58a3bf5fbc986db7c8b17589c9720b4bc6708133 tdreszer Tue Mar 8 16:44:22 2011 -0800 Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels. diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c index 2061c53..226e8ae 100644 --- src/hg/hgFileSearch/hgFileSearch.c +++ src/hg/hgFileSearch/hgFileSearch.c @@ -7,54 +7,45 @@ #include "hdb.h" #include "web.h" #include "mdb.h" #include "hCommon.h" #include "hui.h" #include "fileUi.h" #include "searchTracks.h" #include "cart.h" #include "grp.h" #define FAKE_MDB_MULTI_SELECT_SUPPORT struct hash *trackHash = NULL; // Is this needed? boolean measureTiming = FALSE; /* DON'T EDIT THIS -- use CGI param "&measureTiming=." . */ -#define ANYLABEL "Any" #define FILE_SEARCH "hgfs_Search" #define FILE_SEARCH_FORM "fileSearch" #define FILE_SEARCH_CURRENT_TAB "fsCurTab" #define FILE_SEARCH_ON_FILETYPE "fsFileType" // These are common with trackSearch. Should they be? -#define METADATA_NAME_PREFIX "hgt_mdbVar" -#define METADATA_VALUE_PREFIX "hgt_mdbVal" #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" //#define USE_TABS //#define SUPPORT_COMPOSITE_SEARCH -// Currently selected tab -enum searchTab { - simpleTab = 0, - filesTab = 2, -}; - #ifdef OMIT_SUPPORT_COMPOSITE_SEARCH // make a matchString function to support "contains", "is" etc. and wildcards in contains // ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) || static boolean isNameMatch(struct trackDb *tdb, char *str, char *op) { return str && strlen(str) && ((sameString(op, "is") && !strcasecmp(tdb->shortLabel, str)) || (sameString(op, "is") && !strcasecmp(tdb->longLabel, str)) || (sameString(op, "contains") && containsStringNoCase(tdb->shortLabel, str) != NULL) || (sameString(op, "contains") && containsStringNoCase(tdb->longLabel, str) != NULL)); } static boolean isDescriptionMatch(struct trackDb *tdb, char **words, int wordCount) @@ -84,298 +75,32 @@ found = TRUE; break; } } if(found) numMatches++; else break; } if(numMatches == wordCount) return TRUE; } } return FALSE; } - #endif///def SUPPORT_COMPOSITE_SEARCH -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, FALSE, TRUE); // Files not Tables -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 getFileFormatTypes(char ***pLabels, char ***pTypes) -{ -char *crudeTypes[] = { - ANYLABEL, - "bam", - "bam.bai", - "tagAlign", - "bed.gz", - "bigBed", - "broadPeak", - "narrowPeak", - "fastq", - "bigWig", - "wig" -}; -char *nicerTypes[] = { - ANYLABEL, - "Alignment binary (bam) - binary SAM", - "Alignment binary index (bai) - binary SAM index", - "Alignment tags (tagAlign)", - "bed - browser extensible data", - "bigBed - self index, often remote bed format", - "Peaks Broad (broadPeak) - ENCODE large region peak format", - "Peaks Narrow (narrowPeak) - ENCODE small region peak format", - "Raw Sequence (fastq) - High throughput sequence format", - "Signal (bigWig) - self index, often remote wiggle format", - "Signal (wig) - wiggle format" -}; - -int ix = 0, count = sizeof(crudeTypes)/sizeof(char *); -char **labels; -char **values; -AllocArray(labels, count); -AllocArray(values, count); -for(ix=0;ix<count;ix++) - { - labels[ix] = cloneString(nicerTypes[ix]); - values[ix] = cloneString(crudeTypes[ix]); - } -*pLabels = labels; -*pTypes = 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]; -struct slPair *oneTerm,*whiteList = mdbCvWhiteList(TRUE,FALSE); -int count =0, whiteCount = slCount(whiteList); -char **retVar = needMem(sizeof(char *) * whiteCount); -char **retLab = needMem(sizeof(char *) * whiteCount); - -for(oneTerm=whiteList;oneTerm!=NULL;oneTerm=oneTerm->next) - { - safef(query, sizeof(query), "select count(*) from metaDb where var = '%s'",oneTerm->name); - if(sqlQuickNum(conn,query) > 0) - { - retVar[count] = oneTerm->name; - retLab[count] = oneTerm->val; - count++; - } - } -// Don't do it, unless you clone strings above: slPairFreeValsAndList(&whileList); - -*metaVars = retVar; -*metaLabels = retLab; -return count; -} - -static int printMdbSelects(struct sqlConnection *conn,struct cart *cart,enum searchTab selectedTab,char ***pMdbVar,char ***pMdbVal,int *numMetadataNonEmpty,int cols) -// Prints a table of mdb selects if appropriate and returns number of them -// TODO: move to lib since hgTracks and hgFileSearch share it -{ -// 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(selectedTab!