6ea38c4589a071e814b34a2d5d8a7a9f1829c3ed tdreszer Fri Jan 14 15:02:43 2011 -0800 Added a default sort order. Special code to find .bai files. Common sortable table for both hgFileUi and fileSearch. Added folder link to hgFileUi from file search. diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c index f5b00d4..81e550a 100644 --- src/hg/lib/fileUi.c +++ src/hg/lib/fileUi.c @@ -1,774 +1,764 @@ /* 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" // 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(); if (sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different { // Does not work: rsync -avn rsync://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone // Use ls -log --time=ctime --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone safef(cmd,sizeof(cmd),"ls -log --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/%s/%s/%s/", db,dir,subDir); } else // genome and hgwbeta can use rsync { // Works: rsync -avn rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/ //safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/%s | grep %s", server, db, subDir,dir,fileName,fileName); safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/", server, db, dir, subDir); } //warn("cmd: %s",cmd); 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 && sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different { //-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 && differentString(server,"hgdownload-test.cse.ucsc.edu"))// genome and hgwbeta can use rsync { //-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); 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; } // mark this as done to avoid excessive io savedDb = cloneString(db); savedDir = cloneString(dir); savedSubDir = cloneString(subDir); } // 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; } -sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb) +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; -char *setting = trackDbSetting(parentTdb, FILE_SORT_ORDER); +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); + // Problem with making common fieds as sorable is that it REQUIRES a fixed sort order + char *sortables[] = {"grant","lab","dataType","cell","strain","age","rnaExtract","localization","phase","treatment","antibody","protocol", + "labProtocolId","restrictionEnzyme","control","replicate","expId","labExpId","setType","view","submittedDataVersion","subId", + "dataVersion","dateSubmitted","dateResubmitted","dateUnrestricted",//"labVersion","softwareVersion", + "mapAlgorithm","fragSize","fragLength"}; + // Not included: no:not searchable + // accession no, annotation no, bioRep no, composite no, controlId no, dccInternalNotes no, fileIndex no, fileName no, freezeDate no + // geoSample, geoSeries, insertLength no, labVersion, level no, obtainedBy, origAssembly, privacy no, rank no + // readType, seqPlatform, sex, size no, softwareVersion, tableName no, uniqueness no + + int ix = 0, count = sizeof(sortables)/sizeof(char *); + for (ix=0;ixUntil" + setting = FILE_SORT_ORDER_DEFAULT; + } + sortOrder = needMem(sizeof(sortOrder_t)); + carveSetting = cloneString(setting); + sortOrder->setting = NULL; + } -sortOrder_t *sortOrder = needMem(sizeof(sortOrder_t)); -sortOrder->setting = cloneString(setting); +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(sortOrder->setting,NULL,0); // Get size +sortOrder->count = chopByWhite(carveSetting,NULL,0); // Get size sortOrder->column = needMem(sortOrder->count*sizeof(char*)); -sortOrder->count = chopByWhite(sortOrder->setting,sortOrder->column,sortOrder->count); +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; ixcount; 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;ixcount;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 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. puts("

Data is RESTRICTED FROM USE"); puts("in publication until the restriction date noted for the given data file.

"); struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental"); if (oneFile != NULL) { printf("

\nSupplemental materials may be found here.

\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); } puts("

\nThere are two files within this directory that contain information about the downloads:"); printf("
• files.txt which is a tab-separated file with the name and metadata for each download.\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); printf("
• md5sum.txt which is a list of the md5sum output for each download.\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); puts("

