4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/encode/encodeExp/encodeExp.c src/hg/encode/encodeExp/encodeExp.c index b74a01f..fa91ead 100644 --- src/hg/encode/encodeExp/encodeExp.c +++ src/hg/encode/encodeExp/encodeExp.c @@ -1,537 +1,537 @@ /* encodeExp - manage ENCODE Experiment table (hgFixed.encodeExp) */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "hdb.h" #include "mdb.h" #include "ra.h" #include "portable.h" #include "../../inc/encode/encodeExp.h" static char *encodeExpTableNew = ENCODE_EXP_TABLE "New"; void usage() /* Explain usage and exit. */ { errAbort( "encodeExp - manage ENCODE Experiments table (hgFixed.encodeExp)\n" "usage:\n" " encodeExp <action> [arg]\n" "\n" "actions:\n" " add <exp.ra> add experiments to table from file\n" " acc <id> add accession to experiment (approve it)\n" " dump <exp.ra> output experiment table to file\n" " find <db> <exp.ra> find unassigned experiments in metaDb and create .ra to file\n" " history [<id>] show changes to experiment entry\n" " show <id|accession>[<var>] print experiment (or var from experiment) to stdout\n" /* This command isn't very usable -- recommend using SQL queries instead " id human|mouse <lab> <dataType> <cellType> [<vars>]\n" " return id for experiment (vars as 'var1:val1 var2:val2')\n" */ "\nmanagement actions: (default table \'%s\')\n" " copy <newName> copy table and add update triggers\n" " create create table\n" " drop drop table\n" " rename <newName> rename table and update triggers\n" " restore <exp.ra> restore table from .ra file\n" "\n" " deacc <id> deaccession experiment (remove accession, leave in table)\n" " update <id> <var> <oldval> <newval> change experiment var (must remove accession first)\n" " e.g. update 123 treatment ifnng ifn\n" " remove <id> <why> remove experiment (delete from table)\n" "\n" "options:\n" " -composite limit to specified composite track (affects find)\n" " -mdb specify metaDb table name (default \'%s\') - for test use \n" " -table specify experiment table name (default \'%s\')\n", encodeExpTableNew, MDB_DEFAULT_NAME, ENCODE_EXP_TABLE ); } static struct optionSpec options[] = { {"composite", OPTION_STRING}, {"mdb", OPTION_STRING}, {"table", OPTION_STRING}, {NULL, 0}, }; struct sqlConnection *connExp = NULL; char *composite = NULL, *mdb = NULL, *table = NULL; char *organism = NULL, *lab = NULL, *dataType = NULL, *cellType = NULL, *expVars = NULL; char *var = NULL, *old = NULL, *new = NULL; char *newTable = NULL; char *why = NULL; static struct hash *expKeyHashFromTable(struct sqlConnection *conn, char *table) /* create hash of keys for existing experiments so we can distinguish new ones */ { struct hash *hash = hashNew(0); struct encodeExp *exp = NULL, *exps = NULL; exps = encodeExpLoadAllFromTable(conn, table); while ((exp = slPopHead(&exps)) != NULL) { hashAdd(hash, encodeExpKey(exp), NULL); freez(&exp); } return hash; } void expCreateTable() /* Create table and history */ { verbose(1, "Creating table \'%s\'\n", table); encodeExpTableCreate(connExp, table); } void expDropTable() /* Drop table and history*/ { verbose(1, "Dropping table \'%s\'\n", table); encodeExpTableDrop(connExp, table); } void expAdd(char *file) /* Add rows from .ra file */ { struct hash *ra = NULL; struct lineFile *lf = lineFileOpen(file, TRUE); struct encodeExp *exp; struct hash *oldExps; char *key; /* create hash of keys for existing experiments so we can distinguish new ones */ oldExps = expKeyHashFromTable(connExp, table); verbose(1, "Adding