaded file with cart variable name fileVar.
  * If the file is binary, attempt to decompress it.  Return NULL if no data are found
  * or if there is a problem decompressing binary data.  If retFileName is not NULL */
 {
 struct lineFile *lf = NULL;
 // Depending on whether the file is plain text or binary, different cart variables are present.
@@ -67,115 +67,68 @@
 else if (isNotEmpty(fileBinaryCoords))
     {
     fprintf(stderr, "%s=%s fileBinaryCoords=%s\n", cartVar, fileName, fileBinaryCoords);
     char *binInfo = cloneString(fileBinaryCoords);
     char *words[2];
     char *mem;
     unsigned long size;
     chopByWhite(binInfo, words, ArraySize(words));
     mem = (char *)sqlUnsignedLong(words[0]);
     size = sqlUnsignedLong(words[1]);
     lf = lineFileDecompressMem(TRUE, mem, size);
     }
 return lf;
 }
 
-static char *labelForDb(char *db, boolean addDescription)
-/* If config defines a user-friendly name then return that; otherwise return hGenome(db).
- * If addDescription is set and config defines a description then tack that on. */
-{
-char *label = phyloPlaceDbSetting(db, "name");
-if (isEmpty(label))
-    label = hGenome(db);
-if (addDescription)
-    {
-    char *desc = phyloPlaceDbSetting(db, "description");
-    if (isNotEmpty(desc))
-        {
-        struct dyString *dy = dyStringCreate("%s %s", label, desc);
-        label = dyStringCannibalize(&dy);
-        }
-    }
-return label;
-}
-
-static int labelCmp(const void *va, const void *vb)
-/* Compare two slPairs on their string values -- but treat SARS-CoV-2 as more important. */
-{
-const struct slPair *a = *((struct slPair **)va);
-const struct slPair *b = *((struct slPair **)vb);
-if (sameString((char *)(a->val), "SARS-CoV-2"))
-    return -1;
-else if (sameString((char *)(b->val), "SARS-CoV-2"))
-    return 1;
-return strcmp((char *)(a->val), (char *)(b->val));
-}
-
-
-static struct slName *sortByLabel(struct slName *dbList)
-/* Return a newly allocated version of dbList, sorted by labelForDb value -- but favor SARS-CoV-2. */
-{
-struct slPair *dbLabelList = NULL;
-struct slName *sln;
-for (sln = dbList;  sln != NULL;  sln = sln->next)
-    slPairAdd(&dbLabelList, sln->name, cloneString(labelForDb(sln->name, TRUE)));
-slSort(&dbLabelList, labelCmp);
-struct slName *newList = NULL;
-struct slPair *slp;
-for (slp = dbLabelList;  slp != NULL;  slp = slp->next)
-    slAddHead(&newList, slNameNew(slp->name));
-slReverse(&newList);
-slPairFreeValsAndList(&dbLabelList);
-return newList;
-}
-
-static void selectDb(char **pDb, char **pLabel)
-/* Search for assembly config.ra files in hgPhyloPlaceData.  If there is more than one
- * supported assembly, then make a menu / select input for supported  assemblies;
+static void selectOrg(char **pOrg, char **pLabel)
+/* Search for config files in hgPhyloPlaceData.  If there is more than one
+ * supported organism, then make a menu / select input for supported organisms;
  * reload the page on change. */
 {
-struct slName *supportedDbs = sortByLabel(phyloPlaceDbList(cart));
-if (supportedDbs == NULL)
+struct slPair *orgLabelList = phyloPlaceOrgList(cart);
+if (orgLabelList == NULL)
     errAbort("Sorry, this server is not configured to perform phylogenetic placement.");
-if (!slNameInList(supportedDbs, *pDb))
+if (!slPairFind(orgLabelList, *pOrg))
     {
-    *pDb = cloneString(supportedDbs->name);
+    *pOrg = cloneString(orgLabelList->name);
     }
-*pLabel = labelForDb(*pDb, FALSE);
-char *selectVar = "hpp_ref";
-int supportedDbCount = slCount(supportedDbs);
-if (supportedDbCount > 1)
+*pLabel = phyloPlaceOrgSetting(*pOrg, "name");
+if (isEmpty(*pLabel))
+    *pLabel = *pOrg;
+char *selectVar = orgVar;
+int orgCount = slCount(orgLabelList);
+if (orgCount > 1)
     {
-    char *labels[supportedDbCount];
-    char *values[supportedDbCount];
-    struct slName *sDb;
+    char *labels[orgCount];
+    char *values[orgCount];
+    struct slPair *orgLabel;
     int i;
-    for (sDb = supportedDbs, i = 0;  i < supportedDbCount;  sDb = sDb->next, i++)
+    for (orgLabel = orgLabelList, i = 0;  i < orgCount;  orgLabel = orgLabel->next, i++)
         {
-        values[i] = sDb->name;
-        labels[i] = labelForDb(values[i], TRUE);
+        values[i] = orgLabel->name;
+        labels[i] = orgLabel->val;
         }
     struct dyString *dy = jsOnChangeStart();
     jsDropDownCarryOver(dy, selectVar);
     char *js = jsOnChangeEnd(&dy);
     puts("<p>Choose your pathogen: ");
-    cgiMakeDropListFull(selectVar, labels, values, supportedDbCount, *pDb, "change", js);
+    cgiMakeDropListFull(selectVar, labels, values, orgCount, *pOrg, "change", js);
     puts("</p>");
     }
 else
-    cgiMakeHiddenVar(selectVar, *pDb);
-slNameFreeList(&supportedDbs);
+    cgiMakeHiddenVar(selectVar, *pOrg);
+slPairFreeList(&orgLabelList);
 }
 
