84440373a2ad67b39c36c614687807bda9a423b2 tdreszer Wed Sep 29 11:12:37 2010 -0700 Added definition of multiTrack and changed container to be either multiTrack or Composite. This allows multiTracks (such as multiWigs) to behave as composites in some code paths. diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c index c9d52dd..63c575a 100644 --- src/hg/hgTracks/searchTracks.c +++ src/hg/hgTracks/searchTracks.c @@ -1,804 +1,797 @@ /* 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" static char const rcsid[] = "$Id: searchTracks.c,v 1.11 2010/06/11 18:21:40 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); } // Would like to do a radio button choice ofsorts #define SORT_BY_HIERARCHY #ifdef SORT_BY_HIERARCHY #define SORT_BY_VAR "findTracksSortBy" #define SORT_BY_ABC "abc" #define SORT_BY_HIER "hier" 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 ( tdbIsSuperTrack(a->tdb) && !tdbIsSuperTrack(b->tdb)) + if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb)) return -1; -else if (!tdbIsSuperTrack(a->tdb) && tdbIsSuperTrack(b->tdb)) +else if (!tdbIsFolder(a->tdb) && tdbIsFolder(b->tdb)) return 1; - if ( tdbIsComposite(a->tdb) && !tdbIsComposite(b->tdb)) + if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb)) return -1; -else if (!tdbIsComposite(a->tdb) && tdbIsComposite(b->tdb)) +else if (!tdbIsContainer(a->tdb) && tdbIsContainer(b->tdb)) return 1; - if (!tdbIsCompositeChild(a->tdb) && tdbIsCompositeChild(b->tdb)) + if (!tdbIsContainerChild(a->tdb) && tdbIsContainerChild(b->tdb)) return -1; -else if ( tdbIsCompositeChild(a->tdb) && !tdbIsCompositeChild(b->tdb)) +else if ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb)) return 1; return strcasecmp(a->longLabel, b->longLabel); } #endif///def SORT_BY_HIERARCHY 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); } // 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 ***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. { int i, count = 0; char **retVal; struct slName *termList = mdbValSearch(conn, type, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files count = slCount(termList) + 1; // make room for "Any" AllocArray(retVal, count); retVal[0] = cloneString(ANYLABEL); for(i = 1; termList != NULL;termList = termList->next, i++) { retVal[i] = cloneString(termList->name); } *terms = retVal; 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"}, {"accession", "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 } void doSearchTracks(struct group *groupList) { struct group *group; 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 *descSearch; char *groupSearch = cartOptionalString(cart, "hgt.groupSearch"); boolean doSearch = sameString(cartOptionalString(cart, searchTracks), "Search") || cartUsualInt(cart, "hgt.forceSearch", 0) == 1; struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); struct slRef *tracks = NULL; int numMetadataSelects, tracksFound = 0; int numMetadataNonEmpty = 0; char **mdbVar; char **mdbVal; struct hash *parents = newHash(4); boolean simpleSearch; struct trix *trix; char trixFile[HDB_MAX_PATH_STRING]; char **descWords = NULL; int descWordCount = 0; boolean searchTermsExist = FALSE; int cols; if(sameString(currentTab, "simpleTab")) { descSearch = cartOptionalString(cart, "hgt.simpleSearch"); simpleSearch = TRUE; freez(&nameSearch); freez(&groupSearch); } else { descSearch = cartOptionalString(cart, "hgt.descSearch"); simpleSearch = FALSE; } getSearchTrixFile(database, trixFile, sizeof(trixFile)); trix = trixOpen(trixFile); 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(); } } webStartWrapperDetailedNoArgs(cart, database, "", "Search for Tracks", FALSE, FALSE, FALSE, FALSE); hPrintf("<div style='max-width:1080px;'>"); hPrintf("<form action='%s' name='SearchTracks' id='searchTracks' method='get'>\n\n", hgTracksName()); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo hPrintf("<input type='hidden' name='db' value='%s'>\n", database); hPrintf("<input type='hidden' name='hgt.currentSearchTab' id='currentSearchTab' value='%s'>\n", currentTab); hPrintf("<input type='hidden' name='hgt.delRow' value=''>\n"); hPrintf("<input type='hidden' name='hgt.addRow' value=''>\n"); hPrintf("<input type='hidden' name='hgt.forceSearch' value=''>\n"); hPrintf("<div id='tabs' style='display:none; %s'>\n" "<ul>\n" "<li><a href='#simpleTab'><span>Search</span></a></li>\n" "<li><a href='#advancedTab'><span>Advanced</span></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%%;'><tr><td colspan='2'>"); hPrintf("<input type='text' name='hgt.simpleSearch' id='simpleSearch' value='%s' style='max-width:1000px; width:100%%' onkeyup='findTracksSearchButtonsEnable(true);'>\n", descSearch == NULL ? "" : descSearch); hPrintf("</td></tr><tr><td>"); if (simpleSearch && descSearch) searchTermsExist = TRUE; hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search' style='font-size:14px;'>\n", searchTracks); hPrintf("<input type='button' name='clear' value='Clear' class='clear' style='font-size:14px;' onclick='findTracksClear();'>\n"); hPrintf("<input