70ef68d210fa4b76c16f7b8e8142a8180f75052a tdreszer Fri Jun 17 20:14:06 2011 -0700 Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3. Needs more testing and CSS work. DDCL is working on FF, Chrome and IE. Both Chrome and IE support required tiny changes to the DDCL wigit code. DDCL may still have problems with IE. Other jquery wigits have been tested at a cursory level and work fine. Ajax calls may need an extrat dataType: html param. Dialog (popup) needs CSS tuning. diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c index a931b59..72167c6 100644 --- src/hg/lib/fileUi.c +++ src/hg/lib/fileUi.c @@ -1,974 +1,984 @@ /* fileUi.c - human genome file downloads common controls. */ #include "common.h" #include "hash.h" #include "cheapcgi.h" #include "jsHelper.h" #include "cart.h" #include "hdb.h" #include "fileUi.h" #include "hui.h" #include "obscure.h" #include "mdb.h" #include "jsHelper.h" #include "web.h" // FIXME: Move to hui.h since hui.c also needs this #define ENCODE_DCC_DOWNLOADS "encodeDCC" void fileDbFree(struct fileDb **pFileList) // free one or more fileDb objects { while (pFileList && *pFileList) { struct fileDb *oneFile = slPopHead(pFileList); freeMem(oneFile->fileName); freeMem(oneFile->fileType); freeMem(oneFile->fileDate); freeMem(oneFile->sortFields); freeMem(oneFile->reverse); mdbObjsFree(&(oneFile->mdb)); freeMem(oneFile); } } struct fileDb *fileDbGet(char *db, char *dir, char *subDir, char *fileName) // Returns NULL or if found a fileDb struct with name, size and date filled in. { static char *savedDb = NULL; static char *savedDir = NULL; static char *savedSubDir = NULL; static struct fileDb *foundFiles = NULL;// Use static list to save excess IO struct fileDb *oneFile = NULL; if (foundFiles == NULL || savedDb == NULL || differentString(savedDb, db) || savedDir == NULL || differentString(savedDir,dir) || savedSubDir == NULL || differentString(savedSubDir,subDir)) { // free up any static mem freeMem(savedDb); freeMem(savedDir); freeMem(savedSubDir); fileDbFree(&foundFiles); FILE *scriptOutput = NULL; char buf[1024]; char cmd[512]; char *words[10]; char *server = hDownloadsServer(); boolean useRsync = TRUE; // Works: rsync -avn rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/ if (hIsBetaHost()) safef(cmd,sizeof(cmd),"rsync -n rsync://hgdownload-test.cse.ucsc.edu/goldenPath/%s/%s/%s/beta/", db, dir, subDir); // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu" else safef(cmd,sizeof(cmd),"rsync -n rsync://%s/goldenPath/%s/%s/%s/", server, db, dir, subDir); scriptOutput = popen(cmd, "r"); while(fgets(buf, sizeof(buf), scriptOutput)) { eraseTrailingSpaces(buf); if (!endsWith(buf,".md5sum")) // Just ignore these { int count = chopLine(buf, words); if (count >= 6 && useRsync == FALSE) // hgwdev is same as hgdownloads-test so can't use rsync { //-rw-rw-r-- 5 502826550 2010-10-22 16:51 /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdRawDataRep1.fastq.gz AllocVar(oneFile); oneFile->fileSize = sqlUnsignedLong(words[2]); oneFile->fileDate = cloneString(words[3]); char *atSlash = strrchr(words[5], '/'); if (atSlash != NULL) oneFile->fileName = cloneString(atSlash + 1); else oneFile->fileName = cloneString(words[5]); slAddHead(&foundFiles,oneFile); } else if (count == 5 && useRsync == TRUE)// genome and hgwbeta can use rsync because files are on different machine { //-rw-rw-r-- 26420982 2009/09/29 14:53:30 wgEncodeBroadChipSeq/wgEncodeBroadChipSeqSignalNhlfH4k20me1.wig.gz AllocVar(oneFile); oneFile->fileSize = sqlUnsignedLong(words[1]); oneFile->fileDate = cloneString(words[2]); strSwapChar(oneFile->fileDate,'/','-');// Standardize YYYY-MM-DD, no time oneFile->fileName = cloneString(words[4]); slAddHead(&foundFiles,oneFile); } //warn("File:%s size:%ld",foundFiles->fileName,foundFiles->fileSize); } } pclose(scriptOutput); // mark this as done to avoid excessive io savedDb = cloneString(db); savedDir = cloneString(dir); savedSubDir = cloneString(subDir); if (foundFiles == NULL) { AllocVar(oneFile); oneFile->fileName = cloneString("No files found!"); oneFile->fileDate = cloneString(cmd); slAddHead(&foundFiles,oneFile); warn("No files found for command:\n%s",cmd); return NULL; } } // special code that only gets