 static void newPageStartStuff()
 {
 // Copied these from hgGtexTrackSettings.c which says "// NOTE: This will likely go to web.c".
 puts("<link rel='stylesheet' href='../style/gb.css'>");
 puts("<link rel='stylesheet' href='../style/hgGtexTrackSettings.css'>");
 
 //#*** TODO: move this out to a CSS (hardcoding for now because we're doing a standalone push
 //#*** independent of the release cycle).
 puts("<style>\n"
 "#warnBox {\n"
 "    border: 3px ridge DarkRed;\n"
 "    width:640px;\n"
 "    padding:10px; \n"
@@ -275,141 +228,141 @@
     "{ var $fileInput = $('input[name="fileVarName"]');" \
     "  var $pasteInput = $('textarea[name="pasteVarName"]');" \
     "  if ($fileInput && $fileInput[0] && $fileInput[0].files && !$fileInput[0].files.length &&" \
     "      $pasteInput && !$pasteInput.val()) {" \
     "     alert('Please either choose a file or paste in sequence names/IDs first, ' +" \
     "           'and then click the upload button.');" \
     "     return false; " \
     "   } else if ($fileInput && $fileInput[0] && $fileInput[0].files && " \
     "              !!$fileInput[0].files.length &&" \
     "              $pasteInput && !!$pasteInput.val()) {" \
     "     alert('Sorry, unable to process both a file and pasted-in sequence names/IDs at the ' +" \
     "            'same time.  Please clear one or the other and then click the upload button.');" \
     "     return false; " \
     "   } else { loadingImage.run(); return true; } }"
 
