468608d7e217375418840f1f65ce90884b6c8962 tdreszer Fri Jan 14 16:00:44 2011 -0800 And a little more tweeking. Don't create a default column when all values will be the same diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c index cb5f0e9..6dc1561 100644 --- src/hg/lib/fileUi.c +++ src/hg/lib/fileUi.c @@ -1,764 +1,768 @@ /* 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; } 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); // 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", + char *sortables[] = {"grant","lab","dataType","cell","strain","age","obtainedBy", "rnaExtract","localization","phase","treatment","antibody","protocol", "labProtocolId","restrictionEnzyme","control","replicate","expId","labExpId","setType","view","submittedDataVersion","subId", "dateSubmitted","dateResubmitted","dateUnrestricted","dataVersion"};//"labVersion","softwareVersion", // Not included: no:not searchable // accession no, annotation no, bioRep no, composite no, controlId no, dccInternalNotes no, fileIndex no, fileName no, // fragSize no, fragLength no, freezeDate no, geoSample, geoSeries, insertLength no, labVersion, level no, - // mapAlgorithm, obtainedBy, origAssembly, privacy no, rank no, readType, seqPlatform, sex, + // mapAlgorithm, 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;ix<count;ix++) { // If sortables[ix] is in common vars then then add it to the settings field if (mdbObjContains(commonVars,sortables[ix],NULL)) + { + if (mdbRemoveCommonVar(mdbObjs, sortables[ix])) // Don't bother if all the vals are the same + continue; dyStringPrintf(dySortFields,"%s=%s ",sortables[ix],strSwapChar(cloneString(cvLabel(sortables[ix])),' ','_')); } + } 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 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("<p><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></p>"); struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental"); if (oneFile != NULL) { printf("<p>\n<B>Supplemental materials</b> may be found <A HREF='http://%s/goldenPath/%s/%s/%s/supplemental/' TARGET=ucscDownloads>here</A>.</p>\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); } puts("<p>\nThere are two files within this directory that contain information about the downloads:"); printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s/files.txt' TARGET=ucscDownloads>files.txt</A> which is a tab-separated file with the name and metadata for each download.</LI>\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A> which is a list of the md5sum output for each download.</LI>\n", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track); puts("<P>"); } 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 <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("<i>%d files</i>",filesCount); //puts("<FONT class='subCBcount'></font>"); // 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("<INPUT TYPE=HIDDEN NAME='%s' class='sortOrder' VALUE=\"%s\">",sortOrder->htmlId, sortOrder->sortOrder); printf("</TD>\n"); columnCount++; /*#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS #ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS if (parentTdb == NULL) { printf("<TD align='center' valign='center'> </TD>"); columnCount++; } #endif///def SHOW_FOLDER_FRO_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... 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'>"); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!! // Download button printf("<TD nowrap>"); if (parentTdb) field = parentTdb->track; else field = mdbObjFindValue(oneFile->mdb,"composite"); assert(field != NULL); printf("<A HREF='http://%s/goldenPath/%s/%s/%s/%s' title='Download %s ...' TARGET=ucscDownloads>", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, field, oneFile->fileName, oneFile->fileName); printf("<input type='button' value='Download'>"); printf("</a>"); #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]; if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F")) printf("<TD%s nowrap style='color: #BBBBBB;'>%s</td>",align,field); else printf("<TD%s nowrap>%s</td>",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("<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,"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("<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("<i>%d files</i>\n",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><BR>\n"); if (parentTdb == NULL) printf("<script type='text/javascript'>{$(document).ready(function() {sortTableInitialize($('table.sortable')[0],true,true);});}</script>\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); // 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;ix<ArraySize(commonTerms);ix++) { char *val = mdbRemoveCommonVar(mdbList, commonTerms[ix]);// All mdbs have it and have the same val for it. if (val) dyStringPrintf(dyCommon,"%s=%s ",commonTerms[ix],val); } if (debug && dyStringLen(dyCommon)) warn("These terms are common:%s",dyStringContents(dyCommon)); dyStringFree(&dyCommon); // 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 while(mdbList) { char buf[512]; boolean found = FALSE; struct mdbObj *mdbFile = slPopHead(&mdbList); // First for FileName char *fileName = mdbObjFindValue(mdbFile,"fileName"); if (fileName != NULL) { oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, 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,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); // Print table filesPrintTable(db,tdb,fileList,sortOrder); //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("<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, "composite"); // 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 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("<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 sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbFiles); // No cart, no tdb if (sortOrder != NULL) { // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); } //jsIncludeFile("hui.js",NULL); //jsIncludeFile("ajax.js",NULL); // Print table int filesCount = filesPrintTable(db,NULL,fileList,sortOrder); //fileDbFree(&fileList); // Why bother on this very long running cgi? return filesCount; }