called in debug mode if (sameString(fileName,"listAll")) { for(oneFile=foundFiles;oneFile;oneFile=oneFile->next) warn("%s",oneFile->fileName); return NULL; } // Look up the file and return it struct fileDb *newList = NULL; while (foundFiles) { oneFile = slPopHead(&foundFiles); if (sameString(fileName,oneFile->fileName)) break; // Found means removed from list: shorter list for next file. slAddHead(&newList,oneFile); oneFile = NULL; } if (newList) foundFiles = slCat(foundFiles,newList); // Order does not remain the same if (oneFile != NULL && oneFile->fileType == NULL) { char *suffix = strchr(oneFile->fileName, '.'); if (suffix != NULL && strlen(suffix) > 2) { oneFile->fileType = cloneString(suffix + 1); if (endsWith(oneFile->fileType,".gz")) chopSuffix(oneFile->fileType); } } return oneFile; } static sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb,struct mdbObj *mdbObjs) /* Parses 'fileSortOrder' trackDb/cart instructions and returns a sort order struct or NULL. Some trickiness here. sortOrder->sortOrder is from cart (changed by user action), as is sortOrder->order, But columns are in original tdb order (unchanging)! However, if cart is null, all is from trackDb.ra */ { int ix; sortOrder_t *sortOrder = NULL; char *carveSetting = NULL,*setting = NULL; if (parentTdb) setting = trackDbSetting(parentTdb, FILE_SORT_ORDER); if(setting) { sortOrder = needMem(sizeof(sortOrder_t)); sortOrder->setting = cloneString(setting); carveSetting = sortOrder->setting; } else { if (mdbObjs != NULL) { struct dyString *dySortFields = dyStringNew(512); struct mdbObj *commonVars = mdbObjsCommonVars(mdbObjs); // common vars are already in cv defined order, searchable is also sortable struct mdbVar *var = commonVars->vars; for( ;var != NULL; var = var->next) { if (differentWord(var->var,MDB_VAR_LAB_VERSION) // Exclude certain vars && differentWord(var->var,MDB_VAR_SOFTWARE_VERSION) && cvSearchMethod(var->var) != cvNotSearchable) // searchable is also sortable { if (mdbObjsHasCommonVar(mdbObjs, var->var,TRUE)) // Don't bother if all the vals are the same (missing okay) continue; dyStringPrintf(dySortFields,"%s=%s ",var->var,strSwapChar(cloneString(cvLabel(var->var)),' ','_')); } } if (dyStringLen(dySortFields)) { dyStringAppend(dySortFields,"fileSize=Size fileType=File_Type"); setting = dyStringCannibalize(&dySortFields); } else dyStringFree(&dySortFields); mdbObjsFree(&commonVars); } if(setting == NULL) // Must be in trackDb or not a sortable list of files { #define FILE_SORT_ORDER_DEFAULT "cell=Cell_Line lab=Lab view=View replicate=Rep fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until" setting = FILE_SORT_ORDER_DEFAULT; } sortOrder = needMem(sizeof(sortOrder_t)); carveSetting = cloneString(setting); sortOrder->setting = NULL; } if (parentTdb) { sortOrder->htmlId = needMem(strlen(parentTdb->track)+20); safef(sortOrder->htmlId, (strlen(parentTdb->track)+20), "%s.%s", parentTdb->track,FILE_SORT_ORDER); if(cart != NULL) sortOrder->sortOrder = cloneString(cartOptionalString(cart, sortOrder->htmlId)); } sortOrder->count = chopByWhite(carveSetting,NULL,0); // Get size sortOrder->column = needMem(sortOrder->count*sizeof(char*)); sortOrder->count = chopByWhite(carveSetting,sortOrder->column,sortOrder->count); sortOrder->title = needMem(sortOrder->count*sizeof(char*)); sortOrder->forward = needMem(sortOrder->count*sizeof(boolean)); sortOrder->order = needMem(sortOrder->count*sizeof(int)); for (ix = 0; ix<sortOrder->count; ix++) { // separate out mtaDb var in sortColumn from title sortOrder->title[ix] = strchr(sortOrder->column[ix],'='); // Could be 'cell=Cell_Line' if (sortOrder->title[ix] != NULL) { sortOrder->title[ix][0] = '\0'; sortOrder->title[ix] = strSwapChar(sortOrder->title[ix]+1,'_',' '); // +1 jumps to next char after '=' } else sortOrder->title[ix] = sortOrder->column[ix]; // or could be just 'cell' // Sort order defaults to forward but may be found in a cart var sortOrder->order[ix] = ix+1; sortOrder->forward[ix] = TRUE; if (sortOrder->sortOrder != NULL) { char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder);// find tdb substr in cart current order string if(pos != NULL && pos[strlen(sortOrder->column[ix])] == '=') { int