-static void inputForm(char *db)
+static void inputForm(char *org)
 /* Ask the user for FASTA or VCF. */
 {
 printf("<form action='%s' name='mainForm' method=POST enctype='multipart/form-data'>\n\n",
        "hgPhyloPlace");
 cartSaveSession(cart);
 puts("<div class='readableWidth'>");
 puts("  <div class='gbControl col-md-12'>");
 puts("<div style='font-size: 20px; font-weight: 500; margin-top: 15px; margin-bottom: 10px;'>"
      "Place your sequences in a global phylogenetic tree</div>");
-// If db is not a supported db then switch to the default supported db, and if multiple dbs are
-// supported then make a menu so the user can select.
 char *label = NULL;
-selectDb(&db, &label);
+selectOrg(&org, &label);
 printf("<p>Select your FASTA, VCF or list of sequence names/IDs: ");
 printf("<input type='file' id='%s' name='%s'>",
        seqFileVar, seqFileVar);
 printf("</p><p>or paste in sequence names/IDs:<br>\n");
 cgiMakeTextArea(pastedIdVar, "", 10, 70);
-struct treeChoices *treeChoices = loadTreeChoices(db);
-if (treeChoices)
+if (phyloPlaceOrgSetting(org, "nextcladeIndex") == NULL)
     {
+    // This is not a multi-reference organism, this is an old-style single-reference setup for
+    // which the user can directly choose the tree (i.e. SARS-CoV-2).
+    struct treeChoices *treeChoices = loadTreeChoices(org, org);
     puts("</p><p>");
     printf("Phylogenetic tree version: ");
     char *phyloPlaceTree = cartOptionalString(cart, "phyloPlaceTree");
     cgiMakeDropListWithVals("phyloPlaceTree", treeChoices->descriptions, treeChoices->protobufFiles,
                             treeChoices->count, phyloPlaceTree);
     }
 puts("</p><p>");
 printf("Number of samples per subtree showing sample placement: ");
 int subtreeSize = cartUsualInt(cart, "subtreeSize", 50);
 struct dyString *dy = dyStringCreate("Number of samples in subtree showing neighborhood of "
                                      "placement (max: %d", MAX_SUBTREE_SIZE);
 if (microbeTraceHost() != NULL)
     dyStringPrintf(dy, "; max for MicrobeTrace: %d)", MAX_MICROBETRACE_SUBTREE_SIZE);
 else
     dyStringAppend(dy, ")");
 cgiMakeIntVarWithLimits("subtreeSize", subtreeSize, dy->string, 5, 10, MAX_SUBTREE_SIZE);
 puts("</p><p>");
 cgiMakeOnClickSubmitButton(CHECK_FILE_OR_PASTE_INPUT_JS(seqFileVar, pastedIdVar),
                            "submit", "Upload");
-char *exampleFile = phyloPlaceDbSettingPath(db, "exampleFile");
+char *exampleFile = phyloPlaceOrgSettingPath(org, "exampleFile");
 if (isNotEmpty(exampleFile))
     {
     puts("&nbsp;&nbsp;");
     cgiMakeOnClickSubmitButton("{ loadingImage.run(); return true; }",
                                "exampleButton", "Upload Example File");
-    if (sameString(db, "wuhCor1"))
+    if (sameString(org, "wuhCor1"))
         {
         puts("&nbsp;&nbsp;");
         puts("<a href='https://github.com/russcd/USHER_DEMO/' target=_blank>More example files</a>");
         }
     }
 puts("</p>");
 // Add a loading image to reassure people that we're working on it when they upload a big file
 printf("<div><img id='loadingImg' src='../images/loading.gif' />\n");
 printf("<span id='loadingMsg'></span></div>\n");
 jsInline("$(document).ready(function() {\n"
          "    loadingImage.init($('#loadingImg'), $('#loadingMsg'), "
          "'<p style=\"color: red; font-style: italic;\">Uploading and processing your sequences "
          "may take some time. Please leave this window open while we work on your sequences.</p>');"
          "});\n");
 
