7033f67074594c3d9cc3487f079456928fdf3260 angie Tue Apr 12 13:46:14 2016 -0700 Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist. It has icons for selecting popular species, an autocomplete input for typing in species or common names, as well as a phylogenetic tree display that shows the relationships of the species that we host. It has a menu for selecting the assembly of the selected species' genome and the usual assembly description. refs #15277 diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c index 330bce8..fc5a359 100644 --- src/hg/hgGateway/hgGateway.c +++ src/hg/hgGateway/hgGateway.c @@ -1,310 +1,741 @@ -/* hgGateway - Human Genome Browser Gateway. */ - -/* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ +/* hgGateway: make it easy to select a species and assembly + * + * Copyright (C) 2016 The Regents of the University of California + * + * This CGI has three modes of operation: + * - HTML output for main page (default); most HTML is in hgGateway.html + * - cart-based JSON responses to ajax requests from javascript (using hg/lib/cartJson.c) + * (if CGI param CARTJSON_COMMAND exists) + * - no cart; fast JSON responses to species-search autocomplete requests + * (if CGI param SEARCH_TERM exists) + */ #include "common.h" -#include "linefile.h" -#include "hash.h" -#include "cheapcgi.h" -#include "htmshell.h" -#include "obscure.h" -#include "web.h" #include "cart.h" -#include "hdb.h" -#include "dbDb.h" -#include "hgFind.h" +#include "cartJson.h" +#include "cheapcgi.h" +#include "errCatch.h" +#include "googleAnalytics.h" #include "hCommon.h" -#include "hui.h" -#include "customTrack.h" -#include "hubConnect.h" #include "hgConfig.h" +#include "hdb.h" +#include "htmshell.h" +#include "hubConnect.h" +#include "hui.h" #include "jsHelper.h" -#include "hPrint.h" +#include "jsonParse.h" +#include "obscure.h" // for readInGulp +#include "regexHelper.h" #include "suggest.h" -#include "search.h" -#include "geoMirror.h" #include "trackHub.h" +#include "trix.h" +#include "web.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 */ + +#define SEARCH_TERM "hggw_term" + +static char *maybeGetDescriptionText(char *db) +/* Slurp the description.html file for db into a string (if possible, don't die if + * we can't read it) and return it. */ +{ +struct errCatch *errCatch = errCatchNew(); +char *descText = NULL; +if (errCatchStart(errCatch)) + { + char *htmlPath = hHtmlPath(db); + descText = udcFileReadAll(htmlPath, NULL, 0, NULL); + } +errCatchEnd(errCatch); +// Just ignore errors for now. +return descText; +} + +static int trackHubCountAssemblies(struct trackHub *hub) +/* Return the number of hub's genomes that are hub assemblies, i.e. that have a twoBitPath. */ +{ +int count = 0; +struct trackHubGenome *genome; +for (genome = hub->genomeList; genome != NULL; genome = genome->next) + { + if (isNotEmpty(genome->twoBitPath)) + count++; + } +return count; +} + +static char *trackHubDefaultAssembly(struct trackHub *hub) +/* If hub->defaultDb is an assembly genome, return it; otherwise return the first assembly. + * Don't free result. */ +{ +char *defaultDb = hub->defaultDb; +char *firstAssemblyDb = NULL; +struct trackHubGenome *genome; +for (genome = hub->genomeList; genome != NULL; genome = genome->next) + { + if (isNotEmpty(genome->twoBitPath)) + { + if (sameString(defaultDb, genome->name)) + return defaultDb; + else if (firstAssemblyDb == NULL) + firstAssemblyDb = genome->name; + } + } +return firstAssemblyDb; +} -struct cart *cart = NULL; -struct hash *oldVars = NULL; -char *clade = NULL; -char *organism = NULL; -char *db = NULL; +static void listAssemblyHubs(struct jsonWrite *jw) +/* Write out JSON describing assembly hubs (not track-only hubs) connected in the cart. */ +{ +jsonWriteListStart(jw, "hubs"); +struct hubConnectStatus *status, *statusList = hubConnectStatusListFromCartAll(cart); +for (status = statusList; status != NULL; status = status->next) + { + struct trackHub *hub = status->trackHub; + if (hub == NULL) + continue; + int assemblyCount = trackHubCountAssemblies(hub); + if (assemblyCount > 0) + { + jsonWriteObjectStart(jw, NULL); + jsonWriteString(jw, "name", hub->name); + jsonWriteString(jw, "shortLabel", hub->shortLabel); + jsonWriteString(jw, "longLabel", hub->longLabel); + jsonWriteString(jw, "defaultDb", trackHubDefaultAssembly(hub)); + jsonWriteString(jw, "hubUrl", status->hubUrl); + jsonWriteNumber(jw, "assemblyCount", assemblyCount); + jsonWriteString(jw, "errorMessage", status->errorMessage); + // We