9a49290fedc8b4f9c7a631dedcfe8ac3aa2b4cee chinhli Thu Oct 20 14:10:43 2011 -0700 merge conflict resolved diff --git src/hg/lib/search.c src/hg/lib/search.c index 18e3b7b..5ac30ea 100644 --- src/hg/lib/search.c +++ src/hg/lib/search.c @@ -1,314 +1,311 @@ // Search code which is shared between different CGIs: hgFileSearch and hgTracks(Track Search) #include "search.h" #include "cheapcgi.h" #include "hdb.h" #include "hgConfig.h" #include "hPrint.h" #include "trix.h" #include "mdb.h" #include "subText.h" #include "jsHelper.h" void getSearchTrixFile(char *database, char *buf, int len) // Fill-in the name of the track search trix file { char *trixPath = cfgOptionDefault("browser.trixPath", "/gbdb/$db/trackDb.ix"); struct subText *subList = subTextNew("$db", database); subTextStatic(subList, trixPath, buf, len); } boolean isSearchTracksSupported(char *database, struct cart *cart) // Return TRUE if searchTracks is supported for this database and javascript is supported too { -if (!advancedJavascriptFeaturesEnabled(cart)) - return FALSE; - char trixFile[HDB_MAX_PATH_STRING]; getSearchTrixFile(database, trixFile, sizeof(trixFile)); return fileExists(trixFile); } struct slPair *fileFormatSearchWhiteList() // Gets the whitelist of approved file formats that is allowed for search { char *crudeTypes[] = { "bam", // "bam.bai" is now alway selected with bam, "tagAlign", "bed.gz", "bigBed", "broadPeak", "narrowPeak", "fastq", "bigWig", "wig" // TODO: Add "other" category. TODO: make into multi-select }; char *nicerTypes[] = { "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" }; struct slPair *fileTypes = NULL; int ix = 0, count = sizeof(crudeTypes)/sizeof(char *); for(ix=0;ix<count;ix++) slPairAdd(&fileTypes, crudeTypes[ix],cloneString(nicerTypes[ix])); // Name gets cloned while adding return fileTypes; } char *fileFormatSelectHtml(char *name, char *selected, char *extraHtml) // returns an allocated string of HTML for the fileType select drop down { struct slPair *fileTypes = fileFormatSearchWhiteList(); if (slCount(fileTypes) > 0) { char *dropDownHtml = cgiMakeSingleSelectDropList(name,fileTypes,selected,ANYLABEL,NULL,extraHtml); slPairFreeList(&fileTypes); return dropDownHtml; } return NULL; } struct slPair *mdbSelectPairs(struct cart *cart, struct slPair *mdbVars) // Returns the current mdb vars and vals in the table of drop down selects { // figure out how many metadata selects are visible. int numMetadataSelects = 0; struct slPair *mdbSelectPairs = NULL; if (mdbVars == NULL) return 0; // Get the current number of rows in the table of mdb selects 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++; } // Requesting to add or delete any? 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 if(delSearchSelect) numMetadataSelects--; if(addSearchSelect) numMetadataSelects++; if(numMetadataSelects) { int ix; char buf[256]; for(ix = 0; ix < numMetadataSelects; ix++) { int offset; // used to handle additions/deletions if(addSearchSelect > 0 && ix >= addSearchSelect) offset = 0; // do nothing to offset (i.e. copy data from previous row) else if(delSearchSelect > 0 && ix + 1 >= delSearchSelect) offset = 2; else offset = 1; safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, ix + offset); char *var = cartOptionalString(cart, buf); char *val = NULL; // We need to make sure var is valid in this assembly; if it isn't, reset it to "cell". if(slPairFindVal(mdbVars,var) == NULL) var = "cell"; else { safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, ix + offset); enum cvSearchable searchBy = cvSearchMethod(var); if (searchBy == cvSearchByMultiSelect) { // Multi-selects as comma delimited list of values struct slName *vals = cartOptionalSlNameList(cart,buf); if (vals) { val = slNameListToString(vals,','); // A comma delimited list of values slNameFreeList(&vals); } } else if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByFreeText || searchBy == cvSearchByWildList) val = cloneString(cartUsualString(cart, buf,ANYLABEL)); //else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange) // { // // TO BE IMPLEMENTED // } if (val != NULL && sameString(val, ANYLABEL)) val = NULL; } slPairAdd(&mdbSelectPairs,var,val); // val already cloned } if(delSearchSelect > 0) { 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 slPairAdd(&mdbSelectPairs,"cell", NULL); slPairAdd(&mdbSelectPairs,"antibody",NULL); } slReverse(&mdbSelectPairs); return mdbSelectPairs; } char *mdbSelectsHtmlRows(struct sqlConnection *conn,struct slPair *mdbSelects,struct slPair *mdbVars,int cols,boolean fileSearch) // genereates the html for the table rows containing mdb var and val selects. Assume tableSearch unless fileSearch { struct dyString *output = dyStringNew(1024); dyStringPrintf(output,"<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); struct slPair *mdbSelect = mdbSelects; int row = 0; for(;mdbSelect != NULL; mdbSelect = mdbSelect->next) { char buf[256]; char *dropDownHtml = NULL; #define PLUS_MINUS_BUTTON "<input type='button' id='%sButton%d' value='%c' style='font-size:.7em;' title='%s' onclick='findTracksMdbSelectPlusMinus(this,%d)'>" #define ADD_PM_BUTTON(type,num,value) dyStringPrintf(output,PLUS_MINUS_BUTTON, (type), (num), (value), ((value) == '+' ? "add another row after":"delete"), (num)) dyStringAppend(output,"<tr valign='top' class='mdbSelect'><td nowrap>\n"); row++; if(slCount(mdbSelects) > 2 || row > 2) ADD_PM_BUTTON("minus", row, '-'); else dyStringAppend(output," "); ADD_PM_BUTTON("plus", row, '+'); dyStringAppend(output,"</td><td>and </td><td colspan=3 nowrap>\n"); safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, row); // Left side select of vars dropDownHtml = cgiMakeSingleSelectDropList(buf, mdbVars,mdbSelect->name, NULL,"mdbVar","style='font-size:.9em;' onchange='findTracksMdbVarChanged(this);'"); if (dropDownHtml) { dyStringAppend(output,dropDownHtml); freeMem(dropDownHtml); } // Right side select of vals safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, row); enum cvSearchable searchBy = cvSearchMethod(mdbSelect->name); if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect) { dyStringPrintf(output,"</td>\n<td align='right' id='isLike%i' style='width:10px; white-space:nowrap;'>is%s</td>\n<td nowrap id='%s' style='max-width:600px;'>\n", row,(searchBy == cvSearchByMultiSelect?" among":""),buf); struct slPair *pairs = mdbValLabelSearch(conn, mdbSelect->name, MDB_VAL_STD_TRUNCATION, FALSE, !fileSearch, fileSearch); // not tags, either a file or table search if (slCount(pairs) > 0) { char *dropDownHtml = cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect), buf, pairs,mdbSelect->val, ANYLABEL,"mdbVal","style='min-width:200px; font-size:.9em;' onchange='findTracksMdbValChanged(this);'"); if (dropDownHtml) { dyStringAppend(output,dropDownHtml); freeMem(dropDownHtml); } slPairFreeList(&pairs); } } else if (searchBy == cvSearchByFreeText) { dyStringPrintf(output,"</td><td align='right' id='isLike%i' style='width:10px; white-space:nowrap;'>contains</td>\n<td nowrap id='%s' style='max-width:600px;'>\n", row,buf); dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal freeText' style='max-width:310px; width:310px; font-size:.9em;' onchange='findTracksMdbVarChanged(true);'>\n", buf,(mdbSelect->val ? (char *)mdbSelect->val: "")); } else if (searchBy == cvSearchByWildList) { dyStringPrintf(output,"</td><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", row,buf); dyStringPrintf(output,"<input type='text' name='%s' value='%s' class='mdbVal wildList' title='enter comma separated list of values' style='max-width:310px; width:310px; font-size:.9em;' onchange='findTracksMdbVarChanged(true);'>\n", buf,(mdbSelect->val ? (char *)mdbSelect->val: "")); } //else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange) // { // // TO BE IMPLEMENTED // } dyStringPrintf(output,"<span id='helpLink%i'> </span></td>\n", row); dyStringPrintf(output,"</tr>\n"); } dyStringPrintf(output,"<tr><td colspan='%d' align='right' style='height:10px; max-height:10px;'> </td></tr>", cols); return dyStringCannibalize(&output); } static boolean searchMatchToken(char *string, char *token) { // do this with regex ? Would require all sorts of careful parsing for ()., etc. if (string == NULL) return (token == NULL); if (token == NULL) return TRUE; if (!strchr(token,'*') && !strchr(token,'?')) return (strcasestr(string,token) != NULL); char wordWild[1024]; safef(wordWild,sizeof wordWild,"*%s*",token); return wildMatch(wordWild, string); } boolean searchNameMatches(struct trackDb *tdb, struct slName *wordList) // returns TRUE if all words in preparsed list matches short or long label // A "word" can be "multiple words" (parsed from quoteed string). { if (tdb->shortLabel == NULL || tdb->longLabel == NULL) return (wordList != NULL); struct slName *word = wordList; for(; word != NULL; word = word->next) { if (!searchMatchToken(tdb->shortLabel,word->name) && !searchMatchToken(tdb->longLabel, word->name)) return FALSE; } return TRUE; } boolean searchDescriptionMatches(struct trackDb *tdb, struct slName *wordList) // returns TRUE if all words in preparsed list matches html description page. // A "word" can be "multiple words" (parsed from quoteed string). // Because description contains html, quoted string match has limits. // DANGER: this will alter html of tdb struct (replacing \n with ' ', so the html should not be displayed after. { if (tdb->html == NULL) return (wordList != NULL); if (strchr(tdb->html,'\n')) strSwapChar(tdb->html,'\n',' '); // DANGER: don't own memory. However, this CGI will use html for no other purpose struct slName *word = wordList; for(; word != NULL; word = word->next) { if (!searchMatchToken(tdb->html,word->name)) return FALSE; } return TRUE; }