 puts("  </div>");
 puts("</div>");
 puts("<div class='readableWidth'>");
 puts("  <div class='gbControl col-md-12'>");
 puts("<h2>More information</h2>");
 printf("<p>Upload your %s sequence (FASTA or VCF file) to find the most similar\n"
        "complete, high-coverage samples from \n", label);
-if (sameString(db, "wuhCor1"))
+if (sameString(org, "wuhCor1"))
     {
     puts("<a href='https://www.gisaid.org/' target='_blank'>GISAID</a>\n"
          "or from public sequence databases (INSDC: GenBank/ENA/DDBJ accessed using "
          "<a href='https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049' "
          "target=_blank>NCBI Virus</a>,\n"
          "<a href='https://www.cogconsortium.uk/data/' target=_blank>COG-UK</a> and the\n"
          "<a href='https://bigd.big.ac.cn/ncov/release_genome' "
          "target=_blank>China National Center for Bioinformation</a>), "
          "and your sequence's placement in the phylogenetic tree generated by the\n"
          "<a href='https://github.com/roblanf/sarscov2phylo' target='_blank'>sarscov2phylo</a>\n"
          "pipeline.\n");
     }
 else
     {
-    //#*** TODO get NCBI link from db not hardcoded
+    //#*** TODO get NCBI Virus link that is not hardcoded to MPXV
     puts("public sequence databases (INSDC: GenBank/ENA/DDBJ accessed using "
          "<a href='https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Monkeypox%20virus%20(monkeypox),%20taxid:10244' "
          "target=_blank>NCBI Virus</a>)\n"
          "and your sequence's placement in a global phylogenetic tree.\n"
          );
     }
 puts("Placement is performed by\n"
      "<a href='https://github.com/yatisht/usher' target=_blank>"
      "Ultrafast Sample placement on Existing tRee (UShER)</a> "
      "(<a href='https://www.nature.com/articles/s41588-021-00862-7' target=_blank>"
      "Turakhia <em>et al.</em></a>).  UShER also generates local subtrees to show samples "
      "in the context of the most closely related sequences.  The subtrees can be visualized "
      "as Genome Browser custom tracks and/or using "
      "<a href='https://nextstrain.org' target=_blank>Nextstrain</a>'s interactive display "
      "which supports "
      "<a href='"NEXTSTRAIN_DRAG_DROP_DOC"' "
      "target=_blank>drag-and-drop</a> of local metadata that remains on your computer.\n");
 if (microbeTraceHost())
     printf("If the subtree size is set to %d or smaller, then subtrees can also be visualized in "
            "<a href='https://github.com/CDCgov/MicrobeTrace/wiki' target=_blank>MicrobeTrace</a>, "
            "a network visualization tool that integrates and overlays genomic, laboratory, and "
            "epidemiologic data and offers multiple visualization options of your combined data.\n",
            MAX_MICROBETRACE_SUBTREE_SIZE);
 puts("</p>");
-if (sameString(db, "wuhCor1"))
+if (sameString(org, "wuhCor1"))
     {
     puts("<p>\n"
          "GISAID data displayed in the Genome Browser are subject to GISAID's\n"
          "<a href='https://www.gisaid.org/registration/terms-of-use/' target=_blank>"
          "Terms and Conditions</a>.\n"
          "SARS-CoV-2 genome sequences and metadata are available for download from\n"
          "<a href='https://gisaid.org' target=_blank>GISAID</a> EpiCoV&trade;.\n"
          "</p>");
     puts("<p>\n"
          "<a href='/covid19.html'>COVID-19 Pandemic Resources at UCSC</a></p>\n");
     }
 puts("</div>");
 puts("</div>");
 puts("<div class='readableWidth'>");
 puts("  <div class='gbControl col-md-12'>");
@@ -419,167 +372,150 @@
      "target=_blank>Protected Health Information (PHI)</a>.</h3>\n"
      "If even virus sequence files must remain local on your computer, then you can try "
      "<a href='https://shusher.gi.ucsc.edu/' target=_blank>ShUShER</a> "
      "which runs entirely in your web browser so that no files leave your computer."
      "</p>\n"
      "<p>We do not store your information "
      "(aside from the information necessary to display results)\n"
      "and will not share it with others unless you choose to share your Genome Browser view.</p>\n"
      "<p>In order to enable rapid progress in pandemic research and genomic contact tracing,\n"
      "please share your sequences by submitting them to an "
      "<a href='https://ncbiinsights.ncbi.nlm.nih.gov/2020/08/17/insdc-covid-data-sharing/' "
      "target=_blank>INSDC</a> member institution\n"
      "(<a href='https://submit.ncbi.nlm.nih.gov/sarscov2/' target=_blank>NCBI</a>,\n"
      "<a href='https://www.covid19dataportal.org/submit-data' target=_blank>EMBL-EBI</a>\n"
      "or <a href='https://www.ddbj.nig.ac.jp/ddbj/websub.html' target=_blank>DDBJ</a>)\n");
-if (sameString(db, "wuhCor1"))
+if (sameString(org, "wuhCor1"))
     puts("and <a href='https://www.gisaid.org/' target=_blank>GISAID</a>\n");
 puts(".</p>\n");
 puts("</div>");
 puts("  </div>");
 puts("<div class='readableWidth'>");
 puts("<div class='gbControl col-md-12'>");
 puts("<h2>Tutorial</h2>");
 puts("<iframe width='950' height='535' src='https://www.youtube.com/embed/humQ1NyZOUM' "
      "frameborder='0' allow='accelerometer; autoplay; clipboard-write; encrypted-media; "
      "gyroscope; picture-in-picture' allowfullscreen></iframe>\n"
      "<h3><a href='https://www.cdc.gov/amd/pdf/slidesets/ToolkitModule_3.3-508C.pdf' "
      "target=_blank>Slides for tutorial</a></h3>\n"
      "<h3><a href='https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html' target=_blank>"
      "More tutorials from CDC COVID-19 Genomic Epidemiology Toolkit</a></h3>\n"
      "</p>"
      );
 puts("</div>");
 puts("</div>");
 puts("</form>");
 }
 