type='submit' name='submit' value='Cancel' class='cancel' style='font-size:14px;'>\n"); hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr></table>\n"); //hPrintf("</td><td align='right'><a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr></table>\n"); hPrintf("</div>\n" "<div id='advancedTab' style='width:inherit;'>\n" "<table cellSpacing=0 style='width:inherit;'>\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='hgt.nameSearch' id='nameSearch' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px;'>", 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='hgt.descSearch' id='descSearch' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px;'>", 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 align='right'>is</td>\n"); hPrintf("<td colspan='%d'>", cols - 4); cgiMakeDropListFull("hgt.groupSearch", labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%%;'"); hPrintf("</td></tr>\n"); if (!simpleSearch && groupSearch) searchTermsExist = TRUE; // figure out how many metadata selects are visible. int delSearchSelect = cartUsualInt(cart, "hgt.delRow", 0); // 1-based row to delete int addSearchSelect = cartUsualInt(cart, "hgt.addRow", 0); // 1-based row to insert after 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(delSearchSelect) numMetadataSelects--; if(addSearchSelect) numMetadataSelects++; if(numMetadataSelects) { mdbVar = needMem(sizeof(char *) * numMetadataSelects); mdbVal = needMem(sizeof(char *) * numMetadataSelects); 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) { 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; 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; } if(metaDbExists) { int i; char **mdbVars = NULL; char **mdbVarLabels = NULL; int count = metaDbVars(conn, &mdbVars,&mdbVarLabels); 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; char buf[256]; int len; hPrintf("<tr><td>\n"); if(numMetadataSelects > 2 || i >= 2) { safef(buf, sizeof(buf), "return delSearchSelect(this, %d);", i + 1); hButtonWithOnClick(searchTracks, "-", "delete this row", buf); } else hPrintf(" "); hPrintf("</td><td>\n"); safef(buf, sizeof(buf), "return addSearchSelect(this, %d);", i + 1); hButtonWithOnClick(searchTracks, "+", "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)"); hPrintf("</td><td nowrap style='max-width:600px;'>is\n"); len = getTermArray(conn, &terms, mdbVar[i]); safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1); cgiMakeDropListFull(buf, terms, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px;' onchange='findTracksSearchButtonsEnable(true)'"); if (!simpleSearch && mdbVal[i]) searchTermsExist = TRUE; hPrintf("<span id='helpLink%d'>help</span></td>\n", i + 1); hPrintf("</tr>\n"); } } hPrintf("<tr><td colspan='%d'>\n", cols); hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search' style='font-size:14px;'>\n", searchTracks); hPrintf("<input type='button' name='clear' value='Clear' class='clear' style='font-size:14px;' onclick='findTracksClear();'>\n"); hPrintf("<input type='submit' name='submit' value='Cancel' class='cancel' style='font-size:14px;'>\n"); hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr>\n"); hPrintf("</table>\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; #ifdef SORT_BY_HIERARCHY boolean sortByHierarchy = sameString(cartUsualString(cart,SORT_BY_VAR,SORT_BY_HIER),SORT_BY_HIER); #endif///def SORT_BY_HIERARCHY 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(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next) { struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId); - if (track != NULL && !tdbIsContainerChild(track->tdb)) // NOTE: Not including container children, since they don't seem to be individually viewaable + if (track != NULL) { refAdd(&tracks, track); tracksFound++; } //else // FIXME: Should get to the bottom of why some of these are null // warn("found trix track is NULL."); } #ifdef SORT_BY_HIERARCHY slSort(&tracks, sortByHierarchy? gCmpTrackHierarchy:gCmpTrack); #else///ifndef SORT_BY_HIERARCHY slReverse(&tracks); #endif///ndef SORT_BY_HIERARCHY } 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(mdbVal[i])) { struct slName *tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE); //struct slName *tmp = metaDbSearch(conn, mdbVar[i], mdbVal[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, "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."); } } } } } } } #ifdef SORT_BY_HIERARCHY slSort(&tracks, sortByHierarchy? gCmpTrackHierarchy:gCmpTrack); #else///ifndef SORT_BY_HIERARCHY slSort(&tracks, gCmpTrack); #endif///ndef SORT_BY_HIERARCHY } } hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it if(tracksFound < 1) { if(doSearch) hPrintf("<p>No tracks found</p>\n"); } else { struct hash *tdbHash = makeTrackHash(database, chromName); hPrintf("<form action='%s' name='SearchTracks' id='searchResultsForm' method='post'>\n\n", hgTracksName()); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo #define MAX_FOUND_TRACKS 100 if(tracksFound > MAX_FOUND_TRACKS) { hPrintf("<table class='redBox'><tr><td>Found %d tracks, but only the first %d are displayed.",tracksFound,MAX_FOUND_TRACKS); hPrintf("<BR><B><I>Please narrow search criteria to find fewer tracks.