"); } +static int filesPrintTable(char *db, struct trackDb *parentTdb, struct fileDb *fileList, sortOrder_t *sortOrder) +// 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
in titles for wrapping +printf("\n"); +printf("\n"); +printf("\n"); +printf("\n"); +columnCount++; + +/*#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS +#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS +if (parentTdb == NULL) + { + printf(""); + columnCount++; + } +#endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS +*/ +// Now the columns +int curOrder = 0,ix=0; +if (sortOrder) + { + curOrder = sortOrder->count; + for(ix=0;ixcount;ix++) + { + char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":""); + printf("\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("\n",++curOrder); + columnCount++; + } +printf("\n",++curOrder); +columnCount++; +printf("\n"); + +// Now the files... +struct fileDb *oneFile = fileList; +printf("\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(""); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!! + + // Download button + printf("\n"); + + // Each of the pulled out mdb vars + if (sortOrder) + { + for(ix=0;ixcount;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("",field,niceNumber); + } + else + { + field = oneFile->sortFields[sortOrder->order[ix] - 1]; + if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F")) + printf("%s",align,field); + else + printf("%s",align,field?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("",oneFile->mdb->obj); + } + + // Extras grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; + mdbObjRemoveVars(oneFile->mdb,"fileName fileIndex composite project dccInternalNotes"); // Remove this from mdb now so that it isn't displayed in "extras' + mdbObjReorderVars(oneFile->mdb,"grant lab dataType cell treatment antibody protocol replicate view",FALSE); // Bring to front + mdbObjReorderVars(oneFile->mdb,"subId submittedDataVersion dateResubmitted dataVersion setType inputType controlId tableName",TRUE); // Send to back + field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE); + printf("",field?field:"  "); + + printf("\n"); + } + +printf("\n"); +printf(""); + +// Restriction policy link in first column? +if (restrictedColumn == 1) + printf("", (columnCount - restrictedColumn),ENCODE_DATA_RELEASE_POLICY); + +printf("\n"); +printf("
 "); +int filesCount = slCount(fileList); +if (filesCount > 5) + printf("%d files",filesCount); //puts(""); // Use this style when filterboxes are up and running +//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("",sortOrder->htmlId, sortOrder->sortOrder); +printf(" %sFile NameAdditional Details
"); + if (parentTdb) + field = parentTdb->track; + else + field = mdbObjFindValue(oneFile->mdb,"composite"); + assert(field != NULL); + printf("", + hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, field, oneFile->fileName, oneFile->fileName); + printf(""); + printf(""); + +#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS +#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS + if (parentTdb == NULL) + printf("  ", db,field,field); +#endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS + printf("%s%s",oneFile->fileName); + //// FIXME: " The "..." encapsulation could be rebuilt so it could be called here + //printf(" ...", + // oneFile->mdb->obj,oneFile->mdb->obj); + //printf("%s
Restriction Policy    ",(restrictedColumn > 1 ? (restrictedColumn - 1) : columnCount)); + +// Total +if (filesCount > 5) + printf("%d files\n",filesCount); + +// Restriction policy link in later column? +if (restrictedColumn > 1) + printf("Restriction Policy", columnCount,ENCODE_DATA_RELEASE_POLICY); + +printf("

