533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/lib/search.c src/hg/lib/search.c deleted file mode 100644 index 88dba26..0000000 --- src/hg/lib/search.c +++ /dev/null @@ -1,356 +0,0 @@ -// Search code which is shared between different CGIs: hgFileSearch and hgTracks(Track Search) - -/* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ - -#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); -char *subBuf = hReplaceGbdb(buf); -safecpy(buf, len, subBuf); -freez(&subBuf); -} - -boolean isSearchTracksSupported(char *database, struct cart *cart) -// Return TRUE if searchTracks is supported for this database and javascript is supported too -{ -char trixFile[HDB_MAX_PATH_STRING]; -getSearchTrixFile(database, trixFile, sizeof(trixFile)); -char *trixPath = hReplaceGbdb(trixFile); -bool ret = udcExists(trixPath); -freez(&trixPath); -return ret; -} - -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])); -return fileTypes; -} - -char *fileFormatSelectHtml(char *name, char *selected, char *event, char *javascript, char *style) -// 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, event, javascript, style, NULL); - 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; - - char id[256]; - char javascript[1024]; - - #define PLUS_MINUS_BUTTON "<input type='button' id='%s' value='%c' " \ - "style='font-size:.7em;' title='%s'>" - #define PLUS_MINUS_BUTTON_JS "findTracks.mdbSelectPlusMinus(this,%d);" - #define ADD_PM_BUTTON(type,num,value) \ - safef(id, sizeof id, "%sButton%d", (type), (num)); \ - dyStringPrintf(output,PLUS_MINUS_BUTTON, id, (value), \ - ((value) == '+' ? "add another row after":"delete")); \ - safef(javascript, sizeof javascript, PLUS_MINUS_BUTTON_JS, (num)); \ - jsOnEventById("click", id, javascript); - - 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", - "change", "findTracks.mdbVarChanged(this);", "font-size:.9em;", NULL); - 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", - "change", "findTracks.mdbValChanged(this);", - "min-width:200px; font-size:.9em;", NULL); - 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); - safef(id, sizeof id, "%i_change", row); - dyStringPrintf(output,"<input type='text' name='%s' id='%s' value='%s' class='mdbVal freeText' " - "style='max-width:310px; width:310px; font-size:.9em;'>\n", - buf,id,(mdbSelect->val ? (char *)mdbSelect->val: "")); - jsOnEventById("change", id, "findTracks.mdbVarChanged(true);"); - } - 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); - safef(id, sizeof id, "%i_change", row); - dyStringPrintf(output,"<input type='text' name='%s' id='%s' value='%s' class='mdbVal wildList' " - "title='enter comma separated list of values' " - "style='max-width:310px; width:310px; font-size:.9em;'>\n", - buf,id,(mdbSelect->val ? (char *)mdbSelect->val: "")); - jsOnEventById("change", id, "findTracks.mdbVarChanged(true);"); - } - //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')) // DANGER: don't own memory. - strSwapChar(tdb->html,'\n',' '); // 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; -} -