</I></B></div></td></tr></table>\n"); } #define ENOUGH_FOUND_TRACKS 10 if(tracksFound >= ENOUGH_FOUND_TRACKS) { hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='View in Browser' class='viewBtn'>"); hPrintf(" <FONT class='selCbCount'></font>\n"); } // Set up json for js functionality struct dyString *jsonTdbVars = NULL; hPrintf("<table id='foundTracks'><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"); if(tracksFound >= ENOUGH_FOUND_TRACKS) { #ifdef SORT_BY_HIERARCHY hPrintf("<span style='float:right;'>Sort:"); cgiMakeOnClickRadioButton(SORT_BY_VAR, SORT_BY_ABC, !sortByHierarchy,"onchange=\"findTracksSortNow(this);\""); // FIXME: var is in wrong form! hPrintf("Alphabetically"); cgiMakeOnClickRadioButton(SORT_BY_VAR, SORT_BY_HIER,sortByHierarchy, "onchange=\"findTracksSortNow(this);\""); hPrintf("by Hierarchy </span>\n"); #endif///def SORT_BY_HIERARCHY } hPrintf("</td></tr>\n"); 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); #ifdef SORT_BY_HIERARCHY - if (tdbIsSuperTrack(track->tdb)) + if (tdbIsFolder(track->tdb)) // supertrack hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL1); - if (tdbIsComposite(track->tdb)) + if (tdbIsContainer(track->tdb)) hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3); else #endif///def SORT_BY_HIERARCHY hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2); hPrintf("<td align='center'>\n"); - char name[256]; - safef(name,sizeof(name),"%s_sel",track->track); - boolean checked = FALSE; - #define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>" - if(tdbIsContainerOrCompositeChild(track->tdb)) + + // Determine visibility and checked state + track->visibility = tdbVisLimitedByAncestry(cart, track->tdb, FALSE); + boolean checked = ( track->visibility != tvHide ); + if(tdbIsContainerChild(track->tdb)) { - checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here. Visible=checked&&enabled //track->visibility = limitedVisFromComposite(track); - track->visibility = tdbVisLimitedByAncestry(cart, track->tdb, FALSE); - + 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! - // Only subtracks get "_sel" var - hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY); - } - else - { - track->visibility = tdbVisLimitedByAncestry(cart, track->tdb, FALSE); - checked = ( track->visibility != tvHide ); - if (tdbIsSuperTrackChild(track->tdb)) - hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY); } + // 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 - if (tdbIsSuper(track->tdb)) + if (tdbIsFolder(track->tdb)) { // FIXME: Replace this with select box WITHOUT NAME but with id // HOWEVER, I haven't seen a single supertrack in found tracks so I think they are excluded and this is dead code warn("superTrack: %s '%s' doesn't work yet.",track->track,track->longLabel); superTrackDropDown(cart, track->tdb, superTrackHasVisibleMembers(track->tdb)); } else { char extra[512]; 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 (tdbIsContainerOrComposite(track->tdb) || tdbIsSuper(track->tdb)) + if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb)) { containerTrackCount++; hPrintf(" <a href='hgTrackUi?db=%s&g=%s&hgt_searchTracks=1' title='Configure this container track...'>*</a> ",database,track->track); } hPrintf("</td>\n"); - //if(tdbIsSuper(track->tdb) || tdbIsComposite(track->tdb)) + //if(tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb)) // hPrintf("<td><a target='_top' href='%s' title='Configure track...'>%s</a></td>\n", trackUrl(track->track, NULL), track->shortLabel); //else 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"); if(containerTrackCount > 0) 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>\n"); hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='View in Browser' class='viewBtn'>"); hPrintf(" <FONT class='selCbCount'></font>"); hPrintf("\n</form>\n"); // be done with json hWrites(jsonTdbSettingsUse(&jsonTdbVars)); } if(!doSearch) { hPrintf("<p><b>Recently Done</b><ul>\n" #ifdef SORT_BY_HIERARCHY "<li>Added sort toggle: Alphabetically or by Hierarchy.</li>" #endif///def SORT_BY_HIERARCHY "<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks. (In demo1: only default state composites; demo2: all composites.)</li>" "<li>Metadata variables have been 'white-listed' to only include vetted items. Short text descriptions and vetted list should be reviewed.</li>" "<li>Clicking on shortLabel for found track will popup the description text. Subtracks should show their composite description.</li>" "<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying. Better suggestions?</li>" "<li>Found track list shows only the first 100 tracks with warning to narrow search. Larry suggests this could be done by pages of results in v2.0.</li>\n" "</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"); } hPrintf("</div"); // This div allows the clear button to empty it webEndSectionTables(); }