=simpleTab) - { - 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); - enum mdbCvSearchable searchBy = mdbCvSearchMethod(mdbVar[i]); - if (searchBy == cvsSearchByMultiSelect) - { - // Adding support for multi-selects as comma delimited list of values - struct slName *vals = cartOptionalSlNameList(cart,buf); - if (vals) - { - mdbVal[i] = slNameListToString(vals,','); // A comma delimited list of values - slNameFreeList(&vals); - } - } - else - mdbVal[i] = cloneString(cartUsualString(cart, buf, ANYLABEL)); - - if (mdbVal[i] != NULL && 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; - } - - printf("<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>\n", cols,COLOR_DARKGREY); - for(i = 0; i < numMetadataSelects; i++) - { - char **terms = NULL, **labels = NULL; - char buf[256]; - int len; - - #define PLUS_MINUS_BUTTON "<input type='button' id='%sButton%d' value='%c' style='font-size:.7em;' title='%s' onclick='findTracksMdbSelectPlusMinus(this,%d)'>" - #define PRINT_PM_BUTTON(type,num,value) printf(PLUS_MINUS_BUTTON, (type), (num), (value), ((value) == '+' ? "add another row after":"delete"), (num)) - printf("<tr valign='top' class='mdbSelect'><td nowrap>\n"); - if(numMetadataSelects > 2 || i >= 2) - PRINT_PM_BUTTON("minus", i + 1, '-'); - else - printf(" "); - PRINT_PM_BUTTON("plus", i + 1, '+'); - - printf("</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' style='font-size:.9em;' onchange='findTracksMdbVarChanged(this);'"); - // TODO: move to lib since hgTracks and hgApi share - safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1); - enum mdbCvSearchable searchBy = mdbCvSearchMethod(mdbVar[i]); - if (searchBy == cvsSearchByMultiSelect) - { - printf("</td>\n<td align='right' id='isLike%i' style='width:10px; white-space:nowrap;'>is among</td>\n<td nowrap id='%s' style='max-width:600px;'>\n",i + 1,buf); - #define MULTI_SELECT_CBS_FORMAT "<SELECT MULTIPLE=true name='%s' style='display: none; min-width:200px; font-size:.9em;' class='filterBy mdbVal' onchange='findTracksMdbValChanged(this)'>\n" - printf(MULTI_SELECT_CBS_FORMAT,buf); - len = getTermArray(conn, &labels, &terms, mdbVar[i]); - int tix=0; - for(;tix < len;tix++) - { - char *selected = findWordByDelimiter(terms[tix],',', mdbVal[i]); - printf("<OPTION%s value='%s'>%s</OPTION>\n",(selected != NULL?" SELECTED":""),terms[tix],labels[tix]); - } - printf("</SELECT>\n"); - } - else if (searchBy == cvsSearchBySingleSelect) - { - printf("</td>\n<td align='right' id='isLike%i' style='width:10px; white-space:nowrap;'>is</td>\n<td nowrap id='%s' style='max-width:600px;'>\n",i + 1,buf); - len = getTermArray(conn, &labels, &terms, mdbVar[i]); - cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px; font-size:.9em;' onchange='findTracksMdbValChanged(this);'"); - } - else if (searchBy == cvsSearchByFreeText) - { - printf("</td>\n<td align='right' id='isLike%i' style='width:10px; white-space:nowrap;'>contains</td>\n<td nowrap id='%s' style='max-width:600px;'>\n",i + 1,buf); - printf("<input type='text' name='%s' value='%s' class='mdbVal freeText' style='max-width:310px; width:310px; font-size:.9em;' onchange='findTracksMdbVarChanged(true);'>\n", - buf,(mdbVal[i] ? mdbVal[i]: "")); - } - else if (searchBy == cvsSearchByDateRange || searchBy == cvsSearchByIntegerRange) - { - // TO BE IMPLEMENTED - } - printf("<span id='helpLink%i'> </span></td>\n", i + 1); - printf("</tr>\n"); - } - - printf("<tr><td colspan='%d' align='right' style='height:10px; max-height:10px;'> </td></tr>", cols); - //printf("<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; max-height:20px;'> </td></tr>", cols); - -return numMetadataSelects; -} - #ifdef USE_TABS static struct slRef *simpleSearchForTdbs(struct trix *trix,char **descWords,int descWordCount) // Performs the simple search and returns the found tracks. { struct slRef *foundTdbs = NULL; struct trixSearchResult *tsList; for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next) { struct trackDb *tdb = (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(&foundTdbs, tdb); } } @@ -420,34 +145,30 @@ void doSearch(char *db,char *organism,struct cart *cart,struct trackDb *tdbList) { if (!advancedJavascriptFeaturesEnabled(cart)) { warn("Requires advanced javascript features."); return; } #ifdef SUPPORT_COMPOSITE_SEARCH char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); #endif///def SUPPORT_COMPOSITE_SEARCH char *fileTypeSearch = cartOptionalString(cart, FILE_SEARCH_ON_FILETYPE); char *descSearch=FALSE; boolean doSearch = sameWord(cartUsualString(cart, FILE_SEARCH,"no"), "search"); struct