9b13731e6e466aa0f781179da2d504db2f4c15a9 tdreszer Wed Mar 30 11:28:34 2011 -0700 Made slPairListFromString and slPairListToString optionally handle double quotes. Finally made mdbObjReorderByCv so that priority in cv.ra typeOfTerms is used. diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c index 88fa70c..2f37138 100644 --- src/hg/lib/fileUi.c +++ src/hg/lib/fileUi.c @@ -184,31 +184,37 @@ 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); + // FIXME: Replace with ? cv searchable combined with priority combined with cvDefined? + // A good first step was putting the vars in cv order. Now walk through them, and determine if each should be sortable // Problem with making common fieds as sorable is that it REQUIRES a fixed sort order + // All in priority order (or so) except: obtainedBy,expId,strain,labProtocolId + // All are searchable except: labProtocolId,replicate,submittedDataVersion,dateSubmitted,dateResubmitted,dateUnrestricted + // Solution: use cv order and whether searchable. Define dates as searchable in cv.ra, make searchable: labProtocolId, replicate, submittedDataVersion + // change some orders in cv and other orders here! 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","origAssembly"};//"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, 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)) { @@ -637,33 +643,31 @@ } } } #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 + 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)); @@ -704,119 +708,118 @@ // 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); 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),"composite=%s fileName=?",tdb->track); +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),"composite=%s fileIndex= fileName!=",tdb->track); +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, *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"); + char *fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILENAME); if (fileName != NULL) { oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, fileName); if (oneFile) { slAddHead(&fileList,oneFile); oneFile->mdb = mdbFile; - slAddHead(&mdbFiles,mdbFile); + slAddHead(&mdbFiles,oneFile->mdb); 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"); + fileName = mdbObjFindValue(mdbFile,MDB_VAR_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); - } + slAddHead(&mdbFiles,oneFile->mdb); 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"); } 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(mdbFiles,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print! sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb,mdbFiles); boolean filterable = FALSE; if (sortOrder != NULL) { char *vars = removeCommonMdbVarsNotInSortOrder(mdbFiles,sortOrder); if (vars) { if (debug) warn("These terms are common:%s",vars); freeMem(vars); } // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); // FilterBoxes ? @@ -836,108 +839,107 @@ // 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"); +mdbObjsSortOnVars(&mdbList, MDB_VAR_COMPOSITE); mdbObjRemoveHiddenVars(mdbList); #define FOUND_FILE_LIMIT 1000 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 while(mdbList && fileCount < FOUND_FILE_LIMIT) { boolean found = FALSE; struct mdbObj *mdbFile = slPopHead(&mdbList); - char *composite = mdbObjFindValue(mdbFile,"composite"); + char *composite = mdbObjFindValue(mdbFile,MDB_VAR_COMPOSITE); if (composite != NULL) { // First for FileName - char *fileName = mdbObjFindValue(mdbFile,"fileName"); + char *fileName = mdbObjFindValue(mdbFile,MDB_VAR_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); + slAddHead(&mdbFiles,oneFile->mdb); fileCount++; found = TRUE; if (fileCount == FOUND_FILE_LIMIT) break; } } else fileDbFree(&oneFile); } // Now for FileIndexes - fileName = mdbObjFindValue(mdbFile,"fileIndex"); + fileName = mdbObjFindValue(mdbFile,MDB_VAR_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); - } + slAddHead(&mdbFiles,oneFile->mdb); fileCount++; 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 +mdbObjReorderByCv(mdbFiles,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print! sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbFiles); // No cart, no tdb if (sortOrder != NULL) { // Fill in and sort fileList fileDbSortList(&fileList,sortOrder); } mdbObjRemoveVars(mdbFiles,"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 (mdbList != NULL)