\n"); + +if (parentTdb == NULL) + printf("\n"); + +return filesCount; +} + + 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. { // The basic idea: // 1) tdb of composite or type=downloadsOnly tableless track // 2) All mdb Objs associated with "composite=tdb->track" and having fileName // 3) Verification of each file in its discovered location // 4) Lookup of 'fileSortOrder' // 5) TODO: present filter controls // 6) Presort of files list // 7) make table class=sortable // 8) Final file count // 9) Use trackDb settings to get at html description // Nice to have: Make filtering and sorting persistent (saved to cart) // FIXME: Trick while developing: if (tdb->table != NULL) tdb->track = tdb->table; boolean debug = cartUsualBoolean(cart,"debug",FALSE); int ix; struct sqlConnection *conn = sqlConnect(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); -struct fileDb *fileList = NULL, *oneFile = NULL; - // Get an mdbObj list of all that belong to this track and have a fileName char buf[256]; safef(buf,sizeof(buf),"composite=%s fileName=?",tdb->track); 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),"composite=%s fileIndex= fileName!=",tdb->track); mdbVars = mdbByVarsLineParse(buf); mdbList = slCat(mdbList, mdbObjsQueryByVars(conn,mdbTable,mdbVars)); sqlDisconnect(&conn); if (slCount(mdbList) == 0) { warn("No files specified in metadata for: %s\n%s",tdb->track,tdb->longLabel); return; } // Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; char *commonTerms[] = { "grant", "lab", "dataType", "control", "setType" }; struct dyString *dyCommon = dyStringNew(256); for(ix=0;ixtrack, fileName); if (oneFile) { slAddHead(&fileList,oneFile); oneFile->mdb = mdbFile; + slAddHead(&mdbFiles,mdbFile); found = TRUE; } else if (debug) warn("goldenPath/%s/%s/%s/%s in mdb but not found in directory",db,ENCODE_DCC_DOWNLOADS, tdb->track,fileName); } // Now for FileIndexes + if (fileName && endsWith(fileName,".bam")) // Special to fill in missing .bam.bai's + { + safef(buf,sizeof(buf),"%s.bai",fileName); + fileName = buf; + } + else fileName = mdbObjFindValue(mdbFile,"fileIndex"); if (fileName != NULL) { // Verify existance first oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, fileName); if (oneFile) { slAddHead(&fileList,oneFile); if (found) // if already found then need two mdbObjs (assertable but then this is metadata) oneFile->mdb = mdbObjClone(mdbFile); // Do we really need to clone this? else + { oneFile->mdb = mdbFile; + slAddHead(&mdbFiles,mdbFile); + } found = TRUE; } else if (debug) warn("goldenPath/%s/%s/%s/%s in mdb but not found in directory",db,ENCODE_DCC_DOWNLOADS, tdb->track,fileName); } if (!found) mdbObjsFree(&mdbFile); } if (slCount(fileList) == 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"); } // FilterBoxes ? // Dimensions // cart contents //boolean filterAble = dimensionsExist(tdb); //membersForAll_t* membersForAll = membersForAllSubGroupsGet(tdb,cart); // Now update all files with their sortable fields and sort the list -sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb); +sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb,mdbFiles); if (sortOrder != NULL) { // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); } jsIncludeFile("hui.js",NULL); jsIncludeFile("ajax.js",NULL); // standard preamble filesDownloadsPreamble(db,tdb); -// Table class=sortable -int columnCount = 0; -int restrictedColumn = 0; -printf("\n"); -printf("\n"); -printf("\n"); -printf("\n"); -columnCount++; - -// Now the columns -int curOrder = 0; -if (sortOrder) - { - curOrder = sortOrder->count; - for(ix=0;ixcount;ix++) - { - printf("\n", - sortOrder->order[ix],(sortOrder->forward[ix]?"":" sortRev"), - (sameString("fileSize",sortOrder->column[ix])?"abbr='use' ":""), - 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("\n",++curOrder); - columnCount++; - } -printf("\n",++curOrder); -columnCount++; -printf("\n"); - -// Now the files... -printf("\n"); // 'sorting' is a fib but it conveniently greys the list till the table is initialized. -for(oneFile = fileList;oneFile!= NULL;oneFile=oneFile->next) - { - char *field = NULL; - - printf(""); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!! - - // Download button - printf("\n"); - - // Each of the pulled out mdb vars - if (sortOrder) - { - for(ix=0;ixcount;ix++) - { - if (sameString("fileSize",sortOrder->column[ix])) - { - char niceNumber[128]; - sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize); - field = oneFile->sortFields[sortOrder->order[ix] - 1]; - printf("",field,niceNumber); - } - else - { - field = oneFile->sortFields[sortOrder->order[ix] - 1]; - if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F")) - printf("",field); - else - printf("",field?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("",oneFile->mdb->obj); - } - - // Extras grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; - mdbObjRemoveVars(oneFile->mdb,"fileName fileIndex composite project dccInternalNotes"); // Remove this from mdb now so that it isn't displayed in "extras' - mdbObjReorderVars(oneFile->mdb,"grant lab dataType cell treatment antibody protocol replicate view",FALSE); // Bring to front - mdbObjReorderVars(oneFile->mdb,"subId submittedDataVersion dateResubmitted dataVersion setType inputType controlId tableName",TRUE); // Send to back - field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE); - printf("",field?field:"  "); - - printf("\n"); - } - -printf("\n"); -printf(""); - -// Restriction policy link in first column? -if (restrictedColumn == 1) - printf("", (columnCount - restrictedColumn),ENCODE_DATA_RELEASE_POLICY); - -printf("\n"); -printf("
 "); -int filesCount = slCount(fileList); -if (filesCount > 5) - printf("%d files",filesCount); //puts(""); // Use this style when filterboxes are up and running -//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("",sortOrder->htmlId, sortOrder->sortOrder); -printf("%sFile NameAdditional Details
"); - printf("", - hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track, oneFile->fileName, oneFile->fileName); - printf(""); - printf("%s%s%s%s",oneFile->fileName); - //// FIXME: " The "..." encapsulation could be rebuilt so it could be called here - //printf(" ...", - // oneFile->mdb->obj,oneFile->mdb->obj); - //printf("%s
Restriction Policy    ",(restrictedColumn > 1 ? (restrictedColumn - 1) : columnCount)); +// Print table +filesPrintTable(db,tdb,fileList,sortOrder); -// Total -if (filesCount > 5) - printf("%d files\n",filesCount); - -// Restriction policy link in later column? -if (restrictedColumn > 1) - printf("Restriction Policy", columnCount,ENCODE_DATA_RELEASE_POLICY); - -printf("