-static void mainPage(char *db)
+static void mainPage(char *org)
 {
 // Start web page with new-style header
-webStartGbNoBanner(cart, db, "UShER: Upload");
+webStartGbNoBanner(cart, org, "UShER: Upload");
 jsInit();
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 newPageStartStuff();
 
-// Hidden form for reloading page when hpp_ref select is changed
-static char *saveVars[] = { "hpp_ref" };
+// Hidden form for reloading page when hpp_org select is changed
+static char *saveVars[] = { orgVar };
 jsCreateHiddenForm(cart, cgiScriptName(), saveVars, ArraySize(saveVars));
 
 puts("<div class='row'>"
      "  <div class='row gbSectionBannerLarge'>\n"
      "    <div class='col-md-11'>UShER: Ultrafast Sample placement on Existing tRee</div>\n"
      "    <div class='col-md-1'></div>\n"
      "  </div>\n"
      "</div>\n"
      "<div class='row'>\n");
 if (hgPhyloPlaceEnabled())
     {
-    inputForm(db);
+    inputForm(org);
     }
 else
     {
     puts("  <div class='gbControl col-md-12'>");
     puts("  Sorry, this server is not configured to perform phylogenetic placement.");
     puts("  </div>");
     }
 puts("</div>\n");
 
 newPageEndStuff();
 }
 
-static void resultsPage(char *db, char *refName, struct lineFile *lf)
+static void resultsPage(char *db, char *org, struct lineFile *lf)
 /* QC the user's uploaded sequence(s) or VCF; if input looks valid then run usher
  * and display results. */
 {
-// If refName is a real database or hub then set db to refName.
-if (hDbExists(refName))
-    db = refName;
+// If org is a real database or hub then set db to org.
+if (hDbExists(org))
+    db = org;
 else
     {
     // Not a db -- see if it's a hub that is already connected:
-    struct trackHubGenome *hubGenome = trackHubGetGenomeUndecorated(db);
+    struct trackHubGenome *hubGenome = trackHubGetGenomeUndecorated(org);
     if (hubGenome != NULL)
-        db = refName;
+        db = org;
     // Otherwise we're counting on the config to specify a .2bit file and we won't make CTs.
     }
 webStartGbNoBanner(cart, db, "UShER: Results");
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 newPageStartStuff();
 
 if (issueBotWarning)
     {
     char *ip = getenv("REMOTE_ADDR");
     botDelayMessage(ip, botDelayMillis);
     }
 