might be able to do better than this for taxId, for example if defaultDb is local + // or if hub genomes ever specify taxId... + jsonWriteNumber(jw, "taxId", 0); + jsonWriteObjectEnd(jw); + } + } +jsonWriteListEnd(jw); +} -// TODO REMOVE AFTER AUTOUPGRADE COMPLETE: (added 2014-03-09) -extern struct dyString *dyUpgradeError; -void hgGateway() -/* hgGateway - Human Genome Browser Gateway. */ +static void writeFindPositionInfo(struct jsonWrite *jw, char *db, int taxId, char *hubUrl, + char *position) +/* Write JSON for the info needed to populate the 'Find Position' section. */ +{ +char *genome = hGenome(db); +if (isEmpty(genome)) { -char *defaultPosition = hDefaultPos(db); -char *position = cloneString(cartUsualString(cart, "position", defaultPosition)); -boolean gotClade = hGotClade(); -char *survey = cfgOptionEnv("HGDB_SURVEY", "survey"); -char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel"); -boolean supportsSuggest = FALSE; + jsonWriteStringf(jw, "error", "No genome for db '%s'", db); + } +else + { + jsonWriteString(jw, "db", db); + jsonWriteNumber(jw, "taxId", taxId); + jsonWriteString(jw, "genome", genome); + struct slPair *dbOptions = NULL; + char genomeLabel[PATH_LEN*4]; + if (isNotEmpty(hubUrl)) + { + struct trackHub *hub = hubConnectGetHub(hubUrl); + if (hub == NULL) + { + jsonWriteStringf(jw, "error", "Can't connect to hub at '%s'", hubUrl); + return; + } + struct dbDb *dbDbList = trackHubGetDbDbs(hub->name); + dbOptions = trackHubDbDbToValueLabel(dbDbList); + safecpy(genomeLabel, sizeof(genomeLabel), hub->shortLabel); + jsonWriteString(jw, "hubUrl", hubUrl); + } + else + { + dbOptions = hGetDbOptionsForGenome(genome); + safecpy(genomeLabel, sizeof(genomeLabel), genome); + } + jsonWriteValueLabelList(jw, "dbOptions", dbOptions); + jsonWriteString(jw, "genomeLabel", genomeLabel); + jsonWriteString(jw, "position", position); + char *suggestTrack = NULL; if (! trackHubDatabase(db)) - supportsSuggest = assemblySupportsGeneSuggest(db); + suggestTrack = assemblyGeneSuggestTrack(db); + jsonWriteString(jw, "suggestTrack", suggestTrack); + char *description = maybeGetDescriptionText(db); + //#*** TODO: move jsonStringEscape inside jsonWriteString + char *encoded = jsonStringEscape(description); + jsonWriteString(jw, "description", encoded); + listAssemblyHubs(jw); + } +} -/* JavaScript to copy input data on the change genome button to a hidden form -This was done in order to be able to flexibly arrange the UI HTML -*/ -char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\""; -char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\""; -char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\""; - -/* - If we are changing databases via explicit cgi request, - then remove custom track data which will - be irrelevant in this new database . - If databases were changed then use the new default position too. -*/ +static void setTaxId(struct cartJson *cj, struct hash *paramHash) +/* Set db and genome according to taxId (and/or db) and return the info we'll need + * to fill in the findPosition section. */ +{ +char *taxIdStr = cartJsonRequiredParam(paramHash, "taxId", cj->jw, "setTaxId"); +char *db = cartJsonOptionalParam(paramHash, "db"); +int taxId = atoi(taxIdStr); +if (isEmpty(db)) + db = hDbForTaxon(taxId); +if (isEmpty(db)) + jsonWriteStringf(cj->jw, "error", "No db for taxId '%s'", taxIdStr); +else + { + writeFindPositionInfo(cj->jw, db, taxId, NULL, hDefaultPos(db)); + cartSetString(cart, "db", db); + cartSetString(cart, "position", hDefaultPos(db)); + } +} + +static void setHubDb(struct cartJson *cj, struct hash *paramHash) +/* Set db and genome according to hubUrl (and/or db and hub) and return the info we'll need + * to fill in the findPosition section. */ +{ +char *hubUrl = cartJsonRequiredParam(paramHash, "hubUrl", cj->jw, "setHubDb"); +char *taxIdStr = cartJsonOptionalParam(paramHash, "taxId"); +int taxId = taxIdStr ? atoi(taxIdStr) : -1; +// cart's db was already set by magic handling of hub CGI variables sent along +// with this command. +char *db = cartString(cart, "db"); +if (isEmpty(db)) + jsonWriteStringf(cj->jw, "error", "No db for hubUrl '%s'", hubUrl); +else + writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db)); +} + +static void setDb(struct cartJson *cj, struct hash *paramHash) +/* Set taxId and genome according to db and return the info we'll need to fill in + * the findPosition section. */ +{ +char *db = cartJsonRequiredParam(paramHash, "db", cj->jw, "setDb"); +char *hubUrl = cartJsonOptionalParam(paramHash, "hubUrl"); +int taxId = hTaxId(db); +writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db)); +cartSetString(cart, "db", db); +cartSetString(cart, "position", hDefaultPos(db)); +} + +static void getUiState(struct cartJson *cj, struct hash *paramHash) +/* Write out JSON for hgGateway.js's uiState object using current cart settings. */ +{ +char *db = cartUsualString(cj->cart, "db", hDefaultDb()); +char *position = cartUsualString(cart, "position", hDefaultPos(db)); +char *hubUrl = NULL; +if (trackHubDatabase(db)) + { + struct trackHub *hub = hubConnectGetHubForDb(db); + hubUrl = hub->url; + } +writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position); +// If cart already has a pix setting, pass that along; otherwise the JS will +// set pix according to web browser window width. +int pix = cartUsualInt(cj->cart, "pix", 0); +if (pix) + jsonWriteNumber(cj->jw, "pix", pix); +} + +static void doCartJson() +/* Perform UI commands to update the cart and/or retrieve cart vars & metadata. */ +{ +struct cartJson *cj = cartJsonNew(cart); +cartJsonRegisterHandler(cj, "setTaxId", setTaxId); +cartJsonRegisterHandler(cj, "setDb", setDb); +cartJsonRegisterHandler(cj, "setHubDb", setHubDb); +cartJsonRegisterHandler(cj, "getUiState", getUiState); +cartJsonExecute(cj); +} + +static void doMainPage() +/* Send HTML with javascript to bootstrap the user interface. */ +{ +// Start web page with new banner +char *db = NULL, *genome = NULL, *clade = NULL; +getDbGenomeClade(cart, &db, &genome, &clade, oldVars); +webStartJWest(cart, db, "Genome Browser Gateway"); + +// Edit the HTML in hgGateway.html (see makefile): +puts( +#include "hgGateway.html.h" +); -if (sameString(position, "genome") || sameString(position, "hgBatch")) - position = defaultPosition; +// Set global JS variable hgsid +// We can't just use "var hgsid = " or the other scripts won't see it -- it has to be +// "window.hgsid = ". +puts("<script>"); +printf("window.%s = '%s';\n", cartSessionVarName(), cartSessionId(cart)); +puts("</script>"); + +puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>"); +puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>"); +puts("<script src=\"../js/lodash.3.10.0.compat.min.js\"></script>"); +puts("<script src=\"../js/cart.js\"></script>"); -jsIncludeFile("jquery.js", NULL); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("jquery-ui.js", NULL); -jsIncludeFile("ajax.js", NULL); -jsIncludeFile("autocomplete.js", NULL); -jsIncludeFile("hgGateway.js", NULL); -jsIncludeFile("utils.js", NULL); jsIncludeFile("jquery.watermarkinput.js", NULL); +jsIncludeFile("utils.js",NULL); -puts("<CENTER style='font-size:small;'>" - "The UCSC Genome Browser was created by the \n" - "<A HREF=\"../staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>.\n" - "<BR>" - "Software Copyright (c) The Regents of the University of California.\n" - "All rights reserved.\n" - "</CENTER>\n"); - -puts("<FORM ACTION='../cgi-bin/hgTracks' NAME='mainForm' METHOD='GET' style='display:inline;'>\n" - "<CENTER>" - "<table style='background-color:#FFFEF3; border: 1px solid #CCCC99;'>\n" - "<tr><td>\n"); - -puts("<table><tr>"); -if (gotClade) - puts("<td align=center valign=baseline>group</td>"); -puts("<td align=center valign=baseline>genome</td>\n" - "<td align=center valign=baseline>assembly</td>\n" - "<td align=center valign=baseline>position</td>\n" - "<td align=center valign=baseline>search term</td>\n" - "<td align=center valign=baseline> </td>\n" - "</tr>\n<tr>"); - -if (gotClade) - { - puts("<td align=center>\n"); - printCladeListHtml(organism, onChangeClade); - puts("</td>\n"); - } - -puts("<td align=center>\n"); -if (gotClade) - printGenomeListForCladeHtml(db, onChangeOrg); -else - printGenomeListHtml(db, onChangeOrg); -puts("</td>\n"); - -puts("<td align=center>\n"); -printAssemblyListHtml(db, onChangeDB); -puts("</td>\n"); - -puts("<td align=center>\n"); -hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(db, position)); -hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", addCommasToPos(db, position)); -puts("</td><td align=center>\n"); -hPrintf("<input class='positionInput' type='text' name='hgt.positionInput' id='positionInput' size='45'>\n"); -if(supportsSuggest) - hPrintf("<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(db)); -printf("</td>\n"); - -cartSetString(cart, "position", position); -cartSetString(cart, "db", db); -cartSetString(cart, "org", organism); -if (gotClade) - cartSetString(cart, "clade", clade); - -freez(&defaultPosition); -position = NULL; +// Phylogenetic tree .js file, produced by dbDbTaxonomy.pl: +char *hostCode = (hIsPrivateHost() || hIsPreviewHost()) ? "hgwdev" : "rr"; -puts("<td align=center>"); -hButton("Submit", "submit"); -/* This is a clear submit button that browsers will use by default when enter is pressed in position box. FIXME: This should be done with js onchange event! */ -printf("<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>"); -cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ -puts("</td>\n" - "</tr></table>\n" - "</td></tr>\n"); +//#*** FOR EVALUATION PERIOD ONLY -- TODO: remove! +hostCode = "rr"; +//#*** FOR EVALUATION PERIOD ONLY -puts("<tr><td><CENTER><BR>\n" - "<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> " - "the browser user interface settings to their defaults."); +printf("<script src=\"../js/dbDbTaxonomy.%s.js\"></script>\n", hostCode); -#define SURVEY 1 -#ifdef SURVEY -if (survey && differentWord(survey, "off")) - printf(" <span style='background-color:yellow;'>" - "<A HREF=\"%s\" TARGET=_BLANK><EM><B>%s</EM></B></A></span>", - survey, surveyLabel ? surveyLabel : "Take survey"); -#endif +// Main JS for hgGateway: +puts("<script src=\"../js/hgGateway.js\"></script>"); -puts("<BR>\n" - "</CENTER>\n" - "</td></tr><tr><td><CENTER>\n"); +webIncludeFile("inc/jWestFooter.html"); -puts("<TABLE BORDER=\"0\">"); -puts("<TR>"); +webEndJWest(); +} -if (isSearchTracksSupported(db,cart)) +void doMiddle(struct cart *theCart) +/* Depending on invocation, either perform a query and print out results + * or display the main page. */ { - puts("<TD VALIGN=\"TOP\">"); - cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); - puts("</TD>"); +cart = theCart; +if (cgiOptionalString(CARTJSON_COMMAND)) + doCartJson(); +else + doMainPage(); } -// custom track button. disable hgCustom button on GSID server, until -// necessary additional work is authorized. -puts("<TD VALIGN=\"TOP\">"); +// We find matches from various fields of dbDb: +enum dbDbMatchType { ddmtUndef, ddmtDb, ddmtGenome, ddmtSciName, ddmtDescription }; -/* disable CT for CGB servers for the time being */ -if (!hIsGsidServer() && !hIsCgbServer()) +struct dbDbMatch + // Info about a match of a search term to some field of dbDb, including info that + // helps prioritize matches. { - boolean hasCustomTracks = customTracksExist(cart, NULL); - printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n", - hgCustomName(),hasCustomTracks ? CT_MANAGE_BUTTON_LABEL:CT_ADD_BUTTON_LABEL, - hasCustomTracks ? "Manage your custom tracks" : "Add your own custom tracks" ); + struct dbDbMatch *next; + struct dbDb *dbDb; // the row of dbDb in which a match was found + enum dbDbMatchType type; // which field the match was found in + int offset; // offset of the search term in the dbDb value + boolean isWord; // TRUE if the the search term matches the word at offset + boolean isComplete; // TRUE if the search term matches the entire target string + }; + +static struct dbDbMatch *dbDbMatchNew(struct dbDb *dbDb, enum dbDbMatchType type, int offset, + boolean isWord, boolean isComplete) +/* Allocate and return a new dbDbMatch. Do not free dbDb until done with this. */ +{ +struct dbDbMatch *ddm; +AllocVar(ddm); +ddm->dbDb = dbDb; +ddm->type = type; +ddm->offset = offset; +ddm->isWord = isWord; +ddm->isComplete = isComplete; +return ddm; } -puts("</TD>"); -if (hubConnectTableExists()) +static int dbDbMatchCmp(const void *va, const void *vb) +/* Compare two matches by type, orderKey, offset and genome. */ { - puts("<TD VALIGN=\"TOP\">"); - printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n", - "../cgi-bin/hgHubConnect", "track hubs", "Import tracks"); - puts("</TD>"); +const struct dbDbMatch *a = *((struct dbDbMatch **)va); +const struct dbDbMatch *b = *((struct dbDbMatch **)vb); +int diff = b->isComplete - a->isComplete; +if (diff == 0) + diff = b->isWord - a->isWord; +if (diff == 0 && a->isWord && b->isWord) + diff = a->offset - b->offset; +// Use int values of type, in descending numeric order: +if (diff == 0) + diff = (int)(b->type) - (int)(a->type); +if (diff == 0) + diff = a->dbDb->orderKey - b->dbDb->orderKey; +if (diff == 0) + diff = a->offset - b->offset; +if (diff == 0) + diff = strcmp(a->dbDb->genome, b->dbDb->genome); +return diff; } -// configure button -puts("<TD