ord=1; char* pos2 = sortOrder->sortOrder; for(;*pos2 && pos2 < pos;pos2++) { if(*pos2 == '=') // Discovering sort order in cart ord++; } sortOrder->forward[ix] = (pos[strlen(sortOrder->column[ix]) + 1] == '+'); sortOrder->order[ix] = ord; } } } if (sortOrder->sortOrder == NULL) sortOrder->sortOrder = cloneString(setting); // no order in cart, all power to trackDb return sortOrder; // NOTE cloneString:words[0]==*sortOrder->column[0] and will be freed when sortOrder is freed } static int fileDbSortCmp(const void *va, const void *vb) // Compare two sortable tdb items based upon sort columns. { const struct fileDb *a = *((struct fileDb **)va); const struct fileDb *b = *((struct fileDb **)vb); char **fieldsA = a->sortFields; char **fieldsB = b->sortFields; int ix=0; int compared = 0; while(fieldsA[ix] != NULL && fieldsB[ix] != NULL && compared == 0) { compared = strcmp(fieldsA[ix], fieldsB[ix]) * (a->reverse[ix]? -1: 1); ix++; } return compared; } static void fileDbSortList(struct fileDb **fileList, sortOrder_t *sortOrder) {// If sortOrder struct provided, will update sortFields in fileList, then sort it if (sortOrder && fileList) { struct fileDb *oneFile = NULL; for(oneFile = *fileList;oneFile != NULL;oneFile=oneFile->next) { oneFile->sortFields = needMem(sizeof(char *) * (sortOrder->count + 1)); // +1 Null terminated oneFile->reverse = needMem(sizeof(boolean *) * sortOrder->count); int ix; for(ix=0;ix<sortOrder->count;ix++) { char *field = NULL; if (sameString("fileSize",sortOrder->column[ix])) { char niceNumber[32]; sprintf(niceNumber, "%.15lu", oneFile->fileSize); field = cloneString(niceNumber); } else if (sameString("fileType",sortOrder->column[ix])) field = oneFile->fileType; else field = mdbObjFindValue(oneFile->mdb,sortOrder->column[ix]); if (field) { oneFile->sortFields[sortOrder->order[ix] - 1] = field; oneFile->reverse[ sortOrder->order[ix] - 1] = (sortOrder->forward[ix] == FALSE); } else { oneFile->sortFields[sortOrder->order[ix] - 1] = NULL; oneFile->reverse[ sortOrder->order[ix] - 1] = FALSE; } oneFile->sortFields[sortOrder->count] = NULL; } } slSort(fileList,fileDbSortCmp); } } static char *removeCommonMdbVarsNotInSortOrder(struct mdbObj *mdbObjs,sortOrder_t *sortOrder) { // Removes varaibles common to all mdbObjs and not found in sortOrder. Returns allocated string oh removed var=val pairs if (sortOrder != NULL) { // Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; // However, keep the term if it is in the sortOrder struct dyString *dyCommon = dyStringNew(256); char *commonTerms[] = { "grant", "lab", "dataType", "control", "setType" }; int tIx=0,sIx = 0; for(;tIx<ArraySize(commonTerms);tIx++) { for(sIx = 0; sIx<sortOrder->count && differentString(commonTerms[tIx],sortOrder->column[sIx]); sIx++) ; if (sIx<sortOrder->count) // Found in sort Order so leave it in mdbObjs continue; char *val = mdbRemoveCommonVar(mdbObjs, commonTerms[tIx]); // All mdbs have it and have the same val for it. if (val) dyStringPrintf(dyCommon,"%s=%s ",commonTerms[tIx],val); } return dyStringCannibalize(&dyCommon); } return NULL; } static char *labelWithVocabLink(char *var,char *title,struct slPair *valsAndLabels,boolean tagsNotVals) /* If the parentTdb has a controlledVocabulary setting and the vocabType is found, then label will be wrapped with the link to all relevent terms. Return string is cloned. */ { // Determine if the var is cvDefined. If not, simple link boolean cvDefined = FALSE; struct hash *cvTypesOfTerms = (struct hash *)cvTermTypeHash(); if (cvTypesOfTerms != NULL) { struct hash *cvTermDef = hashFindVal(cvTypesOfTerms,var); if (cvTermDef) cvDefined = SETTING_IS_ON(hashFindVal(cvTermDef,"cvDefined")); } struct dyString *dyLink = dyStringNew(256); if (!cvDefined) dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?type=%s' title='Click for details of \"%s\"' TARGET=ucscVocab>%s</A>", var,title,title); else { dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?%s=",tagsNotVals?"tag":"term"); struct slPair *oneVal = valsAndLabels; for(;oneVal!