 // Allow 10 minutes for big sets of sequences
 lazarusLives(15 * 60);
 
 puts("<div class='row'>"
      "  <div class='row gbSectionBannerLarge'>\n"
      "    <div class='col-md-11'>UShER: Ultrafast Sample placement on Existing tRee</div>\n"
      "    <div class='col-md-1'></div>\n"
      "  </div>\n"
      "</div>\n"
      "<div class='row'>\n");
-// Form submits subtree custom tracks to hgTracks
-printf("<form action='%s' name='resultsForm' method=%s>\n\n",
-       hgTracksName(), cartUsualString(cart, "formMethod", "POST"));
-cartSaveSession(cart);
-cgiMakeHiddenVar("db", db);
 puts("  <div class='gbControl col-md-12'>");
 fflush(stdout);
 
 if (lf != NULL)
     {
     // Use trackLayout to get hgTracks parameters relevant to displaying trees:
     struct trackLayout tl;
     trackLayoutInit(&tl, cart);
     // Do our best to place the user's samples, make custom tracks if successful:
     char *phyloPlaceTree = cartOptionalString(cart, "phyloPlaceTree");
     int subtreeSize = cartUsualInt(cart, "subtreeSize", 50);
-    boolean success = FALSE;
-    char *ctFile = phyloPlaceSamples(lf, db, refName, phyloPlaceTree, measureTiming, subtreeSize,
-                                     tl.fontHeight, &success);
-    if (ctFile)
-        {
-        cgiMakeHiddenVar(CT_CUSTOM_TEXT_VAR, ctFile);
-        if (tl.leftLabelWidthChars < 0 || tl.leftLabelWidthChars == leftLabelWidthDefaultChars)
-            cgiMakeHiddenVar(leftLabelWidthVar, leftLabelWidthForLongNames);
-        cgiMakeButton("submit", "view in Genome Browser");
-        puts("  </div>");
-        puts("</form>");
-        }
-    else if (! success)
+    boolean success = phyloPlaceSamples(lf, db, org, phyloPlaceTree, measureTiming, subtreeSize,
+                                        &tl, cart);
+    if (! success)
         {
         puts("<p></p>");
         puts("  </div>");
-        puts("</form>");
         // Let the user upload something else and try again:
         inputForm(db);
         }
     }
 else
     {
     warn("Unable to read your uploaded data - please choose a file and try again, or click the "
          "&quot;try example&quot; button.");
     // Let the user try again:
     puts("  </div>");
-    puts("</form>");
     inputForm(db);
     }
 puts("</div>\n");
 
 newPageEndStuff();
 }
 
 static boolean serverAuthOk(char *plain, char *salty)
 /* Construct a salted hash of plain and compare it to salty. */
 {
 char *salt = cfgOption(CFG_LOGIN_COOKIE_SALT);
 if (! salt)
     salt = "";
 char *plainMd5 = md5HexForString(plain);
 struct dyString *dySalted = dyStringCreate("%s-%s", salt, plainMd5);
@@ -587,191 +523,205 @@
 boolean ok = sameOk(salty, rightSalty);
 dyStringFree(&dySalted);
 return ok;
 }
 
 INLINE void maybeComment(char *comment)
 /* If comment is nonempty, append it to stderr.  Then print a newline regardless of comment. */
 {
 if (isNotEmpty(comment))
     fprintf(stderr, ": %s", comment);
 fputc('\n', stderr);
 }
 
 #define CONTENT_TYPE "Content-Type: text/plain\n\n"
 
