70e9200a58ef4db6378dae703296d29188ae26b1 tdreszer Fri Dec 17 14:58:43 2010 -0800 Make use of fileUi.h macros and support hgFileUi CGI diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c index 8c8cfd8..0620a63 100644 --- src/hg/lib/fileUi.c +++ src/hg/lib/fileUi.c @@ -1,498 +1,521 @@ /* fileUi.c - human genome file downloads common controls. */ #include "common.h" #include "hash.h" #include "cheapcgi.h" #include "jsHelper.h" #include "cart.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->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); } //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); //warn("found %d files",slCount(foundFiles)); 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; slAddHead(&newList,oneFile); oneFile = NULL; } if (newList) foundFiles = slCat(newList,foundFiles); return oneFile; } sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb) /* 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, "fileSortOrder"); +char *setting = trackDbSetting(parentTdb, FILE_SORT_ORDER); if(setting == NULL) // Must be in trackDb or not a sortable list of files return NULL; sortOrder_t *sortOrder = needMem(sizeof(sortOrder_t)); sortOrder->setting = cloneString(setting); sortOrder->htmlId = needMem(strlen(parentTdb->track)+20); -safef(sortOrder->htmlId, (strlen(parentTdb->track)+20), "%s.fileSortOrder", parentTdb->track); +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->column = needMem(sortOrder->count*sizeof(char*)); sortOrder->count = chopByWhite(sortOrder->setting,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 = cloneString(oneFile->fileName + strlen(oneFile->mdb->obj) + 1); if (endsWith(field,".gz")) chopSuffix(field); } 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); } } 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 filters (tdb dimensions?) and filterComposite style controls // 5) Presort of files list // 6) make table class=sortable // 7) Final file count // Get preamble from dir ?? // Use trackDb settings to get at html description, long and short labels // Recommend different color background to get the point across that these are files, not tracks // 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 memtadata for: %s\n%s",tdb->track,tdb->longLabel); + 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]); 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 while(mdbList) { 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; 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 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; 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); 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("<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 +//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++; // Now the columns int curOrder = 0; if (sortOrder) { curOrder = sortOrder->count; for(ix=0;ix<sortOrder->count;ix++) { printf("<TH class='sortable sort%d%s' %snowrap>%s</TH>\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("<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... -printf("<TBODY class='sortable'>\n"); +printf("<TBODY class='sortable sorting'>\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("<TR valign='top'>"); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!! // Download button printf("<TD>"); printf("<A HREF='http://%s/goldenPath/%s/%s/%s/%s' title='Download %s ...' TARGET=ucscDownloads>", hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track, oneFile->fileName, oneFile->fileName); printf("<input type='button' value='Download'>"); printf("</a></TD>\n"); // Each of the pulled out mdb vars if (sortOrder) { for(ix=0;ix<sortOrder->count;ix++) { 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]; printf("<TD align='center' nowrap>%s</td>",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"); // 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></TABLE><BR>\n"); -printf("<script type='text/javascript'>{$(document).ready(function() {sortTableInitialize($('table.sortable')[0],true,true);});}</script>\n"); +printf("</TBODY><TFOOT class='bgLevel3'>\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); //puts("<FONT class='subCBcount'></font>"); // Use this style when filterboxes are up and running + 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"); // Free mem? }