=NULL;oneVal=oneVal->next) { if (oneVal != valsAndLabels) dyStringAppendC(dyLink,','); dyStringAppend(dyLink,mdbPairVal(oneVal)); } dyStringPrintf(dyLink,"' title='Click for details of each \"%s\"' TARGET=ucscVocab>%s</A>",title,title); } return dyStringCannibalize(&dyLink); } static int filterBoxesForFilesList(char *db,struct mdbObj *mdbObjs,sortOrder_t *sortOrder) { // Will create filterBoxes for each sortOrder field. Returns count of filterBoxes made int count = 0; if (sortOrder != NULL) { struct dyString *dyFilters = dyStringNew(256); int sIx=0; for(sIx = 0;sIx<sortOrder->count;sIx++) { char *var = sortOrder->column[sIx]; enum cvSearchable searchBy = cvSearchMethod(var); if (searchBy != cvSearchBySingleSelect && searchBy != cvSearchByMultiSelect) continue; // Only single selects and multi-select make good candidates for filtering // get all vals for var, then convert to tag/label pairs for filterBys struct slName *vals = mdbObjsFindAllVals(mdbObjs, var); struct slPair *tagLabelPairs = NULL; while(vals != NULL) { struct slName *term = slPopHead(&vals); char *tag = (char *)cvTag(var,term->name); if (tag == NULL) tag = term->name; slPairAdd(&tagLabelPairs,tag,cloneString((char *)cvLabel(term->name))); slNameFree(&term); } // If there is more than one val for this var then create filterBy box for it if (slCount(tagLabelPairs) > 1) { slPairValSortCase(&tagLabelPairs); // should have a list sorted on the label char extraClasses[256]; safef(extraClasses,sizeof extraClasses,"filterTable %s",var); + #ifdef NEW_JQUERY + char *dropDownHtml = cgiMakeMultiSelectDropList(var,tagLabelPairs,NULL,"All",extraClasses,"onchange='filterTable();' onclick='filterTableExclude(this);' style='font-size:.9em;'"); + #else///ifndef NEW_JQUERY char *dropDownHtml = cgiMakeMultiSelectDropList(var,tagLabelPairs,NULL,"All",extraClasses,"onchange='filterTable();' onclick='filterTableExclude(this);'"); + #endif///ndef NEW_JQUERY // Note filterBox has classes: filterBy & {var} if (dropDownHtml) { dyStringPrintf(dyFilters,"<td align='left'>\n<B>%s</B>:<BR>\n%s</td><td width=10> </td>\n", labelWithVocabLink(var,sortOrder->title[sIx],tagLabelPairs,TRUE),dropDownHtml); // TRUE were sending tags, not values freeMem(dropDownHtml); count++; } } if (slCount(tagLabelPairs) > 0) slPairFreeValsAndList(&tagLabelPairs); } // Finally ready to print the filterBys out if (count) { webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); #define FILTERBY_HELP_LINK "<A HREF=\"../goldenPath/help/multiView.html\" TARGET=ucscHelp>help</A>" cgiDown(0.9); printf("<B>Filter files by:</B> (select multiple %sitems - %s)\n<table><tr valign='bottom'>\n", (count >= 1 ? "categories and ":""),FILTERBY_HELP_LINK); printf("%s\n",dyStringContents(dyFilters)); printf("</tr></table>\n"); + #ifdef NEW_JQUERY + printf("<script type='text/javascript'>var newJQuery=true;</script>\n"); + printf("<script type='text/javascript'>$(document).ready(function() { $('.filterBy').each( function(i) { ddclSetup(this,'noneIsAll') });});</script>\n"); + #else///ifndef NEW_JQUERY + printf("<script type='text/javascript'>var newJQuery=false;</script>\n"); printf("<script type='text/javascript'>$(document).ready(function() { $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });});});</script>\n"); + #endif///ndef NEW_JQUERY } dyStringFree(&dyFilters); } return count; } static void filesDownloadsPreamble(char *db, struct trackDb *tdb) { // Do not bother getting preamble.html // 1) It isn't on the RR (yet) // 2) It will likely refer back to the composite for Description info which is included in this page // 3) The rsync-to-tmp-file hurdle isn't worth the effort. cgiDown(0.7); puts("<B>Data is <A HREF='http://genome.ucsc.edu/ENCODE/terms.html'>RESTRICTED FROM USE</a>"); puts("in publication until the restriction date noted for the given data file.</B>"); char *server = hDownloadsServer(); char *subDir = ""; if (hIsBetaHost()) { server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu" subDir = "/beta"; } cgiDown(0.7); puts("Supporting documents:"); printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/files.txt' TARGET=ucscDownloads>files.txt</A></B> is a tab-separated file with the name and metadata for each download.</LI>\n", server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir); printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A></B> is a list of the md5sum output for each download.