0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 angie Fri May 1 10:02:25 2026 -0700 Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table. diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c index d92c273cd02..451030a41eb 100644 --- src/hg/hgPhyloPlace/hgPhyloPlace.c +++ src/hg/hgPhyloPlace/hgPhyloPlace.c @@ -1,787 +1,795 @@ /* 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>"); } +char *ripplesEnabled = phyloPlaceOrgSetting(org, "ripplesEnabled"); +if (isNotEmpty(ripplesEnabled) && SETTING_IS_ON(ripplesEnabled)) + { + printf("Search for potential recombination (limit %d input sequences): ", MAX_RIPPLES_SEARCH); + boolean doRipples = cartUsualBoolean(cart, "doRipples", FALSE); + cgiMakeCheckBox("doRipples", doRipples); + puts("</p><p>"); + } cgiMakeOnClickSubmitButton(CHECK_FILE_OR_PASTE_INPUT_JS(seqFileVar, pastedIdVar), "submit", "Upload"); char *exampleFile = phyloPlaceOrgSettingPath(org, "exampleFile"); if (isNotEmpty(exampleFile)) { puts(" "); cgiMakeOnClickSubmitButton("{ loadingImage.run(); return true; }", "exampleButton", "Upload Example File"); if (sameString(org, "wuhCor1")) { puts(" "); 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™.\n" "</p>"); puts("<p>\n" "<a href='/covid19.html'>COVID-19 Pandemic Resources at UCSC</a></p>\n"); } puts("</div>"); puts("</div>"); // If org directory includes non-empty download.html file then make a Download section char *orgSkipHub = trackHubSkipHubName(org); char downloadHtmlFile[1024]; safef(downloadHtmlFile, sizeof downloadHtmlFile, PHYLOPLACE_DATA_DIR "/%s/download.html", orgSkipHub); struct lineFile *lf = lineFileMayOpen(downloadHtmlFile, TRUE); if (lf != NULL) { char *line = NULL; int size; lineFileNext(lf, &line, &size); if (isNotEmpty(line)) { puts("<div class='readableWidth'>"); puts(" <div class='gbControl col-md-12'>"); puts("<h2>Download public tree files</h2>"); puts(line); while (lineFileNext(lf, &line, &size)) puts(line); puts(" </div>"); puts("</div>"); } lineFileClose(&lf); } 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 " ""try example" 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; }