-static void sendServerCommand(char *db)
+static void sendServerCommand(char *org)
 /* If a recognized server command is requested (with minimal auth to prevent DoS), and usher server
  * is configured, then send the command to the usher server's manager fifo. */
 {
 pushWarnHandler(htmlVaBadRequestAbort);
 pushAbortHandler(htmlVaBadRequestAbort);
 char *plain = cgiOptionalString(serverPlainVar);
 char *salty = cgiOptionalString(serverSaltyVar);
 if (isNotEmpty(plain) && isNotEmpty(salty) && serverAuthOk(plain, salty))
     {
-    if (serverIsConfigured(db))
+    if (serverIsConfigured(org))
         {
         char *command = cgiString(serverCommandVar);
         char *comment = cgiOptionalString(serverCommentVar);
         struct tempName tnCheckServer;
         trashDirFile(&tnCheckServer, "ct", "usher_check_server", ".txt");
         FILE *errFile = mustOpen(tnCheckServer.forCgi, "w");
-        boolean serverUp = serverIsRunning(db, errFile);
+        boolean serverUp = serverIsRunning(org, errFile);
         carefulClose(&errFile);
         if (sameString(command, "start"))
             {
             // This one is really a command for the CGI not the server manager fifo (because the
             // server is not yet running and needs to be started at this point), but uses the
             // same CGI interface.
-            struct treeChoices *treeChoices = loadTreeChoices(db);
+
+            //#*** TODO implement this at the org level, descending into ref subdirs.  For now
+            //#*** this is working because only SARS-CoV-2 has a server and org==ref for it.
+
+            struct treeChoices *treeChoices = loadTreeChoices(org, org);
             if (treeChoices != NULL)
                 {
                 if (serverUp)
-                    errAbort("Server is already running for db %s, see %s",
-                             db, tnCheckServer.forCgi);
+                    errAbort("Server is already running for org %s, see %s",
+                             org, tnCheckServer.forCgi);
                 struct tempName tnServerStartup;
                 trashDirFile(&tnServerStartup, "ct", "usher_server_startup", ".txt");
                 errFile = mustOpen(tnServerStartup.forCgi, "w");
-                fprintf(stderr, "Usher server start for %s", db);
+                fprintf(stderr, "Usher server start for %s", org);
                 maybeComment(comment);
-                boolean success = startServer(db, treeChoices, errFile);
+                boolean success = startServer(org, treeChoices, errFile);
                 carefulClose(&errFile);
                 if (success)
                     {
                     fprintf(stderr, "Spawned usher server background process, details in %s",
                             tnServerStartup.forCgi);
-                    printf(CONTENT_TYPE"Started server for %s\n", db);
+                    printf(CONTENT_TYPE"Started server for %s\n", org);
                     }
                 else
                     errAbort("Unable to spawn usher server background process, details in %s",
                              tnServerStartup.forCgi);
                 }
             else
-                errAbort("No treeChoices for db=%s", db);
+                errAbort("No treeChoices for org=%s", org);
             }
         else if (serverUp)
             {
             if (sameString(command, "reload"))
                 {
-                struct treeChoices *treeChoices = loadTreeChoices(db);
-                fprintf(stderr, "Usher server reload for %s", db);
+                struct treeChoices *treeChoices = loadTreeChoices(org, org);
+                fprintf(stderr, "Usher server reload for %s", org);
                 maybeComment(comment);
-                serverReloadProtobufs(db, treeChoices);
-                printf(CONTENT_TYPE"Sent reload command for %s\n", db);
+                serverReloadProtobufs(org, treeChoices);
+                printf(CONTENT_TYPE"Sent reload command for %s\n", org);
                 }
             else if (sameString(command, "stop"))
                 {
-                fprintf(stderr, "Usher server stop for %s", db);
+                fprintf(stderr, "Usher server stop for %s", org);
                 maybeComment(comment);
-                serverStop(db);
-                printf(CONTENT_TYPE"Sent stop command for %s\n", db);
+                serverStop(org);
+                printf(CONTENT_TYPE"Sent stop command for %s\n", org);
                 }
             else
                 {
                 char commandCopy[16];
                 safecpy(commandCopy, sizeof commandCopy, command);
                 char *words[3];
                 int wordCount = chopLine(commandCopy, words);
                 int val;
                 if (wordCount == 2 && (val = atol(words[1])) > 0)
                     {
                     if (sameString(words[0], "thread"))
                         {
                         fprintf(stderr, "Usher server thread count set to %d", val);
                         maybeComment(comment);
-                        serverSetThreadCount(db, val);
-                        printf(CONTENT_TYPE"Sent thread %d command for %s\n", val, db);
+                        serverSetThreadCount(org, val);
+                        printf(CONTENT_TYPE"Sent thread %d command for %s\n", val, org);
                         }
                     else if (sameString(words[0], "timeout"))
                         {
                         fprintf(stderr, "Usher server timeout set to %d", val);
                         maybeComment(comment);
-                        serverSetTimeout(db, val);
-                        printf(CONTENT_TYPE"Sent timeout %d command for %s\n", val, db);
+                        serverSetTimeout(org, val);
+                        printf(CONTENT_TYPE"Sent timeout %d command for %s\n", val, org);
                         }
                     else
                         errAbort("Unrecognized command '%s'", command);
                     }
                 else
                     errAbort("Unrecognized command '%s'", command);
                 }
             }
         else
             errAbort("Server for %s is down (see %s), cannot send command '%s'",
-                     db, tnCheckServer.forCgi, command);
+                     org, tnCheckServer.forCgi, command);
         }
     else
-        errAbort("Usher server mode not configured for db=%s", db);
+        errAbort("Usher server mode not configured for org=%s", org);
     }
 else
     errAbort("Bad request");
 popWarnHandler();
 popAbortHandler();
 }
 
