c9763e30c4613046362b9d9c47866adafc937ce5 tdreszer Mon Oct 25 15:52:32 2010 -0700 More twiddling with css diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c index 4b8cdef..41dee50 100644 --- src/hg/hgTracks/searchTracks.c +++ src/hg/hgTracks/searchTracks.c @@ -1,962 +1,962 @@ /* Track search code used by hgTracks CGI */ #include "common.h" #include "searchTracks.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 "mdb.h" #include "trix.h" #include "jsHelper.h" #include "imageV2.h" #ifndef TRACK_SEARCH void doSearchTracks(struct group *groupList) { return; } #else///ifdef TRACK_SEARCH #define ANYLABEL "Any" #define TRACK_SEARCH_FORM "trackSearch" #define SEARCH_RESULTS_FORM "searchResults" #define METADATA_NAME_PREFIX "hgt_mdbVar" #define METADATA_VALUE_PREFIX "hgt_mdbVal" #define TRACK_SEARCH_CURRENT_TAB "tsCurTab" #define TRACK_SEARCH_SIMPLE "tsSimple" #define TRACK_SEARCH_ON_NAME "tsName" #define TRACK_SEARCH_ON_GROUP "tsGroup" #define TRACK_SEARCH_ON_DESCR "tsDescr" #define TRACK_SEARCH_SORT "tsSort" 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); } // Would like to do a radio button choice ofsorts enum sortBy { sbRelevance=0, sbAbc =1, sbHierarchy=2, }; static int gCmpTrackHierarchy(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); if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb)) return -1; else if (!tdbIsFolder(a->tdb) && tdbIsFolder(b->tdb)) return 1; if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb)) return -1; else if (!tdbIsContainer(a->tdb) && tdbIsContainer(b->tdb)) return 1; if (!tdbIsContainerChild(a->tdb) && tdbIsContainerChild(b->tdb)) return -1; else if ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb)) return 1; return strcasecmp(a->longLabel, b->longLabel); } 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 strcasecmp(a->longLabel, b->longLabel); } static void findTracksSort(struct slRef **pTrack, boolean simpleSearch, enum sortBy sortBy) { if (sortBy == sbHierarchy) slSort(pTrack, gCmpTrackHierarchy); else if (sortBy == sbAbc) slSort(pTrack, gCmpTrack); else slReverse(pTrack); } // 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 **words, int wordCount) // We parse str and look for every word at the start of any word in track description (i.e. google style). { if(words) { // We do NOT lookup up parent hierarchy for html descriptions. char *html = track->tdb->html; if(!isEmpty(html)) { /* This probably could be made more efficient by parsing the html into some kind of b-tree, but I am assuming that the inner html loop while only happen for 1-2 words for vast majority of the tracks. */ int i, numMatches = 0; html = stripRegEx(html, "<[^>]*>", REG_ICASE); for(i = 0; i < wordCount; i++) { char *needle = words[i]; char *haystack, *tmp = cloneString(html); boolean found = FALSE; while((haystack = nextWord(&tmp))) { char *ptr = strstrNoCase(haystack, needle); if(ptr != NULL && ptr == haystack) { found = TRUE; break; } } if(found) numMatches++; else break; } if(numMatches == wordCount) return TRUE; } } return FALSE; } static int getTermArray(struct sqlConnection *conn, char ***pLabels, char ***pTerms, char *type) // Pull out all term fields from ra entries with given type // Returns count of items found and items via the terms argument. { int ix = 0, count = 0; char **labels; char **values; struct slPair *pairs = mdbValLabelSearch(conn, type, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files count = slCount(pairs) + 1; // make room for "Any" AllocArray(labels, count); AllocArray(values, count); labels[ix] = cloneString(ANYLABEL); values[ix] = cloneString(ANYLABEL); struct slPair *pair = NULL; while((pair = slPopHead(&pairs)) != NULL) { ix++; labels[ix] = pair->name; values[ix] = pair->val; freeMem(pair); } *pLabels = labels; *pTerms = values; return count; } static int metaDbVars(struct sqlConnection *conn, char *** metaVars, char *** metaLabels) // Search the assemblies metaDb table; If name == NULL, we search every metadata field. { char query[256]; #define WHITE_LIST_COUNT 35 #ifdef WHITE_LIST_COUNT #define WHITE_LIST_VAR 0 #define WHITE_LIST_LABEL 1 char *whiteList[WHITE_LIST_COUNT][2] = { {"age", "Age of experimental organism"}, {"antibody", "Antibody or target protein"}, {"origAssembly", "Assembly originally mapped to"}, {"cell", "Cell, tissue or DNA sample"}, {"localization", "Cell compartment"}, {"control", "Control or Input for