VALIGN=\"TOP\">"); -cgiMakeButtonWithMsg("hgTracksConfigPage", "configure tracks and display", - "Configure track selections and browser display"); -puts("</TD>"); - -puts("</TR></TABLE>"); +INLINE void safeAddN(char **pDest, int *pSize, char *src, int len) +/* Copy len bytes of src into dest. Subtract len from *pSize and add len to *pDest, + * for building up a string bit by bit. */ +{ +safencpy(*pDest, *pSize, src, len); +*pSize -= len; +*pDest += len; +} -puts("</CENTER>\n" -"</td></tr></table>\n" -); -puts("</CENTER>"); +INLINE void safeAdd(char **pDest, int *pSize, char *src) +/* Copy src into dest. Subtract len from *pSize and add len to *pDest, + * for building up a string bit by bit. */ +{ +safeAddN(pDest, pSize, src, strlen(src)); +} -if(!cartVarExists(cart, "pix")) - // put a hidden input for pix on page so default value can be filled in on the client side - hPrintf("<input type='hidden' name='pix' value=''>\n"); +static char *boldTerm(char *target, char *term, int offset, enum dbDbMatchType type) +/* Return a string with <b>term</b> swapped in for term at offset. + * If offset is negative and type is ddmtSciName, treat term as an abbreviated species + * name (term = "G. species" vs. target = "Genus species"): bold the first letter of the + * genus and the matching portion of the species. */ +{ +int termLen = strlen(term); +int targetLen = strlen(target); +if (offset + termLen > targetLen) + errAbort("boldTerm: invalid offset (%d) for term '%s' (length %d) in target '%s' (length %d)", + offset, term, termLen, target, targetLen); +else if (offset < 0 && type != ddmtSciName) + errAbort("boldTerm: negative offset (%d) given for type %d", offset, type); +// Allocate enough to have two bolded chunks: +int resultSize = targetLen + 2*strlen("<b></b>") + 1; +char result[resultSize]; +char *p = result; +int size = sizeof(result); +if (offset >= 0) + { + // The part of target before the term: + safeAddN(&p, &size, target, offset); + // The bolded term: + safeAdd(&p, &size, "<b>"); + safeAddN(&p, &size, target+offset, termLen); + safeAdd(&p, &size, "</b>"); + // The rest of the target after the term: + safeAdd(&p, &size, target+offset+termLen); + // Accounting tweak -- we allocate enough for two bolded chunks, but use only one here: + size -= strlen("<b></b>"); + } +else + { + // Term is abbreviated scientific name -- bold the first letter of the genus: + safeAdd(&p, &size, "<b>"); + safeAddN(&p, &size, target, 1); + safeAdd(&p, &size, "</b>"); + // add the rest of the genus: + char *targetSpecies = skipLeadingSpaces(skipToSpaces(target)); + int targetOffset = targetSpecies - target; + safeAddN(&p, &size, target+1, targetOffset-1); + // bold the matching portion of the species: + char *termSpecies = skipLeadingSpaces(skipToSpaces(term)); + termLen = strlen(termSpecies); + safeAdd(&p, &size, "<b>"); + safeAddN(&p, &size, targetSpecies, termLen); + safeAdd(&p, &size, "</b>"); + // add the rest of the species: + safeAdd(&p, &size, targetSpecies+termLen); + } +if (*p != '\0' || size != 1) + errAbort("boldTerm: bad arithmetic (size is %d, *p is '%c')", size, *p); +return cloneStringZ(result, resultSize); +} -puts("</FORM>"); -if (hIsPreviewHost()) +static void writeDbDbMatch(struct jsonWrite *jw, struct dbDbMatch *match, char *term, + char *category) +/* Write out the JSON encoding of a match in dbDb. */ +{ +struct dbDb *dbDb = match->dbDb; +jsonWriteObjectStart(jw, NULL); +jsonWriteString(jw, "genome", dbDb->genome); +if (match->type == ddmtDb) + jsonWriteString(jw, "db", dbDb->name); +// label includes <b> tag to highlight the match for term. +char label[PATH_LEN*4]; +// value is placed in the input box when user selects the item. +char value[PATH_LEN*4]; +if (match->type == ddmtSciName) { -puts("<P>" -"WARNING: This is our preview site. It is a weekly mirror of our internal development server for public access. " -"Data and tools here are under construction, have not been quality reviewed, and are subject to change " -"at any time. We provide this site for early access, with the warning that it is less available " -"and stable than our public site. For high-quality reviewed annotations on our production server, visit " -" <A HREF=\"http://genome.ucsc.edu\">http://genome.ucsc.edu</A>." -"</P><BR>"); + safef(value, sizeof(value), "%s (%s)", dbDb->scientificName, dbDb->genome); + char *bolded = boldTerm(dbDb->scientificName, term, match->offset, match->type); + safef(label, sizeof(label), "%s (%s)", bolded, dbDb->genome); + freeMem(bolded); } -else if (hIsPrivateHost()) +else if (match->type == ddmtGenome) { -puts("<P>WARNING: This is our development and test site. It usually works, but it is filled with tracks in various " -"stages of construction, and others of little interest to people outside of our local group. " -"It is usually slow because we are building databases on it. The documentation is poor. " - "More data than usual is flat out wrong. Maybe you want to go to " - "<A HREF=\"http://genome.ucsc.edu\">genome.ucsc.edu</A> instead."); + safecpy(value, sizeof(value), dbDb->genome); + char *bolded = boldTerm(dbDb->genome, term, match->offset, match->type); + safecpy(label, sizeof(label), bolded); + freeMem(bolded); + } +else if (match->type == ddmtDb) + { + safef(value, sizeof(value), "%s (%s %s)", + dbDb->name, dbDb->genome, dbDb->description); + char *bolded = boldTerm(dbDb->name, term, match->offset, match->type); + safef(label, sizeof(label), "%s (%s %s)", + bolded, dbDb->genome, dbDb->description); + freeMem(bolded); + } +else if (match->type == ddmtDescription) + { + safef(value, sizeof(value), "%s (%s %s)", + dbDb->name, dbDb->genome, dbDb->description); + char *bolded = boldTerm(dbDb->description, term, match->offset, match->type); + safef(label, sizeof(label), "%s (%s %s)", + dbDb->name, dbDb->genome, bolded); + freeMem(bolded); + } +else + errAbort("writeDbDbMatch: unrecognized dbDbMatchType value %d (db %s, term %s)", + match->type, dbDb->name, term); +jsonWriteString(jw, "label", label); +jsonWriteString(jw, "value", value); +jsonWriteNumber(jw, "taxId", dbDb->taxId); +if (isNotEmpty(category)) + jsonWriteString(jw, "category", category); +jsonWriteObjectEnd(jw); } -if (hIsGsidServer()) +int wordMatchOffset(char *term, char *target) +/* If some word of target starts with term (case insensitive), return the offset of + * that word in target; otherwise return -1. */ +{ +if (startsWith(term, target)) + return 0; +int targetLen = strlen(target); +char targetClone[targetLen+1]; +safecpy(targetClone, sizeof(targetClone), target); +char *p = targetClone; +while (nextWord(&p) && p != NULL) { - webNewSection("%s", "Sequence View\n"); - printf("%s","Sequence View is a customized version of the UCSC Genome Browser, which is " - "specifically tailored to provide functions needed for the GSID HIV Data Browser.\n"); + // skip punctuation like parentheses + while (*p != '\0' && ! isalnum(*p)) + p++; + if (startsWith(term, p)) + return p - targetClone; + } +return -1; } -hgPositionsHelpHtml(organism, db); +static void addIfFirstMatch(struct dbDb *dbDb, enum dbDbMatchType type, int offset, char *target, + char *term, struct hash *matchHash, struct dbDbMatch **pMatchList) +/* If target doesn't already have a match in matchHash, compute matchLength and isWord, + * and then add the new match to pMatchList and add target to matchHash. */ +{ +if (! hashLookup(matchHash, target)) + { + char *termInTarget = (offset >= 0) ? target+offset : target; + int matchLength = countSame(term, termInTarget); + // is the match complete up to a word boundary in termInTarget? + boolean isWord = (matchLength == strlen(term) && + (termInTarget[matchLength] == '\0' || isspace(termInTarget[matchLength]))); + boolean isComplete = sameString(term, target); + struct dbDbMatch *match = dbDbMatchNew(dbDb, type, offset, isWord, isComplete); + slAddHead(pMatchList, match); + hashStore(matchHash, target); + } +} -puts("<FORM ACTION=\"../cgi-bin/hgGateway\" METHOD=\"GET\" NAME=\"orgForm\">"); -cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ -if (gotClade) - printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", clade); -else - printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", "mammal"); +static void checkTerm(char *term, char *target, enum dbDbMatchType type, struct dbDb *dbDb, + struct hash *matchHash, struct dbDbMatch **pMatchList) +/* If target starts with term (case-insensitive), and target is not already in matchHash, + * add target to matchHash and add a new match to pMatchList. */ +{ +// Make uppercase version of target for case-insensitive matching. +int targetLen = strlen(target); +char targetUpcase[targetLen + 1]; +safencpy(targetUpcase, sizeof(targetUpcase), target, targetLen); +touppers(targetUpcase); +int offset = wordMatchOffset(term, targetUpcase); +if (offset >= 0) + { + addIfFirstMatch(dbDb, type, offset, targetUpcase, term, matchHash, pMatchList); + } +else if (offset < 0 && type == ddmtSciName && term[0] == targetUpcase[0]) + { + // For scientific names ("Genus species"), see if the user entered the term as 'G. species' + // e.g. term 'P. trog' for target 'Pan troglodytes' + regmatch_t substrArr[3]; + if (regexMatchSubstrNoCase(term, "^[a-z](\\.