d060b70a11099fb693b769c781796b6b577715fb
angie
  Fri Nov 1 12:47:25 2024 -0700
If sessionDataDir is in hg.conf, make a new UI option to request that the Auspice JSON output files don't expire after two days, using sessionDataDir/hgPhyloPlace/ for storage.

diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c
index b8a242d..242ea18 100644
--- src/hg/hgPhyloPlace/hgPhyloPlace.c
+++ src/hg/hgPhyloPlace/hgPhyloPlace.c
@@ -1,756 +1,764 @@
 /* hgPhyloPlace - Upload SARS-CoV-2 or MPXV sequence for placement in phylo tree. */
 
 /* 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
 
 /* 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.
 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 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 slPair *orgLabelList = phyloPlaceOrgList(cart);
 if (orgLabelList == NULL)
     errAbort("Sorry, this server is not configured to perform phylogenetic placement.");
 if (!slPairFind(orgLabelList, *pOrg))
     {
     *pOrg = cloneString(orgLabelList->name);
     }
 *pLabel = phyloPlaceOrgSetting(*pOrg, "name");
 if (isEmpty(*pLabel))
     *pLabel = *pOrg;
 char *selectVar = orgVar;
 int orgCount = slCount(orgLabelList);
 if (orgCount > 1)
     {
     char *labels[orgCount];
     char *values[orgCount];
     struct slPair *orgLabel;
     int i;
     for (orgLabel = orgLabelList, i = 0;  i < orgCount;  orgLabel = orgLabel->next, i++)
         {
         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, orgCount, *pOrg, "change", js);
     puts("</p>");
     }
 else
     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"
 "    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"
 "table.invisalign {\n"
 "    border: 0px;\n"
 "}\n"
 "table.invisalign td {\n "
 "    padding: 5px;\n"
 "}\n"
 "button.fullwidth {\n "
 "    width: 100%;\n"
 "}\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 *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>");
 char *label = NULL;
 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);
 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>");
+char *sessionDataDir = cfgOption("sessionDataDir");
+if (isNotEmpty(sessionDataDir))
+    {
+    puts("Prevent subtree Auspice JSON files from expiring after two days: ");
+    boolean subtreePersist = cartUsualBoolean(cart, "subtreePersist", FALSE);
+    cgiMakeCheckBox("subtreePersist", subtreePersist);
+    puts("</p><p>");
+    }
 cgiMakeOnClickSubmitButton(CHECK_FILE_OR_PASTE_INPUT_JS(seqFileVar, pastedIdVar),
                            "submit", "Upload");
 char *exampleFile = phyloPlaceOrgSettingPath(org, "exampleFile");
 if (isNotEmpty(exampleFile))
     {
     puts("&nbsp;&nbsp;");
     cgiMakeOnClickSubmitButton("{ loadingImage.run(); return true; }",
                                "exampleButton", "Upload Example File");
     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(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 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(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'>");
 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(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 *org)
 {
 // Start web page with new-style header
 webStartGbNoBanner(cart, org, "UShER: Upload");
 jsInit();
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 newPageStartStuff();
 
 // 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(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 *org, struct lineFile *lf)
 /* QC the user's uploaded sequence(s) or VCF; if input looks valid then run usher
  * and display results. */
 {
 // 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(org);
     if (hubGenome != NULL)
         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");
 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 = phyloPlaceSamples(lf, db, org, phyloPlaceTree, measureTiming, subtreeSize,
                                         &tl, cart);
     if (! success)
         {
         puts("<p></p>");
         puts("  </div>");
         // Let the user upload something else and try again:
         inputForm(org);
         }
     }
 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>");
     inputForm(org);
     }
 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 *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(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(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.
 
             //#*** 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 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", org);
                 maybeComment(comment);
                 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", org);
                     }
                 else
                     errAbort("Unable to spawn usher server background process, details in %s",
                              tnServerStartup.forCgi);
                 }
             else
                 errAbort("No treeChoices for org=%s", org);
             }
         else if (serverUp)
             {
             if (sameString(command, "reload"))
                 {
                 struct treeChoices *treeChoices = loadTreeChoices(org, org);
                 fprintf(stderr, "Usher server reload for %s", org);
                 maybeComment(comment);
                 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", org);
                 maybeComment(comment);
                 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(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(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'",
                      org, tnCheckServer.forCgi, command);
         }
     else
         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 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 = phyloPlaceOrgSettingPath(org, "exampleFile");
     struct lineFile *lf = lineFileOpen(exampleFile, TRUE);
     resultsPage(db, org, lf);
     }
 else if (cgiOptionalString(remoteFileVar))
     {
     char *url = cgiString(remoteFileVar);
     struct lineFile *lf = netLineFileOpen(url);
     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, org, lf);
     }
 else if (cgiOptionalString(seqFileVar) || cgiOptionalString(seqFileVar "__filename"))
     {
     struct lineFile *lf = lineFileFromFileInput(cart, seqFileVar);
     resultsPage(db, org, lf);
     }
 else if (isNotEmpty(cgiOptionalString(serverCommandVar)))
     {
     sendServerCommand(org);
     }
 else
     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
     {
     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;
 }