ChIPseq"}, //{"controlId", "ControlId - explicit relationship"}, {"dataType", "Experiment type"}, {"dataVersion", "ENCODE release"}, //{"fragLength", "Fragment Length for ChIPseq"}, //{"freezeDate", "Gencode freeze date"}, //{"level", "Gencode level"}, //{"annotation", "Gencode annotation"}, {"geoSample", "GEO accession"}, {"growthProtocol", "Growth Protocol"}, {"lab", "Lab producing data"}, {"labVersion", "Lab specific details"}, {"labExpId", "Lab specific identifier"}, {"softwareVersion", "Lab specific informatics"}, {"protocol", "Library Protocol"}, {"mapAlgorithm", "Mapping algorithm"}, {"readType", "Paired/Single reads lengths"}, {"grant", "Principal Investigator"}, {"replicate", "Replicate number"}, //{"restrictionEnzyme","Restriction Enzyme used"}, //{"ripAntibody", "RIP Antibody"}, //{"ripTgtProtein", "RIP Target Protein"}, {"rnaExtract", "RNA Extract"}, {"seqPlatform", "Sequencing Platform"}, {"setType", "Experiment or Input"}, {"sex", "Sex of organism"}, {"strain", "Strain of organism"}, {"subId", "Submission Id"}, {"treatment", "Treatment"}, {"view", "View - Peaks or Signals"}, }; // FIXME: The whitelist should be a table or ra // FIXME: The whitelist should be in list order // FIXME: Should read in list, then verify that an mdb val exists. char **retVar = needMem(sizeof(char *) * WHITE_LIST_COUNT); char **retLab = needMem(sizeof(char *) * WHITE_LIST_COUNT); int ix,count; for(ix=0,count=0;ix<WHITE_LIST_COUNT;ix++) { safef(query, sizeof(query), "select count(*) from metaDb where var = '%s'",whiteList[ix][WHITE_LIST_VAR]); if(sqlQuickNum(conn,query) > 0) { retVar[count] = whiteList[ix][WHITE_LIST_VAR]; retLab[count] = whiteList[ix][WHITE_LIST_LABEL]; count++; } } if(count == 0) { freez(&retVar); freez(&retLab); } *metaVars = retVar; *metaLabels = retLab; return count; #else///ifndef WHITE_LIST_COUNT char **retVar; char **retLab; struct slName *el, *varList = NULL; struct sqlResult *sr = NULL; char **row = NULL; safef(query, sizeof(query), "select distinct var from metaDb order by var"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slNameAddHead(&varList, row[0]); sqlFreeResult(&sr); retVar = needMem(sizeof(char *) * slCount(varList)); retLab = needMem(sizeof(char *) * slCount(varList)); slReverse(&varList); //slNameSort(&varList); int count = 0; for (el = varList; el != NULL; el = el->next) { retVar[count] = el->name; retLab[count] = el->name; count++; } *metaVars = retVar; *whiteLabels = retLab; return count; #endif///ndef WHITE_LIST_COUNT } static int printMdbSelects(struct sqlConnection *conn,struct cart *cart,boolean simpleSearch,char ***pMdbVar,char ***pMdbVal,int *numMetadataNonEmpty,int cols) // Prints a table of mdb selects if appropriate and returns number of them { // figure out how many metadata selects are visible. int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after int numMetadataSelects = 0; char **mdbVar = NULL; char **mdbVal = NULL; char **mdbVars = NULL; char **mdbVarLabels = NULL; int i, count = metaDbVars(conn, &mdbVars, &mdbVarLabels); for(;;) { 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(delSearchSelect) numMetadataSelects--; if(addSearchSelect) numMetadataSelects++; if(numMetadataSelects) { mdbVar = needMem(sizeof(char *) * numMetadataSelects); mdbVal = needMem(sizeof(char *) * numMetadataSelects); *pMdbVar = mdbVar; *pMdbVal = mdbVal; int i; for(i = 0; i < numMetadataSelects; i++) { char buf[256]; int offset; // used to handle additions/deletions if(addSearchSelect > 0 && i >= addSearchSelect) offset = 0; // do nothing to offset (i.e. copy data from previous row) else if(delSearchSelect > 0 && i + 1 >= delSearchSelect) offset = 2; else offset = 1; safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, i + offset); mdbVar[i] = cloneString(cartOptionalString(cart, buf)); if(!simpleSearch) { int j; boolean found = FALSE; // We need to make sure mdbVar[i] is valid in this assembly; if it isn't, reset it to "cell". for(j = 0; j < count && !found; j++) if(sameString(mdbVars[j], mdbVar[i])) found = TRUE; if(found) { safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, i + offset); mdbVal[i] = cloneString(cartOptionalString(cart, buf)); if(sameString(mdbVal[i], ANYLABEL)) mdbVal[i] = NULL; } else { mdbVar[i] = cloneString("cell"); mdbVal[i] = NULL; } if(!isEmpty(mdbVal[i])) (*numMetadataNonEmpty)++; } } if(delSearchSelect > 0) { char buf[255]; safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1); cartRemove(cart, buf); safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1); cartRemove(cart, buf); } } else { // create defaults numMetadataSelects = 2; mdbVar = needMem(sizeof(char *) * numMetadataSelects); mdbVal = needMem(sizeof(char *) * numMetadataSelects); mdbVar[0] = "cell"; mdbVar[1] = "antibody"; mdbVal[0] = ANYLABEL; mdbVal[1] = ANYLABEL; } hPrintf("<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; max-height:20px;'><em style='color:%s; width:200px;'>ENCODE terms</em></td></tr>", cols,COLOR_DARKGREY); for(i = 0; i < numMetadataSelects; i++) { char **terms = NULL, **labels = NULL; char buf[256]; int len; #define PRINT_BUTTON(name,value,msg,js) printf("<input type='submit' name='%s' value='%s' style='font-size:.7em;' title='%s' onclick='%s'>", (name), (value), (msg), (js)); hPrintf("<tr><td>\n"); if(numMetadataSelects > 2 || i >= 2) { safef(buf, sizeof(buf), "return delSearchSelect(this, %d);", i + 1); PRINT_BUTTON(TRACK_SEARCH, "-", "delete this row", buf); } else hPrintf(" "); hPrintf("</td><td>\n"); safef(buf, sizeof(buf), "return addSearchSelect(this, %d);", i + 1); PRINT_BUTTON(TRACK_SEARCH, "+", "add another row after this row", buf); hPrintf("</td><td>and </td><td colspan=3 nowrap>\n"); safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, i + 1); - cgiDropDownWithTextValsAndExtra(buf, mdbVarLabels, mdbVars,count,mdbVar[i],"class='mdbVar' onchange='findTracksMdbVarChanged(this);'"); + cgiDropDownWithTextValsAndExtra(buf, mdbVarLabels, mdbVars,count,mdbVar[i],"class='mdbVar' style='font-size:.9em;' onchange='findTracksMdbVarChanged(this);'"); hPrintf("</td><td nowrap style='max-width:600px;'>is\n"); len = getTermArray(conn, &labels, &terms, mdbVar[i]); safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1); - cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px;' onchange='findTracksSearchButtonsEnable(true);'"); + cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px; font-size:.9em;' onchange='findTracksSearchButtonsEnable(true);'"); hPrintf("<span id='helpLink%d'>help</span></td>\n", i + 1); hPrintf("</tr>\n"); } hPrintf("<tr><td colspan='%d' align='right' style='height:10px; max-height:10px;'> </td></tr>", cols); //hPrintf("<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; max-height:20px;'> </td></tr>", cols); return numMetadataSelects; } static struct slRef *simpleSearchForTracksstruct(struct trix *trix,char **descWords,int descWordCount) // Performs the simple search and returns the found tracks. { struct slRef *tracks = NULL; struct trixSearchResult *tsList; for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next) { struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId); if (track != NULL) // It is expected that this is NULL (e.g. when the trix references trackDb tracks which have no tables) { refAdd(&tracks, track); } } return tracks; } static struct slRef *advancedSearchForTracks(struct sqlConnection *conn,struct group *groupList, char **descWords,int descWordCount, char *nameSearch, char *descSearch, char *groupSearch, int numMetadataNonEmpty,int numMetadataSelects,char **mdbVar,char **mdbVal) // Performs the advanced search and returns the found tracks. { int tracksFound = 0; struct slRef *tracks = NULL; 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 slName *el, *metaTracks = NULL; int i; for(i = 0; i < numMetadataSelects; i++) { if(!isEmpty(mdbVal[i])) { struct slName *tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE); if(metaTracks == NULL) metaTracks = tmp; else metaTracks = slNameIntersection(metaTracks, tmp); } } for (el = metaTracks; el != NULL; el = el->next) hashAddInt(matchingTracks, el->name, 1); struct group *group; 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, "contains")) && (isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) && (!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL)) { if (track != NULL) { tracksFound++; refAdd(&tracks, track); } else warn("found group track is NULL."); } if (track->subtracks != NULL) { struct track *subTrack; for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next) { if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, "contains")) && (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); if (track != NULL) { tracksFound++; refAdd(&tracks, subTrack); } else warn("found subtrack is NULL."); } } } } } } } } return tracks; } #define MAX_FOUND_TRACKS 100 static void findTracksPageLinks(int tracksFound, int startFrom) { if (tracksFound <= MAX_FOUND_TRACKS) return; // Opener int willStartAt = 0; int curPage = (startFrom/MAX_FOUND_TRACKS) + 1; int endAt = startFrom+MAX_FOUND_TRACKS; if (endAt > tracksFound) endAt = tracksFound; hPrintf("<span><em style='font-size:.9em;'>Listing %d - %d of %d tracks</em> ",startFrom+1,endAt,tracksFound); // << and < if (startFrom >= MAX_FOUND_TRACKS) { hPrintf("<a href='../cgi-bin/hgTracks?%s=Search&%s=0' title='First page of found tracks' onclick='return findTracksPage(\"%s\",0);'>«</a> ", TRACK_SEARCH,TRACK_SEARCH_PAGER,TRACK_SEARCH_PAGER); willStartAt = startFrom - MAX_FOUND_TRACKS; hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Previous page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>‹</a> ", TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt); } // page number links int lastPage = (tracksFound/MAX_FOUND_TRACKS); if ((tracksFound % MAX_FOUND_TRACKS) > 0) lastPage++; int thisPage = curPage - 3; // Window of 3 pages above and below if (thisPage < 1) thisPage = 1; for (;thisPage <= lastPage && thisPage <= curPage + 3; thisPage++) { if (thisPage != curPage) { willStartAt = ((thisPage - 1) * MAX_FOUND_TRACKS); endAt = willStartAt+ MAX_FOUND_TRACKS; if (endAt > tracksFound) endAt = tracksFound; hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Page %d (%d - %d) tracks' onclick='return findTracksPage(\"%s\",%d);'>%d</a> ", TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,thisPage,willStartAt+1,endAt,TRACK_SEARCH_PAGER,willStartAt,thisPage); } else hPrintf(" <em style='color:%s;'>%d</em> ",COLOR_DARKGREY,thisPage); } // > and >> if ((startFrom + MAX_FOUND_TRACKS) < tracksFound) { willStartAt = startFrom + MAX_FOUND_TRACKS; hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Next page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>›</a> ", TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt); willStartAt = tracksFound - (tracksFound % MAX_FOUND_TRACKS); if (willStartAt == tracksFound) willStartAt -= MAX_FOUND_TRACKS; hPrintf(" <a href='../cgi-bin/hgTracks?%s=Search&%s=%d' title='Last page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>»</a></span>\n", TRACK_SEARCH,TRACK_SEARCH_PAGER,willStartAt,TRACK_SEARCH_PAGER,willStartAt); } } static void displayFoundTracks(struct cart *cart, struct slRef *tracks, int tracksFound,enum sortBy sortBy) // Routine for displaying found tracks { hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it if(tracksFound < 1) { hPrintf("<p>No tracks found</p>\n"); } else { struct hash *tdbHash = makeTrackHash(database, chromName); hPrintf("<form action='%s' name='%s' id='%s' method='post'>\n\n", hgTracksName(),SEARCH_RESULTS_FORM,SEARCH_RESULTS_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo int startFrom = 0; hPrintf("<table id='foundTracks'>\n"); // Opening view in browser button and foundTracks count #define ENOUGH_FOUND_TRACKS 10 if(tracksFound >= ENOUGH_FOUND_TRACKS) { hPrintf("<tr><td nowrap colspan=3>\n"); - hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' style='font-size:.8em;'>"); + hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='return to browser' class='viewBtn' style='font-size:.8em;'>"); hPrintf(" <FONT class='selCbCount'></font>\n"); startFrom = cartUsualInt(cart,TRACK_SEARCH_PAGER,0); if (startFrom > 0 && startFrom < tracksFound) { int countUp = 0; for(countUp=0; countUp < startFrom;countUp++) { if (slPopHead(&tracks) == NULL) // memory waste break; } } hPrintf("</td><td align='right' valign='bottom'>\n"); findTracksPageLinks(tracksFound,startFrom); hPrintf("</td></tr>\n"); } // Begin foundTracks table //hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n"); hPrintf("<tr><td colspan='2'>\n"); hPrintf("</td><td align='right'>\n"); #define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracksCheckAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>" hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER); hPrintf(PM_BUTTON,"true", "plus_all", "add_sm.gif", "Select"); hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect"); hPrintf("</td><td><b>Visibility</b></td><td colspan=2> <b>Track Name</b>\n"); // Sort options? if(tracksFound >= ENOUGH_FOUND_TRACKS) { hPrintf("<span style='float:right;'>Sort:"); cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "0", (sortBy == sbRelevance),"onchange=\"findTracksSortNow(this);\""); hPrintf("by Relevance"); cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "1", (sortBy == sbAbc), "onchange=\"findTracksSortNow(this);\""); hPrintf("Alphabetically"); cgiMakeOnClickRadioButton(TRACK_SEARCH_SORT, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\""); hPrintf("by Hierarchy </span>\n"); } hPrintf("</td></tr>\n"); // Set up json for js functionality struct dyString *jsonTdbVars = NULL; int trackCount=0; boolean containerTrackCount = 0; struct slRef *ptr; while((ptr = slPopHead(&tracks))) { if(++trackCount > MAX_FOUND_TRACKS) break; struct track *track = (struct track *) ptr->val; jsonTdbSettingsBuild(&jsonTdbVars, track); if (tdbIsFolder(track->tdb)) // supertrack hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n","#EED5B7");//"#DEB887");//"#E6B426");//#FCECC0//COLOR_LTGREY);//COLOR_LTGREEN);//COLOR_TRACKLIST_LEVEL1); else if (tdbIsContainer(track->tdb)) hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3); else hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2); hPrintf("<td align='center'>\n"); // Determine visibility and checked state track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE); boolean checked = ( track->visibility != tvHide ); if(tdbIsContainerChild(track->tdb)) { //track->visibility = limitedVisFromComposite(track); checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here. Visible=checked&&enabled checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set! } // Setup the check box #define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>" if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb)) // subtracks and folder children get "_sel" var. ("_sel" var is temporary on folder children) hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY); #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' onclick='findTracksClickedOne(this,true);'%s>" hPrintf(CB_SEEN,track->track,(checked?" CHECKED":"")); hPrintf("</td><td>\n"); // Setup the visibility drop down #define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>" hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var char extra[512]; if (tdbIsFolder(track->tdb)) { safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track); hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra); } else { safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track); hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra); } // If this is a container track, allow configuring... if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb)) { containerTrackCount++; hPrintf(" <a href='hgTrackUi?db=%s&g=%s&%s=Search' title='Configure this container track...'><IMG SRC='../images/folderWrench.png'></a> ",database,track->track,TRACK_SEARCH); } hPrintf("</td>\n"); // shortLabel has description popup and longLabel has "..." metadata hPrintf("<td><a target='_top' onclick=\"hgTrackUiPopUp('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel); hPrintf("<td>%s", track->longLabel); compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash); hPrintf("</td></tr>\n"); } //hPrintf("</table>\n"); // Closing view in browser button and foundTracks count hPrintf("<tr><td nowrap colspan=3>"); hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn' style='font-size:.8em;'>"); hPrintf(" <FONT class='selCbCount'></font>"); if(tracksFound >= ENOUGH_FOUND_TRACKS) { hPrintf("</td><td align='right' valign='top'>\n"); findTracksPageLinks(tracksFound,startFrom); hPrintf("</td></tr>\n"); } hPrintf("</table>\n"); if(containerTrackCount > 0) hPrintf("<BR><IMG SRC='../images/folderWrench.png'> Tracks so marked are containers which group related data tracks. Containers may need additional configuration (by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can be viewed in the browser.<BR>\n"); //hPrintf("* Tracks so marked are containers which group related data tracks. These may not be visible unless further configuration is done. Click on the * to configure these.<BR><BR>\n"); hPrintf("\n</form>\n"); // be done with json hWrites(jsonTdbSettingsUse(&jsonTdbVars)); } #ifdef OMIT if(!doSearch) { hPrintf("<p><b>Recently Done</b><ul>\n" "<li>Can now page through found tracks 100 at a time.</li>" "<li>Added <IMG SRC='../images/folderWrench.png'> icon for contqainers with a configuration link. Is this okay?</li>" "<li>SuperTracks can now be found.</li>" "<li>Configuration of superTrack children's vis should result in proper superTrack reshaping. (This is really an hgTrackUi feature.)</li>" "<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>" "<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks. (In demo1: only default state composites; demo2: all composites.)</li>" "<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying. Better suggestions?</li>" "</ul></p>" "<p><b>Suggested improvments:</b><ul>\n" "<li>The metadata values will not be white-listed, but it would be nice to have more descriptive text for them. A short label added to cv.ra?</li>" "<li>Look and feel of found track list (here) and composite subtrack list (hgTrackUi) should converge. Jim suggests look and feel of hgTracks 'Configure Tracks...' list instead.</li>" "<li>Drop-down list of terms (cells, antibodies, etc.) should be multi-select with checkBoxes as seen in filterComposites. Perhaps saved for v2.0.</li>" "</ul></p>\n"); } #endif///def OMIT hPrintf("</div>"); // This div allows the clear button to empty it } void doSearchTracks(struct group *groupList) { if (!advancedJavascriptFeaturesEnabled(cart)) { warn("Requires advanced javascript features."); return; } struct group *group; char *groups[128]; char *labels[128]; int numGroups = 1; groups[0] = ANYLABEL; labels[0] = ANYLABEL; char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab"); char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); char *descSearch; char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP); boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0; struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); int numMetadataSelects, tracksFound = 0; int numMetadataNonEmpty = 0; char **mdbVar = NULL; char **mdbVal = NULL; #ifdef ONE_FUNC struct hash *parents = newHash(4); #endif///def ONE_FUNC boolean simpleSearch; struct trix *trix; char trixFile[HDB_MAX_PATH_STRING]; char **descWords = NULL; int descWordCount = 0; boolean searchTermsExist = FALSE; int cols; char buf[512]; if(sameString(currentTab, "simpleTab")) { descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE); simpleSearch = TRUE; freez(&nameSearch); freez(&groupSearch); } else { descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR); simpleSearch = FALSE; } trackList = getTrackList(&groupList, -2); // global makeGlobalTrackHash(trackList); // NOTE: This is necessary when container cfg by '*' results in vis changes // This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping. #ifdef SUBTRACKS_HAVE_VIS parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated #endif///def SUBTRACKS_HAVE_VIS getSearchTrixFile(database, trixFile, sizeof(trixFile)); trix = trixOpen(trixFile); slSort(&groupList, gCmpGroup); for (group = groupList; group != NULL; group = group->next) { groupTrackListAddSuper(cart, group); if (group->trackList != NULL) { groups[numGroups] = cloneString(group->name); labels[numGroups] = cloneString(group->label); numGroups++; if (numGroups >= ArraySize(groups)) internalErr(); } } safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database)); webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE); hPrintf("<div style='max-width:1080px;'>"); hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo safef(buf, sizeof(buf), "%lu", clock1()); cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache hPrintf("<input type='hidden' name='db' value='%s'>\n", database); hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW); hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER); hPrintf("<div id='tabs' style='display:none; %s'>\n" "<ul>\n" - "<li><a href='#simpleTab'><B style='font-size:.8em;'>Search</B></a></li>\n" - "<li><a href='#advancedTab'><B style='font-size:.8em;'>Advanced</B></a></li>\n" + "<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n" + "<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n" "</ul>\n" "<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;"); -hPrintf("<table style='width:100%%; font-size:.8em;'><tr><td colspan='2'>"); +hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>"); hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n", TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch); if (simpleSearch && descSearch) searchTermsExist = TRUE; hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>"); //hPrintf("</td></tr></table>"); -hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search' style='font-size:.7em;'>\n", TRACK_SEARCH); -hPrintf("<input