| ) *([a-z]+)", substrArr, ArraySize(substrArr))) + { + char *termSpecies = term + substrArr[2].rm_so; + char *targetSpecies = skipLeadingSpaces(skipToSpaces(targetUpcase)); + if (targetSpecies && startsWithNoCase(termSpecies, targetSpecies)) + { + // Keep the negative offset since we can't just bold one chunk of target... + addIfFirstMatch(dbDb, type, offset, targetUpcase, term, matchHash, pMatchList); + } + } + } +} -printf("<input type=\"hidden\" name=\"org\" value=\"%s\">\n", organism); -printf("<input type=\"hidden\" name=\"db\" value=\"%s\">\n", db); -puts("</FORM><BR>"); +static struct dbDbMatch *searchDbDb(struct dbDb *dbDbList, char *term) +/* Search various fields of dbDb for matches to term and sort by relevance. */ +{ +struct dbDbMatch *matchList = NULL; +struct hash *matchHash = hashNew(0); +struct dbDb *dbDb; +for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next) + { + checkTerm(term, dbDb->name, ddmtDb, dbDb, matchHash, &matchList); + // Skip experimental stuff on hgwdev with bogus taxId unless the db name matches term. + if (dbDb->taxId >= 2) + { + checkTerm(term, dbDb->genome, ddmtGenome, dbDb, matchHash, &matchList); + checkTerm(term, dbDb->scientificName, ddmtSciName, dbDb, matchHash, &matchList); + } + // dbDb.description is a little too much for autocomplete ("br" would match dozens + // of Broad assemblies), but we do need to recognize "GRC". + if (startsWith("GR", term)) + checkTerm(term, dbDb->description, ddmtDescription, dbDb, matchHash, &matchList); + } +slSort(&matchList, dbDbMatchCmp); +return matchList; } -void doMiddle(struct cart *theCart) -/* Set up pretty web display and save cart in global. */ +// Assembly hub match: + +struct aHubMatch + // description of an assembly hub db { -char *scientificName = NULL; -cart = theCart; + struct aHubMatch *next; + char *shortLabel; // hub shortLabel + char *hubUrl; // hub url + char *aDb; // assembly db hosted by hub + }; + +static struct aHubMatch *aHubMatchNew(char *shortLabel, char *hubUrl, char *aDb) +/* Allocate and return a description of an assembly hub db. */ +{ +struct aHubMatch *match; +AllocVar(match); +match->shortLabel = cloneString(shortLabel); +match->hubUrl = cloneString(hubUrl); +match->aDb = cloneString(aDb); +return match; +} -if(cgiIsOnWeb()) - checkForGeoMirrorRedirect(cart); -getDbGenomeClade(cart, &db, &organism, &clade, oldVars); -if (! hDbIsActive(db)) +static struct aHubMatch *filterTrixSearchMatches(struct dbDb *dbDbList, + struct trixSearchResult *tsrList) +/* Collect the assembly hub matches (not track hub matches) from a search in hub trix files. */ +{ +if (tsrList == NULL) + return NULL; +struct aHubMatch *aHubMatchList = NULL; +// Make a hash of local dbs so we can tell which hub dbs must be assembly hubs +// not track hubs. +struct hash *localDbs = hashNew(0); +struct dbDb *dbDb; +for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next) + hashStore(localDbs, dbDb->name); + +// tsrList gives hub URLs which we can then look up in hubPublic. +struct dyString *query = sqlDyStringCreate("select shortLabel,hubUrl,dbList from %s " + "where hubUrl in (", + hubPublicTableName()); +struct trixSearchResult *tsr; +for (tsr = tsrList; tsr != NULL; tsr = tsr->next) { - db = hDefaultDb(); - organism = hGenome(db); - clade = hClade(organism); + if (tsr != tsrList) + dyStringAppend(query, ", "); + dyStringPrintf(query, "'%s'", tsr->itemId); } -scientificName = hScientificName(db); -if (hIsGsidServer()) - cartWebStart(theCart, db, "GSID %s Sequence View (UCSC Genome Browser) Gateway \n", organism); -else +dyStringAppendC(query, ')'); +struct sqlConnection *conn = hConnectCentral(); +struct sqlResult *sr = sqlGetResult(conn, query->string); +char **row; +while ((row = sqlNextRow(sr)) != NULL) { - char buffer[128]; - - /* tell html routines *not* to escape htmlOut strings*/ - htmlNoEscape(); - buffer[0] = 0; - if ((scientificName != NULL) && (*scientificName != 0)) + char *shortLabel = row[0]; + char *hubUrl = row[1]; + struct slName *dbName, *dbList = slNameListFromComma(row[2]); + for (dbName = dbList; dbName != NULL; dbName = dbName->next) + if (! hashLookup(localDbs, dbName->name)) { - if (sameString(clade,"ancestor")) - safef(buffer, sizeof(buffer), "(<I>%s</I> Ancestor) ", scientificName); - else - safef(buffer, sizeof(buffer), "(<I>%s</I>) ", scientificName); + slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name)); } - cartWebStart(theCart, db, "%s %s%s Gateway\n", trackHubSkipHubName(organism), buffer, hBrowserName()); - htmlDoEscape(); + } +slReverse(&aHubMatchList); +hDisconnectCentral(&conn); +return aHubMatchList; } -cartFlushHubWarnings(); -hgGateway(); +static void writeAssemblyHubMatches(struct jsonWrite *jw, struct aHubMatch *aHubMatchList) +/* Write out JSON for each assembly in each assembly hub that matched the search term. */ +{ +struct aHubMatch *aHubMatch; +for (aHubMatch = aHubMatchList; aHubMatch != NULL; aHubMatch = aHubMatch->next) + { + jsonWriteObjectStart(jw, NULL); + jsonWriteString(jw, "genome", aHubMatch->shortLabel); + jsonWriteString(jw, "db", aHubMatch->aDb); + jsonWriteString(jw, "hubUrl", aHubMatch->hubUrl); + jsonWriteString(jw, "hubName", hubNameFromUrl(aHubMatch->hubUrl)); + // Add a category label for customized autocomplete-with-categories. + char category[PATH_LEN*4]; + safef(category, sizeof(category), "Assembly Hub: %s", aHubMatch->shortLabel); + jsonWriteString(jw, "category", category); + jsonWriteString(jw, "value", aHubMatch->aDb); + // Use just the db as label, since shortLabel is included in the category label. + jsonWriteString(jw, "label", aHubMatch->aDb); + jsonWriteObjectEnd(jw); + } +} -// TODO REMOVE AFTER AUTOUPGRADE COMPLETE: (added 2014-03-09) -if (dyUpgradeError) - warn("%s", dyUpgradeError->string); +static struct aHubMatch *searchPublicHubs(struct dbDb *dbDbList, char *term) +/* Search for term in public hub trix files -- return a list of matches to assembly hubs + * (i.e. hubs that host an assembly with 2bit etc as opposed to only providing tracks.) */ +{ +struct aHubMatch *aHubMatchList = NULL; +char *trixFile = cfgOptionEnvDefault("HUBSEARCHTRIXFILE", "hubSearchTrixFile", + hReplaceGbdb("/gbdb/hubs/public.ix")); +if (fileExists(trixFile)) + { + struct trix *trix = trixOpen(trixFile); + char termCopy[strlen(term)+1]; + safecpy(termCopy, sizeof(termCopy), term); + tolowers(termCopy); + char *words[512]; + int wordCount = chopByWhite(termCopy, words, ArraySize(words)); + struct trixSearchResult *tsrList = trixSearch(trix, wordCount, words, tsmFirstFive); + aHubMatchList = filterTrixSearchMatches(dbDbList, tsrList); + trixClose(&trix); + } +return aHubMatchList; +} -cartWebEnd(); +static char *getSearchTermUpperCase() +/* If we don't have the SEARCH_TERM cgi param, exit with an HTTP Bad Request response. + * If we do, convert it to upper case for case-insensitive matching and return it. */ +{ +pushAbortHandler(htmlVaBadRequestAbort); +char *term = cgiOptionalString(SEARCH_TERM); +touppers(term); +if (isEmpty(term)) + errAbort("Missing required CGI parameter %s", SEARCH_TERM); +popAbortHandler(); +return term; } -char *excludeVars[] = {NULL}; +static void lookupTerm() +/* Look for matches to term in hgcentral and print as JSON for autocomplete if found. */ +{ +char *term = getSearchTermUpperCase(); + +// Write JSON response with list of matches +puts("Content-Type:text/javascript\n"); + +struct dbDb *dbDbList = hDbDbList(); +struct dbDbMatch *matchList = searchDbDb(dbDbList, term); +struct aHubMatch *aHubMatchList = searchPublicHubs(dbDbList, term); +struct jsonWrite *jw = jsonWriteNew(); +jsonWriteListStart(jw, NULL); +// Write out JSON for dbDb matches, if any; add category if we found assembly hub matches too. +char *category = aHubMatchList ? "UCSC databases" : NULL; +struct dbDbMatch *match; +for (match = matchList; match != NULL; match = match->next) + writeDbDbMatch(jw, match, term, category); +// Write out assembly hub matches, if any. +writeAssemblyHubMatches(jw, aHubMatchList); +jsonWriteListEnd(jw); +puts(jw->dy->string); +jsonWriteFree(&jw); +} int main(int argc, char *argv[]) -/* Process command line. */ +/* Process CGI / command line. */ { -long enteredMainTime = clock1000(); -oldVars = hashNew(10); +/* Null terminated list of CGI Variables we don't want to save + * permanently. */ +char *excludeVars[] = {SEARCH_TERM, CARTJSON_COMMAND, NULL,}; cgiSpoof(&argc, argv); - setUdcCacheDir(); - - -cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); -cgiExitTime("hgGateway", enteredMainTime); +if (cgiOptionalString(SEARCH_TERM)) + // Skip the cart for speedy searches + lookupTerm(); +else + cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }