0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55
angie
  Fri Jun 2 11:40:19 2023 -0700
Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.

diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c
index f68e460..e77277f 100644
--- src/hg/hgPhyloPlace/hgPhyloPlace.c
+++ src/hg/hgPhyloPlace/hgPhyloPlace.c
@@ -1,737 +1,761 @@
 /* hgPhyloPlace - Upload SARS-CoV-2 or MPXV sequence for placement in phylo tree. */
 
 /* Copyright (C) 2020-2022 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 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.
 char *filePlainContents = cartOptionalString(cart, fileVar);
 char cartVar[2048];
 safef(cartVar, sizeof cartVar, "%s__binary", fileVar);
 char *fileBinaryCoords = cartOptionalString(cart, cartVar);
 // Also get the file name for error reporting.
 safef(cartVar, sizeof cartVar, "%s__filename", fileVar);
 char *fileName = cartOptionalString(cart, cartVar);
 if (fileName == NULL)
     fileName = "<uploaded data>";
 if (isNotEmpty(filePlainContents))
     {
     lf = lineFileOnString(fileName, TRUE, cloneString(trimSpaces(filePlainContents)));
     }
 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)
 /* The assembly hub name is just the accession; make a special label for hMPXV.  Otherwise just
  * return hGenome(db). */
 {
-char *label = NULL;
-if (sameString(trackHubSkipHubName(db), "GCF_014621545.1"))
-    label = cloneString("hMPXV");
-else if (sameString(trackHubSkipHubName(db), "GCF_002815475.1"))
-    label = cloneString("RSV-A");
-else if (sameString(trackHubSkipHubName(db), "GCF_000855545.1"))
-    label = cloneString("RSV-B");
-else
+char *label = phyloPlaceDbSetting(db, "name");
+if (isEmpty(label))
     label = hGenome(db);
 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)));
+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;
  * reload the page on change. */
 {
-struct slName *supportedDbs = phyloPlaceDbList(cart);
+struct slName *supportedDbs = sortByLabel(phyloPlaceDbList(cart));
 if (supportedDbs == NULL)
     errAbort("Sorry, this server is not configured to perform phylogenetic placement.");
 if (!slNameInList(supportedDbs, *pDb))
     {
     *pDb = cloneString(supportedDbs->name);
     }
 *pLabel = labelForDb(*pDb);
 int supportedDbCount = slCount(supportedDbs);
 if (supportedDbCount > 1)
     {
     char *labels[supportedDbCount];
     char *values[supportedDbCount];
     struct slName *sDb;
     int i;
     for (sDb = supportedDbs, i = 0;  i < supportedDbCount;  sDb = sDb->next, i++)
         {
         values[i] = sDb->name;
         labels[i] = labelForDb(values[i]);
         }
     char *selectVar = "db";
     struct dyString *dy = jsOnChangeStart();
     jsDropDownCarryOver(dy, selectVar);
     char *js = jsOnChangeEnd(&dy);
     puts("<p>Choose your pathogen: ");
     cgiMakeDropListFull(selectVar, labels, values, supportedDbCount, *pDb, "change", js);
     puts("</p>");
     }
 else
     cgiMakeHiddenVar("db", *pDb);
 slNameFreeList(&supportedDbs);
 }
 
 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"
 "    margin:10px;\n"
 "    text-align:left;\n"
 "}\n"
 "\n"
 "#warnHead {\n"
 "    color: DarkRed;\n"
 "}\n"
 ".readableWidth {\n"
 "    max-width: 70em;\n"
 "}\n"
 "table.seqSummary, table.seqSummary th, table.seqSummary td {\n"
 "    border: 1px gray solid;\n"
 "    padding: 5px;\n"
 "}\n"
 ".tooltip {\n"
 "    position: relative;\n"
 "    display: inline-block;\n"
 "    border-bottom: 1px dotted black;\n"
 "}\n"
 "\n"
 ".tooltip .tooltiptext {\n"
 "    visibility: hidden;\n"
 "    background-color: lightgray;\n"
 "    text-align: center;\n"
 "    position: absolute;\n"
 "    z-index: 1;\n"
 "    opacity: 0;\n"
 "    width: 220px;\n"
 "    padding: 5px;\n"
 "    left: 105%;\n"
 "    transition: opacity .6s;\n"
 "    line-height: 1em;\n"
 "}\n"
 "\n"
 ".tooltip:hover .tooltiptext {\n"
 "    visibility: visible;\n"
 "    opacity: .9;\n"
 "}\n"
 "td.qcExcellent {\n"
 "    background-color: #44ff44;\n"
 "}\n"
 "td.qcGood {\n"
 "    background-color: #88ff88;\n"
 "}\n"
 "td.qcMeh {\n"
 "    background-color: #ffcc44;\n"
 "}\n"
 "td.qcBad {\n"
 "    background-color: #ff8888;\n"
 "}\n"
 "td.qcFail {\n"
 "    background-color: #ff6666;\n"
 "}\n"
 ".gbSectionBannerLarge {\n"
 "    padding: 10px;\n"
 "    margin-top: 6px;\n"
 "    margin-right: 0;\n"
 "    background-color: #4c759c;  /* light blue */\n"
 "    color: white;\n"
 "    font-weight: bold;\n"
 "    font-size: 22px;\n"
 "}\n"
 "h2 { font-size: 18px; }\n"
 "h3 { font-size: 16px; }\n"
 "</style>\n"
      );
 
 
 
 // Container for bootstrap grid layout
 puts(
 "<div class='container-fluid'>\n");
 }
 
 static void newPageEndStuff()
 {
 puts(
 "</div>");
 jsIncludeFile("utils.js", NULL);
 webIncludeFile("inc/gbFooter.html");
 webEndJWest();
 }
 
 #define CHECK_FILE_OR_PASTE_INPUT_JS(fileVarName, pasteVarName) \
     "{ 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)
 /* 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);
 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)
     {
     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);
 cgiMakeIntVarWithLimits("subtreeSize", subtreeSize,
                         "Number of samples in subtree showing neighborhood of placement",
                         5, 10, 5000);
 puts("</p><p>");
 cgiMakeOnClickSubmitButton(CHECK_FILE_OR_PASTE_INPUT_JS(seqFileVar, pastedIdVar),
                            "submit", "Upload");
 char *exampleFile = phyloPlaceDbSettingPath(db, "exampleFile");
 if (isNotEmpty(exampleFile))
     {
     puts("&nbsp;&nbsp;");
     cgiMakeOnClickSubmitButton("{ loadingImage.run(); return true; }",
                                "exampleButton", "Upload Example File");
     if (sameString(db, "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"))
     {
     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
     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.</p>\n");
 if (sameString(db, "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'>");
 puts("<h2>Privacy and sharing</h2>");
 puts("<h3>Please do not upload "
      "<a href='https://en.wikipedia.org/wiki/Protected_health_information#United_States' "
      "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"))
     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)
 {
 // Start web page with new-style header
 webStartGbNoBanner(cart, db, "UShER: Upload");
 jsInit();
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 newPageStartStuff();
 
 // Hidden form for reloading page when db select is changed
 static char *saveVars[] = { "db" };
 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);
     }
 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, struct lineFile *lf)
 /* QC the user's uploaded sequence(s) or VCF; if input looks valid then run usher
  * and display results. */
 {
 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);
 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, 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)
         {
         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);
 char *rightSalty = md5HexForString(dySalted->string);
 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)
 /* 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))
         {
         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);
         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);
             if (treeChoices != NULL)
                 {
                 if (serverUp)
                     errAbort("Server is already running for db %s, see %s",
                              db, 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);
                 maybeComment(comment);
                 boolean success = startServer(db, 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);
                     }
                 else
                     errAbort("Unable to spawn usher server background process, details in %s",
                              tnServerStartup.forCgi);
                 }
             else
                 errAbort("No treeChoices for db=%s", db);
             }
         else if (serverUp)
             {
             if (sameString(command, "reload"))
                 {
                 struct treeChoices *treeChoices = loadTreeChoices(db);
                 fprintf(stderr, "Usher server reload for %s", db);
                 maybeComment(comment);
                 serverReloadProtobufs(db, treeChoices);
                 printf(CONTENT_TYPE"Sent reload command for %s\n", db);
                 }
             else if (sameString(command, "stop"))
                 {
                 fprintf(stderr, "Usher server stop for %s", db);
                 maybeComment(comment);
                 serverStop(db);
                 printf(CONTENT_TYPE"Sent stop command for %s\n", db);
                 }
             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);
                         }
                     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);
                         }
                     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);
         }
     else
         errAbort("Usher server mode not configured for db=%s", db);
     }
 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);
 
 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(db, "exampleFile");
     struct lineFile *lf = lineFileOpen(exampleFile, TRUE);
     resultsPage(db, lf);
     }
 else if (cgiOptionalString(remoteFileVar))
     {
     char *url = cgiString(remoteFileVar);
     struct lineFile *lf = netLineFileOpen(url);
     resultsPage(db, lf);
     }
 else if (isNotEmpty(trimSpaces(cgiOptionalString(pastedIdVar))))
     {
     char *pastedIds = cgiString(pastedIdVar);
     struct lineFile *lf = lineFileOnString("pasted names/IDs", TRUE, pastedIds);
     resultsPage(db, lf);
     }
 else if (cgiOptionalString(seqFileVar) || cgiOptionalString(seqFileVar "__filename"))
     {
     struct lineFile *lf = lineFileFromFileInput(cart, seqFileVar);
     resultsPage(db, lf);
     }
 else if (isNotEmpty(cgiOptionalString(serverCommandVar)))
     {
     sendServerCommand(db);
     }
 else
     mainPage(db);
 }
 
 #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
     {
     char cwd[4096];
     getcwd(cwd, sizeof cwd);
     dyStringPrintf(dy, "%s/%s", cwd, PHYLOPLACE_DATA_DIR);
     }
 if (isNotEmpty(oldValue))
     dyStringPrintf(dy, ":%s", oldValue);
 setenv(LD_LIBRARY_PATH, dyStringCannibalize(&dy), TRUE);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 /* Null terminated list of CGI Variables we don't want to save to cart */
 char *excludeVars[] = {"submit", "Submit",
                        seqFileVar, seqFileVar "__binary", seqFileVar "__filename",
                        pastedIdVar, remoteFileVar,
                        serverCommandVar, serverCommentVar, serverPlainVar, serverSaltyVar,
                        NULL};
 enteredMainTime = clock1000();
 issueBotWarning = earlyBotCheck(enteredMainTime, "hgPhyloPlace", delayFraction, 0, 0, "html");
 
 cgiSpoof(&argc, argv);
 oldVars = hashNew(10);
 addLdLibraryPath();
 
 cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
 cgiExitTime("hgPhyloPlace", enteredMainTime);
 return 0;
 }