type='button' name='clear' value='Clear' class='clear' style='font-size:.7em;' onclick='findTracksClear();'>\n"); -hPrintf("<input type='submit' name='submit' value='Cancel' class='cancel' style='font-size:.7em;'>\n"); +hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH); +hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n"); +hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); hPrintf("</div>\n"); // Advanced tab hPrintf("<div id='advancedTab' style='width:inherit;'>\n" - "<table cellSpacing=0 style='width:inherit; font-size:.8em;'>\n"); + "<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n"); cols = 7; // Track Name contains hPrintf("<tr><td colspan=3></td>"); hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); -hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px;'>", +hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>", TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch); hPrintf("</td></tr>\n"); // Description contains hPrintf("<tr><td colspan=2></td><td align='right'>and </td>"); hPrintf("<td><b style='max-width:100px;'>Description:</b></td>"); hPrintf("<td align='right'>contains</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); -hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px;'>", +hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>", TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch); hPrintf("</td></tr>\n"); if (!simpleSearch && descSearch) searchTermsExist = TRUE; hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n"); -hPrintf("<td><b style='max-width:100px;'>Group</b></td>"); +hPrintf("<td><b style='max-width:100px;'>Group:</b></td>"); hPrintf("<td align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); -cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%;'"); +cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'"); hPrintf("</td></tr>\n"); if (!simpleSearch && groupSearch) searchTermsExist = TRUE; // Metadata selects require careful accounting if(metaDbExists) numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols); else numMetadataSelects = 0; hPrintf("</table>\n"); -hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search' style='font-size:.7em;'>\n", TRACK_SEARCH); -hPrintf("<input type='button' name='clear' value='Clear' class='clear' style='font-size:.7em;' onclick='findTracksClear();'>\n"); -hPrintf("<input type='submit' name='submit' value='Cancel' class='cancel' style='font-size:.7em;'>\n"); +hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH); +hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n"); +hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); //hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n"); hPrintf("</div>\n</div>\n"); hPrintf("</form>\n"); hPrintf("</div>"); // Restricts to max-width:1000px; if(descSearch != NULL && !strlen(descSearch)) descSearch = NULL; if(groupSearch != NULL && sameString(groupSearch, ANYLABEL)) groupSearch = NULL; if(!isEmpty(descSearch)) { char *tmp = cloneString(descSearch); char *val = nextWord(&tmp); struct slName *el, *descList = NULL; int i; while (val != NULL) { slNameAddTail(&descList, val); descWordCount++; val = nextWord(&tmp); } descWords = needMem(sizeof(char *) * descWordCount); for(i = 0, el = descList; el != NULL; i++, el = el->next) descWords[i] = strLower(el->name); } if (doSearch && simpleSearch && descWordCount <= 0) doSearch = FALSE; if(doSearch) { // Now search struct slRef *tracks = NULL; if(simpleSearch) tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount); else tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal); // Sort and Print results enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); tracksFound = slCount(tracks); if(tracksFound > 1) findTracksSort(&tracks,simpleSearch,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); } hFreeConn(&conn); webNewSection("About Track Search"); if(metaDbExists) - hPrintf("<p>Search for terms in track descriptions, groups, names, and ENCODE " + hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE " "metadata. If multiple terms are entered, only tracks with all terms " "will be part of the results."); else hPrintf("<p>Search for terms in track descriptions, groups, and names. " "If multiple terms are entered, only tracks with all terms " "will be part of the results."); hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n"); webEndSectionTables(); } #endif///def TRACK_SEARCH