7a04fb667a40f234c3dd89a72698962edeb3fd7b larrym Thu Jun 10 20:24:01 2010 +0000 use trix search for simple search; style related code review changes per jim diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c index 53db8e7..6bbfbad 100644 --- src/hg/hgTracks/searchTracks.c +++ src/hg/hgTracks/searchTracks.c @@ -1,485 +1,529 @@ /* Track search code used by hgTracks CGI */ #include "common.h" #include "hCommon.h" #include "memalloc.h" #include "obscure.h" #include "dystring.h" #include "hash.h" #include "cheapcgi.h" #include "hPrint.h" #include "htmshell.h" #include "cart.h" #include "hgTracks.h" #include "web.h" #include "jksql.h" #include "hdb.h" +#include "trix.h" -static char const rcsid[] = "$Id: searchTracks.c,v 1.9 2010/06/03 05:52:42 larrym Exp $"; +static char const rcsid[] = "$Id: searchTracks.c,v 1.10 2010/06/10 20:24:01 larrym Exp $"; #define ANYLABEL "Any" #define METADATA_NAME_PREFIX "hgt.metadataName" #define METADATA_VALUE_PREFIX "hgt.metadataValue" static int gCmpGroup(const void *va, const void *vb) /* Compare groups based on label. */ { const struct group *a = *((struct group **)va); const struct group *b = *((struct group **)vb); return strcmp(a->label, b->label); } static int gCmpTrack(const void *va, const void *vb) /* Compare tracks based on longLabel. */ { const struct slRef *aa = *((struct slRef **)va); const struct slRef *bb = *((struct slRef **)vb); const struct track *a = ((struct track *) aa->val); const struct track *b = ((struct track *) bb->val); return strcmp(a->longLabel, b->longLabel); } // XXXX make a matchString function to support "contains", "is" etc. and wildcards in contains // ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) || static boolean isNameMatch(struct track *track, char *str, char *op) { return str && strlen(str) && ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) || (sameString(op, "is") && !strcasecmp(track->longLabel, str)) || (sameString(op, "contains") && containsStringNoCase(track->shortLabel, str) != NULL) || (sameString(op, "contains") && containsStringNoCase(track->longLabel, str) != NULL)); } -static boolean isDescriptionMatch(struct track *track, char *str, struct hash *trackMetadata) -{ +static boolean isDescriptionMatch(struct track *track, char **words, int wordCount) // We parse str and look for every word ANYWHERE in track description (i.e. google style). // XXXX currently quite primitive; do stemming, strip html markup ?? // trackMetaData contains tracks already found via metadata searches. +{ boolean found = FALSE; -if(str && strlen(str)) +if(words) { char *html = track->tdb->html; - if(html == NULL || !strlen(html)) + if(isEmpty(html)) { // XXXX is there a cleaner way to find parent? struct trackDb *parent = track->tdb->parent; while(parent != NULL && (parent->html == NULL || !strlen(parent->html))) parent = parent->parent; if(parent != NULL) html = parent->html; } - if(html && strlen(html)) + if(!isEmpty(html)) { - char *tmp = cloneString(str); - char *val = nextWord(&tmp); - while (val != NULL) + int i; + for(i = 0; i < wordCount; i++) { + char *val = words[i]; if(strstrNoCase(html, val) == NULL) { - struct hashEl *el; found = FALSE; - for(el = hashLookup(trackMetadata, track->track); el != NULL; el = hashLookupNext(el)) - if(sameWord((char *) el->val, val)) break; - found = el != NULL; } else found = TRUE; - if(found) - val = nextWord(&tmp); - else - break; } } } return found; } -static int getTermList(struct sqlConnection *conn, char ***terms, char *type) -{ +static int getTermArray(struct sqlConnection *conn, char ***terms, char *type) // Pull out all