experiments from file \'%s\' to table \'%s\'\n", file, table); while ((ra = raNextRecord(lf)) != NULL) { exp = encodeExpFromRa(ra); key = encodeExpKey(exp); if (hashLookup(oldExps, key) == NULL) { verbose(2, "Adding new experiment: %s\n", key); encodeExpAdd(connExp, table, exp); } else verbose(2, "Old experiment: %s\n", key); } } void expRestoreTable(char *file) /* Fill empty table with experiments in .ra file with id's */ { struct hash *ra = NULL; struct lineFile *lf = lineFileOpen(file, TRUE); struct encodeExp *exp; int ix = 1; int expId; char *accession; char *key; verbose(1, "Restoring experiments from file \'%s\' to table \'%s\'\n", file, table); if (sqlRowCount(connExp, sqlCheckIdentifier(table)) != 0) errAbort("ERROR: table for restore must exist and be empty"); while ((ra = raNextRecord(lf)) != NULL) { exp = encodeExpFromRa(ra); /* save accession and id as we may stomp on these for to-delete experiments */ accession = cloneString(exp->lab); expId = exp->ix; key = encodeExpKey(exp); while (ix < expId) { exp->accession = "DELETED"; exp->ix = ix; verbose(3, "Adding row for deleted experiment %d\n", ix); encodeExpAdd(connExp, table, exp); ix++; } /* restore accession and id */ exp->accession = accession; exp->ix = expId; encodeExpAdd(connExp, table, exp); verbose(3, "Adding row for experiment %d: %s\n", ix, key); ix++; } verbose(1, "To complete restore, delete rows where accession=DELETED\n"); } void expRenameTable() /* Rename table and update history table triggers */ { verbose(1, "Renaming table %s to %s\n", table, newTable); encodeExpTableRename(connExp, table, newTable); } void expCopyTable() /* Rename table and update history table triggers */ { verbose(1, "Copying table %s to %s\n", table, newTable); encodeExpTableCopy(connExp, table, newTable); } void expAcc(int id) /* Add accession to an existing experiment (approve it)*/ { char *acc = encodeExpAddAccession(connExp, table, id); verbose(1, "Added accession: %s\n", acc); } void expDeacc(int id) /* Decession an experiment (remove accession but leave in table)*/ { verbose(1, "Removing accession from id: %d\n", id); encodeExpRemoveAccession(connExp, table, id); } void expRemove(int id, char *why) /* Remove an experiment (delete from table) */ { struct encodeExp *exp = encodeExpGetByIdFromTable(connExp, table, id); if (exp == NULL) errAbort("Id %d not found in experiment table %s", id, table); verbose(1, "Deleting experiment id %d\n", id); encodeExpRemove(connExp, table, exp, why); } void expShow(int id) /* Print experiment in .ra format to stdout */ { struct encodeExp *exp = encodeExpGetByIdFromTable(connExp, table, id); if (exp == NULL) errAbort("Id %d not found in experiment table %s", id, table); if (var == NULL) encodeExpToRaFile(exp, stdout); else { char *val = encodeExpGetField(exp, var); if (val != NULL) puts(val); } } void expHistory(int id) /* Show changes to an existing experiment */ { // TODO: Libify int i; char **row; struct dyString *dy = sqlDyStringCreate("select * from %sHistory", table); if (id != 0) dyStringPrintf(dy, " where %s=%d ", ENCODE_EXP_FIELD_IX, id); dyStringPrintf(dy, " order by updateTime, %s", ENCODE_EXP_FIELD_IX); struct sqlResult *sr = sqlGetResult(connExp, dyStringCannibalize(&dy)); while ((row = sqlNextRow(sr)) != NULL) { for (i = 0; i < ENCODEEXP_NUM_COLS+2; i++) // history has 2 additional fields: action and user { printf("%s\t", row[i]); } puts("\n"); } sqlFreeResult(&sr); } void expDump(char *file) /* Output rows to .ra file */ { struct encodeExp *exp = NULL, *exps = NULL; verbose(1, "Dumping table %s to %s\n", table, file); FILE *f = mustOpen(file, "w"); exps = encodeExpLoadAllFromTable(connExp, table); while ((exp = slPopHead(&exps)) != NULL) encodeExpToRaFile(exp, f); carefulClose(&f); } void expFind(char *assembly, char *file) /* Find experiments in metaDb and output .ra file */ { verbose(1, "Finding experiments in %s:%s\n", assembly, mdb); struct sqlConnection *connMeta; struct mdbObj *meta = NULL, *metas = NULL; struct encodeExp *exp = NULL, *exps = NULL; struct hash *oldExps, *newExps; char *key; int expNum = 0; FILE *f = mustOpen(file, "w"); /* create hash of keys for existing experiments so we can distinguish new ones */ oldExps = expKeyHashFromTable(connExp, table); newExps = hashNew(0); /* read mdb objects from database */ connMeta = sqlConnect(assembly); metas = mdbObjsQueryAll(connMeta, mdb); verbose(2, "Found %d objects\n", slCount(metas)); /* order so that oldest have lowest ids */ mdbObjsSortOnVars(&metas, "dateSubmitted lab dataType cell"); /* create new experiments */ while ((meta = slPopHead(&metas)) != NULL) { if (!mdbObjIsEncode(meta)) continue; if (composite != NULL && !mdbObjInComposite(meta, composite)) continue; exp = encodeExpFromMdb(connMeta,assembly,meta); if (exp == NULL) continue; key = encodeExpKey(exp); verbose(3, "key: %s\n", key); if (hashLookup(newExps, key) == NULL && hashLookup(oldExps, key) == NULL) { verbose(2, "Found new experiment - Date: %s Experiment %d: %s\n", mdbObjFindValue(meta, "dateSubmitted"), ++expNum, key); /* save new experiment */ hashAdd(newExps, key, NULL); slAddHead(&exps, exp); } /* Skip other metas belonging to the same exp by: struct mdbVar *edvs = mdbObjFindEncodeEdvs(connMeta,meta); // Can't use encodeExpVars(exp) because of "None" issues assert(edvs != NULL); char *expVars = slPairListToString(edvs,FALSE); // don't bother with quoting since edvs should not have spaces struct mdbObj *mdbExpObjs = mdbObjsFilterByVars(&metas,expVars,TRUE,TRUE); freeMem(expVars); mdbVarsFree(&edvs); // If you want to do this, then encodeExpFromMdb() above should be replaced with encodeExpFromMdbVars() mdbObjFree(&mdbExpObjs); // Filtering destroyed sort order // NOTE: Given the re-sort, this may not prove much more efficient mdbObjsSortOnVars(&metas, "dateSubmitted lab dataType cell"); */ } /* write out experiments in .ra format */ slReverse(&exps); while ((exp = slPopHead(&exps)) != NULL) { exp->organism = organism; encodeExpToRaFile(exp, f); } carefulClose(&f); sqlDisconnect(&connMeta); } void expId() /* Print id */ { struct encodeExp *exps = NULL; int count; struct slPair *varPairs = NULL; /* transform var:val to var=val. Can't use var=val on command-line as it conflicts with standard options processing */ if (expVars == NULL) varPairs = NULL; else { memSwapChar(expVars, strlen(expVars), ':', '='); varPairs = slPairListFromString(expVars,FALSE); // don't expect quoted EDVs which should always be simple tokens. } exps = encodeExpGetFromTable(organism, lab, dataType, cellType, varPairs, table); count = slCount(exps); verbose(2, "Results: %d\n", count); if (count == 0) errAbort("Experiment not found in table %s", table); if (count > 1) errAbort("Found more than 1 match for experiment"); printf("%d\n", exps->ix); } void expUpdate(int id) /* Modify an experiment. Changes value of one field or expVar for id specified. * Aborts if experiment has an accession (must deaccession first) */ { encodeExpUpdate(connExp, table, id, var, new, old); verbose(1, "Modified