sqlConnection *conn = hAllocConn(db); boolean metaDbExists = sqlTableExists(conn, "metaDb"); -int numMetadataSelects; -int numMetadataNonEmpty = 0; -char **mdbVar = NULL; -char **mdbVal = NULL; #ifdef ONE_FUNC struct hash *parents = newHash(4); #endif///def ONE_FUNC char **descWords = NULL; int descWordCount = 0; boolean searchTermsExist = FALSE; // FIXME: Why is this needed? int cols; #ifdef USE_TABS enum searchTab selectedTab = simpleTab; char *currentTab = cartUsualString(cart, FILE_SEARCH_CURRENT_TAB, "simpleTab"); if(sameString(currentTab, "simpleTab")) { selectedTab = simpleTab; descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE); @@ -565,43 +286,54 @@ printf("</td></tr>\n"); if (selectedTab==filesTab && groupSearch) searchTermsExist = TRUE; #endif///def SUPPORT_COMPOSITE_SEARCH // Track Type is (drop down) #ifdef SUPPORT_COMPOSITE_SEARCH printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); #else///ifndef SUPPORT_COMPOSITE_SEARCH printf("<tr><td colspan=2></td><td align='right'> </td>\n"); #endif///ndef SUPPORT_COMPOSITE_SEARCH //printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); // Bring back "and" if using "Track Name,Description or Group printf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>"); printf("<td align='right'>is</td>\n"); printf("<td colspan='%d'>", cols - 4); -char **formatTypes = NULL; -char **formatLabels = NULL; -int formatCount = getFileFormatTypes(&formatLabels, &formatTypes); -cgiMakeDropListFull(FILE_SEARCH_ON_FILETYPE, formatLabels, formatTypes, formatCount, fileTypeSearch, "class='fileTypeSearch' style='min-width:40%; font-size:.9em;'"); +char *dropDownHtml = fileFormatSelectHtml(FILE_SEARCH_ON_FILETYPE,fileTypeSearch,"style='min-width:40%; font-size:.9em;'"); +if (dropDownHtml) + { + puts(dropDownHtml); + freeMem(dropDownHtml); + } printf("</td></tr>\n"); if (selectedTab==filesTab && fileTypeSearch) searchTermsExist = TRUE; -// Metadata selects require careful accounting +// mdb selects +struct slPair *mdbSelects = NULL; if(metaDbExists) - numMetadataSelects = printMdbSelects(conn, cart, selectedTab, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols); -else - numMetadataSelects = 0; + { + struct slPair *mdbVars = mdbVarsRelevant(conn); + mdbSelects = mdbSelectPairs(cart,selectedTab, mdbVars); + char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols); + if (output) + { + printf(output); + freeMem(output); + } + slPairFreeList(&mdbVars); + } printf("</table>\n"); printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", FILE_SEARCH); printf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n"); printf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); //printf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n"); printf("</div>\n"); #ifdef USE_TABS printf("</div>\n"); // End tabs div #endif///def USE_TABS printf("</form>\n"); printf("</div>"); // Restricts to max-width:1000px; @@ -624,73 +356,63 @@ 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 && selectedTab==simpleTab && descWordCount <= 0) doSearch = FALSE; if(doSearch) { - // Convert to slPair list - int ix=0; - struct slPair *mdbPairs = NULL; - for(ix = 0; ix < numMetadataSelects; ix++) - { - if(!isEmpty(mdbVal[ix])) - slAddHead(&mdbPairs,slPairNew(mdbVar[ix],mdbVal[ix])); - } - slReverse(&mdbPairs); - // Now search #ifdef USE_TABS struct slRef *foundTdbs = NULL; if(selectedTab==simpleTab) { foundTdbs = simpleSearchForTdbs(trix,descWords,descWordCount); // What to do now? if (measureTiming) uglyTime("Searched for tracks"); // Sort and Print results if(selectedTab!=filesTab) { enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); int tracksFound = slCount(foundTdbs); if(tracksFound > 1) findTracksSort(&tracks,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); if (measureTiming) uglyTime("Displayed found files"); } } else if(selectedTab==filesTab && mdbPairs != NULL) #endif///def USE_TABS { - fileSearchResults(db, conn, mdbPairs, fileTypeSearch); + fileSearchResults(db, conn, mdbSelects, fileTypeSearch); if (measureTiming) uglyTime("Searched for files"); } - slPairFreeList(&mdbPairs); + slPairFreeList(&mdbSelects); } hFreeConn(&conn); webNewSection("About Downloadable Files Search"); if(metaDbExists) printf("<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 printf("<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."); printf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n"); webEndSectionTables(); }