term fields from ra entries with given type // Returns count of items found and items via the terms argument. +{ struct sqlResult *sr = NULL; char **row = NULL; char query[256]; struct slName *termList = NULL; int i, count = 0; -char **retval; +char **retVal; safef(query, sizeof(query), "select distinct val from metaDb where var = '%s'", type); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { slNameAddHead(&termList, row[0]); count++; } sqlFreeResult(&sr); slSort(&termList, slNameCmpCase); count++; // make room for "Any" -retval = needMem(sizeof(char *) * count); -retval[0] = cloneString(ANYLABEL); +AllocArray(retVal, count); +retVal[0] = cloneString(ANYLABEL); for(i = 1; termList != NULL;termList = termList->next, i++) { - retval[i] = cloneString(termList->name); + retVal[i] = cloneString(termList->name); } -*terms = retval; +*terms = retVal; return count; } static struct slName *metaDbSearch(struct sqlConnection *conn, char *name, char *val, char *op) -{ // Search the assembly's metaDb table for var; If name == NULL, we search every metadata field. // Search is via mysql, so it's case-insensitive. -struct slName *retval = NULL; +{ +struct slName *retVal = NULL; char query[256]; struct sqlResult *sr = NULL; char **row = NULL; if(sameString(op, "contains")) if(name == NULL) safef(query, sizeof(query), "select obj from metaDb where val like '%%%s%%'", val); else safef(query, sizeof(query), "select obj from metaDb where var = '%s' and val like '%%%s%%'", name, val); else if(name == NULL) safef(query, sizeof(query), "select distinct obj from metaDb where val = '%s'", val); else safef(query, sizeof(query), "select obj from metaDb where var = '%s' and val = '%s'", name, val); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { - slNameAddHead(&retval, row[0]); + slNameAddHead(&retVal, row[0]); } sqlFreeResult(&sr); -return retval; +return retVal; } static int metaDbVars(struct sqlConnection *conn, char *** metaValues) -{ // Search the assemblies metaDb table; If name == NULL, we search every metadata field. +{ char query[256]; struct sqlResult *sr = NULL; char **row = NULL; int i; struct slName *el, *varList = NULL; -char **retval; +char **retVal; safef(query, sizeof(query), "select distinct var from metaDb"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slNameAddHead(&varList, row[0]); sqlFreeResult(&sr); -retval = needMem(sizeof(char *) * slCount(varList)); +retVal = needMem(sizeof(char *) * slCount(varList)); slNameSort(&varList); for (el = varList, i = 0; el != NULL; el = el->next, i++) - retval[i] = el->name; -*metaValues = retval; + retVal[i] = el->name; +*metaValues = retVal; return i; } void doSearchTracks(struct group *groupList) { struct group *group; char *ops[] = {"is", "contains"}; char *op_labels[] = {"is", "contains"}; char *groups[128]; char *labels[128]; int numGroups = 1; groups[0] = ANYLABEL; labels[0] = ANYLABEL; char *currentTab = cartUsualString(cart, "hgt.currentSearchTab", "simpleTab"); char *nameSearch = cartOptionalString(cart, "hgt.nameSearch"); char *nameOp = cartOptionalString(cart, "hgt.nameOp"); char *descSearch; char *groupSearch = cartOptionalString(cart, "hgt.groupSearch"); boolean doSearch = sameString(cartOptionalString(cart, searchTracks), "Search"); struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); struct slRef *tracks = NULL; int numMetadataSelects, tracksFound = 0; int numMetadataNonEmpty = 0; char **metadataName; char **metadataValue; struct hash *parents = newHash(4); boolean simpleSearch; +struct trix *ix; +char ixFile[HDB_MAX_PATH_STRING]; +char **descWords = NULL; +int descWordCount = 0; if(sameString(currentTab, "simpleTab")) { descSearch = cartOptionalString(cart, "hgt.simpleSearch"); simpleSearch = TRUE; freez(&nameSearch); freez(&groupSearch); } else { descSearch = cartOptionalString(cart, "hgt.descSearch"); simpleSearch = FALSE; } +safef(ixFile, sizeof(ixFile), "/gbdb/%s/trackDb.ix", database); +ix = trixOpen(ixFile); getTrackList(&groupList, -2); slSort(&groupList, gCmpGroup); for (group = groupList; group != NULL; group = group->next) { if (group->trackList != NULL) { groups[numGroups] = cloneString(group->name); labels[numGroups] = cloneString(group->label); numGroups++; if (numGroups >= ArraySize(groups)) internalErr(); } } -hPrintf("<form action='%s' name='SearchTracks' method='get'>\n\n", hgTracksName()); +hPrintf("<form action='%s' name='SearchTracks' id='searchTracks' method='get'>\n\n", hgTracksName()); webStartWrapperDetailedNoArgs(cart, database, "", "Track Search (prototype!)", FALSE, FALSE, FALSE, FALSE); hPrintf("<input type='hidden' name='db' value='%s'>\n", database); -fprintf(stderr, "currentTab: %s\n", currentTab); hPrintf("<input type='hidden' name='hgt.currentSearchTab' id='hgt.currentSearchTab' value='%s'>\n", currentTab); hPrintf("<div id='tabs'>\n" "<ul>\n" "<li><a href='#simpleTab'><span>Search</span></a></li>\n" "<li><a href='#advancedTab'><span>Advanced Search</span></a></li>\n" "</ul>\n" "<div id='simpleTab'>\n"); -hPrintf("<input type='text' name='hgt.simpleSearch' value='%s' size='80'>\n", descSearch == NULL ? "" : descSearch); +hPrintf("<input type='text' name='hgt.simpleSearch' id='simpleSearch' value='%s' size='80'>\n", descSearch == NULL ? "" : descSearch); hPrintf("</div>\n" "<div id='advancedTab'>\n" "<table>\n"); hPrintf("<tr><td></td><td></td><td><b>Description:</b></td><td>contains</td>\n"); -hPrintf("<td><input type='text' name='hgt.descSearch' value='%s' size='80'></td></tr>\n", descSearch == NULL ? "" : descSearch); +hPrintf("<td><input type='text' name='hgt.descSearch' id='descSearch' value='%s' size='80'></td></tr>\n", descSearch == NULL ? "" : descSearch); hPrintf("<tr><td></td><td>and</td><td><b>Track Name:</b></td><td>\n"); cgiMakeDropListFull("hgt.nameOp", op_labels, ops, ArraySize(ops), nameOp == NULL ? "contains" : nameOp, NULL); -hPrintf("</td>\n<td><input type='text' name='hgt.nameSearch' value='%s'></td></tr>\n", nameSearch == NULL ? "" : nameSearch); +hPrintf("</td>\n<td><input type='text' name='hgt.nameSearch' id='nameSearch' value='%s'></td></tr>\n", nameSearch == NULL ? "" : nameSearch); hPrintf("<tr><td></td><td>and</td>\n"); hPrintf("<td><b>Group</b></td><td>is</td>\n<td>\n"); cgiMakeDropListFull("hgt.groupSearch", labels, groups, numGroups, groupSearch, NULL); hPrintf("</td></tr>\n"); // figure out how many metadata selects are visible. for(numMetadataSelects = 0;;) { char buf[256]; safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1); char *str = cartOptionalString(cart, buf); if(isEmpty(str)) break; else numMetadataSelects++; } if(numMetadataSelects) { metadataName = needMem(sizeof(char *) * numMetadataSelects); metadataValue = needMem(sizeof(char *) * numMetadataSelects); int i; for(i = 0; i < numMetadataSelects; i++) { char buf[256]; safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, i + 1); metadataName[i] = cartOptionalString(cart, buf); if(!simpleSearch) { safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, i + 1); metadataValue[i] = cartOptionalString(cart, buf); if(sameString(metadataValue[i], ANYLABEL)) metadataValue[i] = NULL; if(!isEmpty(metadataValue[i])) numMetadataNonEmpty++; } } } else { // create defaults numMetadataSelects = 2; metadataName = needMem(sizeof(char *) * numMetadataSelects); metadataValue = needMem(sizeof(char *) * numMetadataSelects); metadataName[0] = "cell"; metadataName[1] = "antibody"; metadataValue[0] = ANYLABEL; metadataValue[1] = ANYLABEL; } -fprintf(stderr, "numMetadataSelects: %d: %d\n", numMetadataSelects, numMetadataNonEmpty); - if(metaDbExists) { int i; char **metaValues = NULL; int count = metaDbVars(conn, &metaValues); for(i = 0; i < numMetadataSelects; i++) { char **terms; char buf[256]; int len; hPrintf("<tr><td>\n"); if(i == 0) hPrintf(" \n"); else hButtonWithOnClick("hgt.ignoreme", "+", "add a select", "alert('add a select is not yet implemented'); return false;"); hPrintf("</td><td>and</td>\n"); hPrintf("</td><td>\n"); safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, i + 1); cgiMakeDropListClassWithStyleAndJavascript(buf, metaValues, count, metadataName[i], NULL, NULL, "onchange=metadataSelectChanged(this)"); hPrintf("</td><td>is</td>\n<td>\n"); - len = getTermList(conn, &terms, metadataName[i]); + len = getTermArray(conn, &terms, metadataName[i]); safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1); cgiMakeDropListFull(buf, terms, terms, len, metadataValue[i], NULL); hPrintf("</td></tr>\n"); } } hPrintf("</table>\n"); -// hPrintf("<u><a onclick=\"alert('add a select not yet implemented')\" title=\"add a select\">+</a></u>"); hPrintf("</div>\n</div>\n"); -hPrintf("<input type='submit' name='%s' value='Search'>\n", searchTracks); +hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search'>\n", searchTracks); hPrintf("<input type='submit' name='submit' value='Cancel'>\n"); hPrintf("</form>\n"); if(descSearch != NULL && !strlen(descSearch)) descSearch = NULL; if(groupSearch != NULL && sameString(groupSearch, ANYLABEL)) groupSearch = NULL; -if(doSearch && ((nameSearch != NULL && strlen(nameSearch)) || descSearch != NULL || groupSearch != NULL || numMetadataNonEmpty)) + +if(!isEmpty(descSearch)) + { + char *tmp = cloneString(descSearch); + char *val = nextWord(&tmp); + struct slName *el, *descList = NULL; + int i; + + while (val != NULL) + { + slNameAddTail(&descList, val); + val = nextWord(&tmp); + } + descWordCount = slCount(descList); + descWords = needMem(sizeof(char *) * descWordCount); + for(i = 0, el = descList; el != NULL; i++, el = el->next) + descWords[i] = strLower(el->name); + + } + +if(doSearch) + { + if(simpleSearch) + { + struct trixSearchResult *tsList; + struct hash *trackHash = newHash(0); + + // Create a hash of tracks, so we can map the track name into a track struct. + for (group = groupList; group != NULL; group = group->next) + { + struct trackRef *tr; + for (tr = group->trackList; tr != NULL; tr = tr->next) + { + struct track *track = tr->track; + hashAdd(trackHash, track->track, track); + struct track *subTrack = track->subtracks; + for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next) + hashAdd(trackHash, subTrack->track, subTrack); + } + } + for(tsList = trixSearch(ix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next) + { + struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId); + refAdd(&tracks, track); + tracksFound++; + } + slReverse(&tracks); + } + else if(!isEmpty(nameSearch) || descSearch != NULL || groupSearch != NULL || numMetadataNonEmpty) { // First do the metaDb searches, which can be done quickly for all tracks with db queries. struct hash *matchingTracks = newHash(0); struct hash *trackMetadata = newHash(0); struct slName *el, *metaTracks = NULL; int i; + for(i = 0; i < numMetadataSelects; i++) { if(!isEmpty(metadataValue[i])) { struct slName *tmp = metaDbSearch(conn, metadataName[i], metadataValue[i], "is"); if(metaTracks == NULL) metaTracks = tmp; else metaTracks = slNameIntersection(metaTracks, tmp); } } for (el = metaTracks; el != NULL; el = el->next) hashAddInt(matchingTracks, el->name, 1); if(metaDbExists && !isEmpty(descSearch)) { // Load all metadata words for each track to facilitate metadata search. char query[256]; struct sqlResult *sr = NULL; char **row; safef(query, sizeof(query), "select obj, val from metaDb"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *str = cloneString(row[1]); hashAdd(trackMetadata, row[0], str); } sqlFreeResult(&sr); } for (group = groupList; group != NULL; group = group->next) { if(groupSearch == NULL || sameString(group->name, groupSearch)) { if (group->trackList != NULL) { struct trackRef *tr; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, nameOp)) && - (isEmpty(descSearch) || isDescriptionMatch(track, descSearch, trackMetadata)) && + (isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) && (!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL)) { tracksFound++; refAdd(&tracks, track); } if (track->subtracks != NULL) { struct track *subTrack; for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next) { if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, nameOp)) && - (isEmpty(descSearch) || isDescriptionMatch(subTrack, descSearch, trackMetadata)) && + (isEmpty(descSearch) || isDescriptionMatch(subTrack, descWords, descWordCount)) && (!numMetadataNonEmpty || hashLookup(matchingTracks, subTrack->track) != NULL)) { // XXXX to parent hash. - use tdb->parent instead. hashAdd(parents, subTrack->track, track); tracksFound++; refAdd(&tracks, subTrack); } } } } } } } slSort(&tracks, gCmpTrack); + } + } + if(tracksFound) { hPrintf("<p>%d tracks found:</p>\n", tracksFound); hPrintf("<form action='%s' name='SearchTracks' method='post'>\n\n", hgTracksName()); hButton("submit", "save"); hButtonWithOnClick("hgt.ignoreme", "show all", "show all found tracks", "alert('show all not yet implemented'); return false;"); hPrintf("<table>\n"); - hPrintf("<tr bgcolor='#666666'><td><br /></td><td><b>Name</b></td><td><b>Description</b></td><td><b>Group</b></td></tr>\n"); + hPrintf("<tr bgcolor='#666666'><td><br /></td><td><b>Name</b></td><td><b>Description</b></td></tr>\n"); struct slRef *ptr; while((ptr = slPopHead(&tracks))) { struct track *track = (struct track *) ptr->val; // trackDbOutput(track->tdb, stderr, ',', '\n'); hPrintf("<tr bgcolor='#EEEEEE'>\n"); hPrintf("<td>\n"); if (tdbIsSuper(track->tdb)) { superTrackDropDown(cart, track->tdb, superTrackHasVisibleMembers(track->tdb)); } else { hTvDropDownClassVisOnly(track->track, track->visibility, track->canPack, (track->visibility == tvHide) ? "hiddenText" : "normalText", trackDbSetting(track->tdb, "onlyVisibility")); } hPrintf("</td>\n"); - hPrintf("<td>%s</td>\n", track->shortLabel); + hPrintf("<td>%s", track->shortLabel); + compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE); + hPrintf("</td>\n"); hPrintf("<td><a target='_top' href='%s'>%s</a></td>\n", trackUrl(track->track, NULL), track->longLabel); - // How do we get subtrack's parent? - struct track *parent = NULL; - if(hashLookup(parents, track->track) != NULL) - parent = (struct track *) hashLookup(parents, track->track)->val; - hPrintf("<td>%s</td>\n", parent != NULL ? parent->longLabel : track->group != NULL ? track->group->label : ""); hPrintf("</tr>\n"); } hPrintf("</table>\n"); hButton("submit", "save"); hPrintf("\n</form>\n"); } else { + if(doSearch) hPrintf("<p>No tracks found</p>\n"); } - } webEndSectionTables(); }