 static void doMiddle(struct cart *theCart)
 /* Set up globals and make web page */
 {
 cart = theCart;
 char *db = NULL, *genome = NULL;
 // Get the current db from the cart
 getDbAndGenome(cart, &db, &genome, oldVars);
-// The currently selected pathogen reference sequence may or may not be a db/hub.
-char *refName = cartOptionalString(cart, "hpp_ref");
-if (isEmpty(refName))
-    refName = cloneString(db);
+// The currently selected organism may or may not be a db/hub.
+char *org = cartOptionalString(cart, orgVar);
+if (isEmpty(org))
+    {
+    // If orgVar is not found but old cart var is set, use it and then remove it to tidy up.
+    org = cartOptionalString(cart, "hpp_ref");
+    if (isNotEmpty(org))
+        cartRemove(cart, "hpp_ref");
+    }
+if (isEmpty(org))
+    {
+    // Default to db
+    org = cloneString(db);
+    }
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 measureTiming = cartUsualBoolean(cart, "measureTiming", measureTiming);
 
 char *submitLabel = cgiOptionalString("submit");
 char *newExampleButton = cgiOptionalString("exampleButton");
 if ((submitLabel && sameString(submitLabel, "try example")) ||
     (newExampleButton && sameString(newExampleButton, "Upload Example File")))
     {
-    char *exampleFile = phyloPlaceDbSettingPath(refName, "exampleFile");
+    char *exampleFile = phyloPlaceOrgSettingPath(org, "exampleFile");
     struct lineFile *lf = lineFileOpen(exampleFile, TRUE);
-    resultsPage(db, refName, lf);
+    resultsPage(db, org, lf);
     }
 else if (cgiOptionalString(remoteFileVar))
     {
     char *url = cgiString(remoteFileVar);
     struct lineFile *lf = netLineFileOpen(url);
-    resultsPage(db, refName, lf);
+    resultsPage(db, org, lf);
     }
 else if (isNotEmpty(trimSpaces(cgiOptionalString(pastedIdVar))))
     {
     char *pastedIds = cgiString(pastedIdVar);
     struct lineFile *lf = lineFileOnString("pasted names/IDs", TRUE, pastedIds);
-    resultsPage(db, refName, lf);
+    resultsPage(db, org, lf);
     }
 else if (cgiOptionalString(seqFileVar) || cgiOptionalString(seqFileVar "__filename"))
     {
     struct lineFile *lf = lineFileFromFileInput(cart, seqFileVar);
-    resultsPage(db, refName, lf);
+    resultsPage(db, org, lf);
     }
 else if (isNotEmpty(cgiOptionalString(serverCommandVar)))
     {
-    sendServerCommand(refName);
+    sendServerCommand(org);
     }
 else
-    mainPage(refName);
+    mainPage(org);
 }
 
 #define LD_LIBRARY_PATH "LD_LIBRARY_PATH"
 
 static void addLdLibraryPath()
 /* usher requires a tbb lib that is not in the yum package tbb-devel, so for now
  * I'm adding the .so files to hgPhyloPlaceData.  Set environment variable LD_LIBRARY_PATH
  * to pick them up from there. */
 {
 char *oldValue = getenv(LD_LIBRARY_PATH);
 struct dyString *dy = dyStringNew(0);
 if (startsWith("/", PHYLOPLACE_DATA_DIR))
     dyStringAppend(dy, PHYLOPLACE_DATA_DIR);
 else
     {