id %d in table %s\n", id, table); } int encodeExp(char *command, char *file, char *assembly, int id) /* manage ENCODE experiments table */ { connExp = sqlConnect(ENCODE_EXP_DATABASE); if (assembly != NULL) { organism = hOrganism(assembly); strLower(organism); } if (sameString(command, "create")) expCreateTable(); else if (sameString(command, "drop")) expDropTable(); else if (sameString(command, "copy")) expCopyTable(); else if (sameString(command, "rename")) expRenameTable(); else if (sameString(command, "restore")) expRestoreTable(file); else if (sameString(command, "add")) expAdd(file); else if (sameString(command, "remove")) expRemove(id, why); else if (sameString(command, "acc")) expAcc(id); else if (sameString(command, "deacc")) expDeacc(id); else if (sameString(command, "show")) expShow(id); else if (sameString(command, "history")) expHistory(id); else if (sameString(command, "dump")) expDump(file); else if (sameString(command, "find")) expFind(assembly, file); else if (sameString(command, "id")) expId(); else if (sameString(command, "update")) expUpdate(id); else { errAbort("ERROR: Unknown command %s\n", command); usage(); } sqlDisconnect(&connExp); return(0); } int main(int argc, char *argv[]) /* Process command line. */ { char *assembly = NULL; char *file = NULL; int id = 0; optionInit(&argc, argv, options); if (argc < 2) usage(); char *command = argv[1]; table = optionVal("table", (sameString(command, "copy") || sameString(command, "create") || sameString(command, "drop") || sameString(command, "rename") || sameString(command, "restore") || sameString(command, "deacc") || sameString(command, "update") || sameString(command, "remove")) ? encodeExpTableNew: ENCODE_EXP_TABLE); mdb = optionVal("mdb", MDB_DEFAULT_NAME); composite = optionVal("composite", NULL); verbose(2, "Experiment table name: %s\n", table); if (sameString("find", command)) { if (argc < 3) { errAbort("ERROR: Missing assembly\n"); usage(); } else assembly = argv[2]; if (argc < 4) { errAbort("ERROR: Missing .ra file\n"); usage(); } else file = argv[3]; } else if (sameString("add", command) || sameString("dump", command) || sameString("restore", command)) { if (argc < 3) { errAbort("ERROR: Missing .ra file\n"); usage(); } else file = argv[2]; } else if (sameString("id", command)) { if (argc < 6) usage(); else { organism = argv[2]; lab = argv[3]; dataType = argv[4]; cellType = argv[5]; if (argc > 6) expVars = argv[6]; } } else if ( sameString("acc", command) || sameString("deacc", command) || sameString("remove", command) || sameString("update", command) || sameString("show", command)) { if (argc < 3) { errAbort("ERROR: Missing id\n"); } else { char *arg = argv[2]; if (startsWith(ENCODE_EXP_ACC_PREFIX, arg)) // prefix plus single char for organism arg += strlen(ENCODE_EXP_ACC_PREFIX) + 1; id = atoi(arg); if (id < 1) errAbort("ERROR: Bad id %d\n", id); if (sameString("remove", command)) { if (argc < 4) errAbort("ERROR: remove must include why"); else why = argv[3]; } else if (sameString("update", command)) { if (argc < 6) usage(); var = argv[3]; old = argv[4]; new = argv[5]; } else if (sameString("show", command) && argc == 4) var = argv[3]; } } else if (sameString("history", command)) { if (argc > 2) id = atoi(argv[2]); } else if (sameString("rename", command) || sameString("copy", command)) { if (argc < 3) errAbort("ERROR: Missing new tablename\n"); if (argc != 3) usage(); newTable = argv[2]; } encodeExp(command, file, assembly, id); return 0; }