\n"); - -// Free mem? +//fileDbFree(&fileList); // Why bother on this very long running cgi? } 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("


No files found.

\n"); return 0; } // Now sort mdbObjs so that composites will stay together and lookup of files will be most efficient mdbObjsSortOnVars(&mdbList, "composite"); // Verify file existance and make fileList of those found -struct fileDb *fileList = NULL, *oneFile = NULL; +struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files +struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files while(mdbList) { boolean found = FALSE; struct mdbObj *mdbFile = slPopHead(&mdbList); char *composite = mdbObjFindValue(mdbFile,"composite"); if (composite != NULL) { // First for FileName char *fileName = mdbObjFindValue(mdbFile,"fileName"); if (fileName != NULL) { oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName); if (oneFile) { //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,mdbFile); found = TRUE; continue; } } else fileDbFree(&oneFile); } // Now for FileIndexes fileName = mdbObjFindValue(mdbFile,"fileIndex"); if (fileName != NULL) { // Verify existance first oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName); if (oneFile) { //warn("%s == %s",fileType,oneFile->fileType); if (isEmpty(fileType) || sameWord(fileType,"Any") || (oneFile->fileType && sameWord(fileType,oneFile->fileType))) { slAddHead(&fileList,oneFile); if (found) // if already found then need two mdbObjs (assertable but then this is metadata) oneFile->mdb = mdbObjClone(mdbFile); // Do we really need to clone this? else + { oneFile->mdb = mdbFile; + slAddHead(&mdbFiles,mdbFile); + } found = TRUE; continue; } else fileDbFree(&oneFile); } } } if (!found) mdbObjsFree(&mdbFile); } if (slCount(fileList) == 0) { printf("

No files found.