</LI>\n", server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir); struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental"); if (oneFile != NULL) { printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' TARGET=ucscDownloads>Supplemental materials</A></B> contains additional files provided by the laboratory related to these downloads.</LI>\n", server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir); } } static int filesPrintTable(char *db, struct trackDb *parentTdb, struct fileDb *fileList, sortOrder_t *sortOrder,boolean filterable) // Prints filesList as a sortable table. Returns count { // Table class=sortable int columnCount = 0; int restrictedColumn = 0; char *nowrap = (sortOrder->setting != NULL ? " nowrap":""); // Sort order trackDb setting found so rely on <BR> in titles for wrapping printf("<TABLE class='sortable' style='border: 2px outset #006600;'>\n"); printf("<THEAD class='sortable'>\n"); printf("<TR class='sortable' valign='bottom'>\n"); printf("<TD align='center' valign='center'> "); int filesCount = slCount(fileList); if (filesCount > 5) printf("<em><span class='filesCount'></span>%d files</em>",filesCount); //if (sortOrder) // NOTE: This could be done to preserve sort order FIXME: However hgFileUi would need form OR changes would need to be ajaxed over AND hgsid would be needed. // printf("<INPUT TYPE=HIDDEN NAME='%s' class='sortOrder' VALUE=\"%s\">",sortOrder->htmlId, sortOrder->sortOrder); printf("</TD>\n"); columnCount++; /*#define SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS #ifdef SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS if (parentTdb == NULL) { printf("<TD align='center' valign='center'> </TD>"); columnCount++; } #endif///def SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS */ // Now the columns int curOrder = 0,ix=0; if (sortOrder) { curOrder = sortOrder->count; for(ix=0;ix<sortOrder->count;ix++) { char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":""); printf("<TH class='sortable sort%d%s' %s%s%s>%s</TH>\n", sortOrder->order[ix],(sortOrder->forward[ix]?"":" sortRev"), (sameString("fileSize",sortOrder->column[ix])?"abbr='use' ":""), nowrap,align,sortOrder->title[ix]); // keeing track of sortOrder columnCount++; if (sameWord(sortOrder->column[ix],"dateUnrestricted")) restrictedColumn = columnCount; } } //#define INCLUDE_FILENAMES #ifndef INCLUDE_FILENAMES else #endif///defn INCLUDE_FILENAMES { printf("<TH class='sortable sort%d' nowrap>File Name</TH>\n",++curOrder); columnCount++; } printf("<TH class='sortable sort%d' align='left' nowrap>Additional Details</TH>\n",++curOrder); columnCount++; printf("</TR></THEAD>\n"); // Now the files... char *server = hDownloadsServer(); char *subDir = ""; if (hIsBetaHost()) { server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu" subDir = "/beta"; } struct fileDb *oneFile = fileList; printf("<TBODY class='sortable sorting'>\n"); // 'sorting' is a fib but it conveniently greys the list till the table is initialized. for( ;oneFile!= NULL;oneFile=oneFile->next) { oneFile->mdb->next = NULL; // mdbs were in list for generating sortOrder, but list no longer needed char *field = NULL; printf("<TR valign='top'%s>",filterable?" class='filterable'":""); // Download button printf("<TD nowrap>"); if (parentTdb) field = parentTdb->track; else field = mdbObjFindValue(oneFile->mdb,"composite"); assert(field != NULL); printf("<input type='button' value='Download' onclick=\"window.location='http://%s/goldenPath/%s/%s/%s%s/%s';\" title='Download %s ...'>", server,db,ENCODE_DCC_DOWNLOADS, field, subDir, oneFile->fileName, oneFile->fileName); #define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS #ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS if (parentTdb == NULL) printf(" <A href='../cgi-bin/hgFileUi?db=%s&g=%s' title='Navigate to downloads page for %s set...'