\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 -//sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb); -//if (sortOrder != NULL) -// { -// // Fill in and sort fileList -// fileDbSortList(&fileList,sortOrder); -// } - -//jsIncludeFile("hui.js",NULL); -//jsIncludeFile("ajax.js",NULL); - -// Table class=sortable -int columnCount = 0; -//int restrictedColumn = 0; -printf("
\n"); -printf("\n"); -printf("\n"); -printf("\n"); -columnCount++; - -// Now the columns -struct slPair *onePair; -for(onePair=varValPairs; onePair != NULL; onePair=onePair->next) - { - printf("\n",onePair->name); - columnCount++; - } -printf("\n"); -columnCount++; -printf("\n"); -columnCount++; -printf("\n"); -columnCount++; -printf("\n", ENCODE_DATA_RELEASE_POLICY); -//printf("\n"); -columnCount++; -//restrictedColumn = columnCount; -//#define INCLUDE_FILENAMES -#ifdef INCLUDE_FILENAMES -printf("\n"); -columnCount++; -#endif///defn INCLUDE_FILENAMES -printf("\n"); -columnCount++; -printf("\n"); - -// Now the files... -printf("\n"); -for(oneFile = fileList;oneFile!= NULL;oneFile=oneFile->next) - { - char *field = NULL; - - printf(""); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!! - - // Download button - printf(""); - - // Each of the pulled out mdb vars - for(onePair=varValPairs; onePair != NULL; onePair=onePair->next) +sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbFiles); // No cart, no tdb +if (sortOrder != NULL) { - field = mdbObjFindValue(oneFile->mdb,onePair->name); - printf("",field?field:"  "); - mdbObjRemoveVars(oneFile->mdb,onePair->name); // Remove this from mdb now so that it isn't displayed in "extras' - } - char niceNumber[128]; - sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize); - printf("",niceNumber); - printf("",oneFile->fileType?oneFile->fileType:"  "); - field = mdbObjFindValue(oneFile->mdb,"dateSubmitted"); - printf("",field?field:"  "); - field = mdbObjFindValue(oneFile->mdb,"dateUnrestricted"); - //printf("",field?dateIsOld(field,"%F")?"  ":field:"  "); - if(field) - printf("",dateIsOld(field,"%F")?" style='color: #BBBBBB;'":"",field); - else - printf(""); -#ifdef INCLUDE_FILENAMES - printf("",oneFile->fileName); -#endif///def INCLUDE_FILENAMES - - // Extras grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std; - mdbObjRemoveVars(oneFile->mdb,"dateSubmitted dateUnrestricted fileName fileIndex composite project dccInternalNotes"); // Remove this from mdb now so that it isn't displayed in "extras' - mdbObjReorderVars(oneFile->mdb,"grant lab dataType cell treatment antibody protocol replicate view",FALSE); // Bring to front - mdbObjReorderVars(oneFile->mdb,"subId submittedDataVersion dateResubmitted dataVersion setType inputType controlId tableName",TRUE); // Send to back - field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE); - printf("",field?field:"  "); - - printf("\n"); + // Fill in and sort fileList + fileDbSortList(&fileList,sortOrder); } -printf("\n"); -printf(""); - -printf("\n"); -printf("
 "); -int filesCount = slCount(fileList); -if (filesCount > 5) - printf("%d files",filesCount); //puts(""); // Use this style when filterboxes are up and running -printf("%sSizeFile TypeSubmittedRestricted
Until		Restricted
Until		File NameAdditional Details
"); - field = mdbObjFindValue(oneFile->mdb,"composite"); - assert(field != NULL); - printf("", - hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, field?field:"  ", oneFile->fileName, oneFile->fileName); - printf(""); - printf(""); -//#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS -#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS - field = mdbObjFindValue(oneFile->mdb,"composite"); - if (field) - { - // TODO Look up trackDb.fileSortOrder. If found, then offer "folder" icon with link to page - // Instead, always offer hgFileUi link and have hgFileUi figure out what to do - printf("  ", db,field,field); - } -#endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS - puts("%s%s%s%s%s%s  %s%s
    ",columnCount); -//printf("    ",(restrictedColumn > 1 ? (restrictedColumn - 1) : columnCount)); - -// Total -if (filesCount > 5) - printf("%d files\n",filesCount); +//jsIncludeFile("hui.js",NULL); +//jsIncludeFile("ajax.js",NULL); -// Restriction policy link in later column? -//if (restrictedColumn > 1) -// printf("Restriction Policy", columnCount,ENCODE_DATA_RELEASE_POLICY); +// Print table +int filesCount = filesPrintTable(db,NULL,fileList,sortOrder); -printf("
\n"); -// Free mem? -fileDbFree(&fileList); +//fileDbFree(&fileList); // Why bother on this very long running cgi? return filesCount; }