><IMG SRC='../images/folderC.png'></a> ", db,field,field); #endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS printf("</TD>\n"); // Each of the pulled out mdb vars if (sortOrder) { for(ix=0;ix<sortOrder->count;ix++) { char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":" align='center'"); if (sameString("fileSize",sortOrder->column[ix])) { char niceNumber[128]; sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize); field = oneFile->sortFields[sortOrder->order[ix] - 1]; printf("<TD abbr='%s' align='right' nowrap>%s</td>",field,niceNumber); } else { field = oneFile->sortFields[sortOrder->order[ix] - 1]; boolean isFieldEmpty = cvTermIsEmpty(sortOrder->column[ix],field); char class[128]; class[0] = '\0'; if (filterable) { enum cvSearchable searchBy = cvSearchMethod(sortOrder->column[ix]); if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect) { char *cleanClass = NULL; if (isFieldEmpty) cleanClass = "None"; else { cleanClass = (char *)cvTag(sortOrder->column[ix],field); // class should be tag if (cleanClass == NULL) cleanClass = field; } safef(class,sizeof class," class='%s %s'",sortOrder->column[ix],cleanClass); } } if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F")) printf("<TD%s nowrap style='color: #BBBBBB;'%s>%s</td>",align,class,field); else printf("<TD%s nowrap%s>%s</td>",align,class,isFieldEmpty?" ":field); if (!sameString("fileType",sortOrder->column[ix])) mdbObjRemoveVars(oneFile->mdb,sortOrder->column[ix]); // Remove this from mdb now so that it isn't displayed in "extras' } } } #ifndef INCLUDE_FILENAMES else #endif///ndef INCLUDE_FILENAMES { // fileName printf("<TD nowrap>%s",oneFile->fileName); //// FIXME: " The "..." encapsulation could be rebuilt so it could be called here //printf(" <A HREF='#a_meta_%s' onclick='return metadataShowHide(\"%s\",true,true);' title='Show metadata details...'>...</A>", // oneFile->mdb->obj,oneFile->mdb->obj); //printf("<DIV id='div_%s_meta' style='display:none;'></div></td>",oneFile->mdb->obj); } // Extras grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; mdbObjRemoveVars(oneFile->mdb,MDB_VAR_FILENAME " " MDB_VAR_FILEINDEX " " MDB_VAR_COMPOSITE " " MDB_VAR_PROJECT); // Remove this from mdb now so that it isn't displayed in "extras' field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE); printf("<TD nowrap>%s</td>",field?field:" "); printf("</TR>\n"); } printf("</TBODY><TFOOT class='bgLevel1'>\n"); printf("<TR valign='top'>"); // Restriction policy link in first column? if (restrictedColumn == 1) printf("<TH colspan=%d><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>Restriction Policy</A></TH>", (columnCount - restrictedColumn),ENCODE_DATA_RELEASE_POLICY); printf("<TD colspan=%d> ",(restrictedColumn > 1 ? (restrictedColumn - 1) : columnCount)); // Total if (filesCount > 5) printf("<em><span class='filesCount'></span>%d files</em>",filesCount); // Restriction policy link in later column? if (restrictedColumn > 1) printf("</TD><TH colspan=%d align='left'><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>Restriction Policy</A>", columnCount,ENCODE_DATA_RELEASE_POLICY); printf("</TD></TR>\n"); printf("</TFOOT></TABLE>\n"); if (parentTdb == NULL) printf("<script type='text/javascript'>{$(document).ready(function() {sortTableInitialize($('table.sortable')[0],true,true);});}</script>\n"); return filesCount; } static int filesFindInDir(char *db, struct mdbObj **pmdbFiles, struct fileDb **pFileList, char *fileType, int limit,boolean *exceededLimit) // Prints list of files in downloads directories matching mdb search terms. Returns count { int fileCount = 0; // Verify file existance and make fileList of those found struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files struct mdbObj *mdbList = *pmdbFiles; while (mdbList && (limit == 0 || fileCount < limit)) { boolean found = FALSE; struct mdbObj *mdbFile = slPopHead(&mdbList); char *composite = mdbObjFindValue(mdbFile,MDB_VAR_COMPOSITE); if (composite == NULL) { mdbObjsFree(&mdbFile); continue; } // First for FileName char *fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILENAME); if (fileName == NULL) { mdbObjsFree(&mdbFile); continue; } //#define NO_FILENAME_LISTS #ifdef NO_FILENAME_LISTS oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName); if (oneFile == NULL) { mdbObjsFree(&mdbFile); continue; } //warn("%s == %s",fileType,oneFile->fileType); if (isEmpty(fileType) || sameWord(fileType,"Any") || (oneFile->fileType && sameWord(fileType,oneFile->fileType))) { slAddHead(&fileList,oneFile); oneFile->mdb = mdbFile; slAddHead(&mdbFiles,oneFile->mdb); found = TRUE; fileCount++; if (limit > 0 && fileCount >= limit) break; } else fileDbFree(&oneFile); #else///ifndef NO_FILENAME_LISTS struct slName *fileSet = slNameListFromComma(fileName); struct slName *md5Set = NULL; char *md5sums = mdbObjFindValue(mdbFile,MDB_VAR_MD5SUM); if (md5sums != NULL) md5Set = slNameListFromComma(md5sums); while (fileSet != NULL) { struct slName *file = slPopHead(&fileSet); struct slName *md5 = NULL; if (md5Set) md5 = slPopHead(&md5Set); oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, file->name); if (oneFile == NULL) { slNameFree(&file); if (md5) slNameFree(&md5); continue; } //warn("%s == %s",fileType,oneFile->fileType); if (isEmpty(fileType) || sameWord(fileType,"Any") || (oneFile->fileType && startsWithWordByDelimiter(fileType,'.',oneFile->fileType))) // Starts with! This ensures both bam and bam.bai are found. { slAddHead(&fileList,oneFile); if (found) // if already found then need two mdbObjs (assertable but then this is metadata) oneFile->mdb = mdbObjClone(mdbFile); // Yes clone this as differences will occur else oneFile->mdb = mdbFile; if (md5 != NULL) mdbObjSetVar(oneFile->mdb,MDB_VAR_MD5SUM,md5->name); else mdbObjRemoveVars(oneFile->mdb,MDB_VAR_MD5SUM); slAddHead(&mdbFiles,oneFile->mdb); found = TRUE; fileCount++; if (limit > 0 && fileCount >= limit) { slNameFreeList(&fileSet); if (md5Set) slNameFreeList(&md5Set); break; } } else fileDbFree(&oneFile); slNameFree(&file); if (md5) slNameFree(&md5); } #endif///ndef NO_FILENAME_LISTS // FIXME: This support of fileIndex and implicit bam.bai's should be removed when mdb is cleaned up. // Now for FileIndexes if (limit == 0 || fileCount < limit) { char buf[512]; if (strchr(fileName,',') == NULL && endsWith(fileName,".bam")) // Special to fill in missing .bam.bai's { safef(buf,sizeof(buf),"%s.bai",fileName); fileName = buf; } else { fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILEINDEX); // This mdb var should be going away. if (fileName == NULL) continue; } // Verify existance first oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName); // NOTE: won't be found if already found in comma delimited fileName! if (oneFile == NULL) continue; //warn("%s == %s",fileType,oneFile->fileType); if (isEmpty(fileType) || sameWord(fileType,"Any") || (oneFile->fileType && sameWord(fileType,oneFile->fileType)) || (oneFile->fileType && sameWord(fileType,"bam") && sameWord("bam.bai",oneFile->fileType))) // TODO: put fileType matching into search.c lib code to segregate index logic. { slAddHead(&fileList,oneFile); if (found) // if already found then need two mdbObjs (assertable but then this is metadata) oneFile->mdb = mdbObjClone(mdbFile); else oneFile->mdb = mdbFile; mdbObjRemoveVars(oneFile->mdb,MDB_VAR_MD5SUM); slAddHead(&mdbFiles,oneFile->mdb); fileCount++; found = TRUE; continue; } else fileDbFree(&oneFile); } if (!found) mdbObjsFree(&mdbFile); } *pmdbFiles = mdbFiles; *pFileList = fileList; if (exceededLimit != NULL) *exceededLimit = FALSE; if (mdbList != NULL) { if (exceededLimit != NULL) *exceededLimit = TRUE; mdbObjsFree(&mdbList); } return fileCount; } void filesDownloadUi(char *db, struct cart *cart, struct trackDb *tdb) // UI for a "composite like" track: This will list downloadable files associated with // a single trackDb entry (composite or of type "downloadsOnly". The list of files // will have links to their download and have metadata information associated. // The list will be a sortable table and there may be filtering controls. { boolean debug = cartUsualBoolean(cart,"debug",FALSE); struct sqlConnection *conn = hAllocConn(db); char *mdbTable = mdbTableName(conn,TRUE); // Look for sandBox name first if(mdbTable == NULL) errAbort("TABLE NOT FOUND: '%s.%s'.\n",db,MDB_DEFAULT_NAME); // Get an mdbObj list of all that belong to this track and have a fileName char buf[256]; safef(buf,sizeof(buf),"%s=%s %s=?",MDB_VAR_COMPOSITE,tdb->track,MDB_VAR_FILENAME); struct mdbByVar *mdbVars = mdbByVarsLineParse(buf); struct mdbObj *mdbList = mdbObjsQueryByVars(conn,mdbTable,mdbVars); // Now get Indexes But be sure not to duplicate entries in the list!!! safef(buf,sizeof(buf),"%s=%s %s= %s!=",MDB_VAR_COMPOSITE,tdb->track,MDB_VAR_FILEINDEX,MDB_VAR_FILENAME); mdbVars = mdbByVarsLineParse(buf); mdbList = slCat(mdbList, mdbObjsQueryByVars(conn,mdbTable,mdbVars)); mdbObjRemoveHiddenVars(mdbList); hFreeConn(&conn); if (slCount(mdbList) == 0) { warn("No files specified in metadata for: %s\n%s",tdb->track,tdb->longLabel); return; } // Verify file existance and make fileList of those found struct fileDb *fileList = NULL; // Will contain found files int fileCount = filesFindInDir(db, &mdbList, &fileList, NULL, 0, NULL); assert(fileCount == slCount(fileList)); if (fileCount == 0) { warn("No downloadable files currently available for: %s\n%s",tdb->track,tdb->longLabel); return; // No files so nothing to do. } if (debug) { warn("The following files are in goldenPath/%s/%s/%s/ but NOT in the mdb:",db,ENCODE_DCC_DOWNLOADS, tdb->track); fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "listAll"); } jsIncludeFile("hui.js",NULL); jsIncludeFile("ajax.js",NULL); // standard preamble filesDownloadsPreamble(db,tdb); // Now update all files with their sortable fields and sort the list mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print! sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb,mdbList); boolean filterable = FALSE; if (sortOrder != NULL) { char *vars = removeCommonMdbVarsNotInSortOrder(mdbList,sortOrder); if (vars) { if (debug) warn("These terms are common:%s",vars); freeMem(vars); } // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); // FilterBoxes filterable = (filterBoxesForFilesList(db,mdbList,sortOrder) > 0); } // Print table filesPrintTable(db,tdb,fileList,sortOrder,filterable); //fileDbFree(&fileList); // Why bother on this very long running cgi? //mdbObjsFree(&mdbList); } int fileSearchResults(char *db, struct sqlConnection *conn, struct slPair *varValPairs, char *fileType) // Prints list of files in downloads directories matching mdb search terms. Returns count { struct sqlConnection *connLocal = conn; if (conn == NULL) connLocal = hAllocConn(db); struct mdbObj *mdbList = mdbObjRepeatedSearch(connLocal,varValPairs,FALSE,TRUE); if (conn == NULL) hFreeConn(&connLocal); if (slCount(mdbList) == 0) { printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n"); return 0; } // Now sort mdbObjs so that composites will stay together and lookup of files will be most efficient mdbObjsSortOnVars(&mdbList, MDB_VAR_COMPOSITE); mdbObjRemoveHiddenVars(mdbList); #define FOUND_FILE_LIMIT 1000 struct fileDb *fileList = NULL; // Will contain found files int filesExpected = slCount(mdbList); boolean exceededLimit = FALSE; int fileCount = filesFindInDir(db, &mdbList, &fileList, fileType, FOUND_FILE_LIMIT, &exceededLimit); assert(fileCount == slCount(fileList)); if (fileCount == 0) { printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n"); return 0; // No files so nothing to do. } // TODO Could sort on varValPairs by creating a sortOrder struct of them //// Now update all files with their sortable fields and sort the list mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print! sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbList); // No cart, no tdb if (sortOrder != NULL) { // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); } mdbObjRemoveVars(mdbList,"tableName"); // Remove this from mdb now so that it isn't displayed in "extras' //jsIncludeFile("hui.js",NULL); //jsIncludeFile("ajax.js",NULL); // Print table printf("<DIV id='filesFound'>"); if (exceededLimit) { // What is the expected count? Difficult to say because of comma delimited list in fileName. if (filesExpected <= FOUND_FILE_LIMIT) filesExpected = FOUND_FILE_LIMIT + 1; printf("<DIV class='redBox' style='width: 380px;'>Too many files found. Displaying first %d of at least %d.<BR>Narrow search parameters and try again.</DIV><BR>\n", fileCount,filesExpected); //warn("Too many files found. Displaying first %d of at least %d.<BR>Narrow search parameters and try again.\n", fileCount,filesExpected); } fileCount = filesPrintTable(db,NULL,fileList,sortOrder,FALSE); // FALSE=Don't offer more filtering on the file search page printf("</DIV><BR>\n"); //fileDbFree(&fileList); // Why bother on this very long running cgi? //mdbObjsFree(&mdbList); return fileCount; }