src/utils/raSqlQuery/raSqlQuery.c 1.11
1.11 2009/11/20 09:59:30 kent
Adding parent,key,noInherit options and implementing inheritance.
Index: src/utils/raSqlQuery/raSqlQuery.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/raSqlQuery/raSqlQuery.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/utils/raSqlQuery/raSqlQuery.c 20 Nov 2009 07:41:56 -0000 1.10
+++ src/utils/raSqlQuery/raSqlQuery.c 20 Nov 2009 09:59:30 -0000 1.11
@@ -13,8 +13,16 @@
#include "rql.h"
static char const rcsid[] = "$Id$";
+static char *clQueryFile = NULL;
+static char *clQuery = NULL;
+static char *clKey = "track";
+static char *clParentField = "subTrack";
+static char *clNoInheritField = "noInherit";
+static boolean clMerge = FALSE;
+static boolean clParent = FALSE;
+
void usage()
/* Explain usage and exit. */
{
errAbort(
@@ -31,26 +39,28 @@
"Count is not followed by anything. The 'where' clause is optional, and if it\n"
"exists it can contain expressions involving fields, numbers, strings, arithmetic, 'and'\n"
"'or' and so forth. Unlike SQL there is no 'from' claus.\n"
"Other options:\n"
- " -merge=keyField - If there are multiple raFiles, records with the same keyField will be\n"
+ " -key=keyField - Use the as the key field for merges and parenting. Default %s\n"
+ " -parent - Merge together inheriting on parentField\n"
+ " -parentField=field - Use field as the one that tells us who is our parent. Default %s\n"
+ " -noInheritField=field - If field is present don't inherit fields from parent\n"
+ " -merge - If there are multiple raFiles, records with the same keyField will be\n"
" merged together with fields in later files overriding fields in earlier files\n"
- " -skipMissing - If merging, skip records without keyfield rather than abort\n"
"The output will be to stdout, in the form of a .ra file if the select command is used\n"
"and just a simple number if the count command is used\n"
+ , clKey, clParentField
);
}
-static char *clQueryFile = NULL;
-static char *clQuery = NULL;
-static char *clMerge = NULL;
-static boolean clSkipMissing = FALSE;
-
static struct optionSpec options[] = {
{"queryFile", OPTION_STRING},
{"query", OPTION_STRING},
- {"merge", OPTION_STRING},
- {"skipMissing", OPTION_BOOLEAN},
+ {"merge", OPTION_BOOLEAN},
+ {"key", OPTION_STRING},
+ {"parent", OPTION_BOOLEAN},
+ {"parentField", OPTION_STRING},
+ {"noInheritField", OPTION_STRING},
{NULL, 0},
};
struct rqlEval rqlEvalOnRecord(struct rqlParse *p, struct raRecord *ra);
@@ -74,9 +84,28 @@
}
}
}
-static struct raRecord *readRaRecords(int inCount, char *inNames[], char *mergeField, struct lm *lm)
+static void mergeParentRecord(struct raRecord *record, struct raRecord *parent, struct lm *lm)
+/* Merge in parent record. This only updates fields that are in parent but not record. */
+{
+struct raField *parentField;
+for (parentField= parent->fieldList; parentField!= NULL; parentField= parentField->next)
+ {
+ struct raField *oldField = raRecordField(record, parentField->name);
+ if (oldField == NULL)
+ {
+ struct raField *newField;
+ lmAllocVar(lm, newField);
+ newField->name = parentField->name;
+ newField->val = parentField->val;
+ slAddTail(&record->fieldList, newField);
+ }
+ }
+}
+
+static struct raRecord *readRaRecords(int inCount, char *inNames[],
+ char *mergeField, struct lm *lm)
/* Scan through files, merging records on mergeField if it is non-NULL. */
{
if (inCount <= 0)
return NULL;
@@ -168,13 +197,77 @@
}
fprintf(out, "\n");
}
-void raSqlQuery(int inCount, char *inNames[], struct lineFile *query, char *mergeField, struct lm *lm,
- FILE *out)
+static void addMissingKeys(struct raRecord *list, char *keyField)
+/* Add key to all raRecords that don't already have it. */
+{
+struct raRecord *rec;
+for (rec = list; rec != NULL; rec = rec->next)
+ {
+ if (rec->key == NULL)
+ rec->key = raRecordField(rec, keyField);
+ }
+}
+
+static struct raRecord *findParent(struct raRecord *rec,
+ char *parentFieldName, char *noInheritFieldName, struct hash *hash)
+/* Find parent field if possible. */
+{
+struct raField *noInheritField = raRecordField(rec, noInheritFieldName);
+if (noInheritField != NULL)
+ return NULL;
+struct raField *parentField = raRecordField(rec, parentFieldName);
+if (parentField == NULL)
+ return NULL;
+char *parentLine = parentField->val;
+int len = strlen(parentLine);
+char buf[len+1];
+strcpy(buf, parentLine);
+char *parentName = firstWordInLine(buf);
+struct raRecord *parent = hashFindVal(hash, parentName);
+if (parent == NULL)
+ warn("%s is a subTrack of %s, but %s doesn't exist", rec->key->val,
+ parentField->val, parentField->val);
+return parent;
+}
+
+static void inheritFromParents(struct raRecord *list, char *parentField, char *noInheritField,
+ struct lm *lm)
+/* Go through list. If an element has a parent field, then fill in non-existent fields from
+ * parent. */
+{
+/* Build up hash of records indexed by key field. */
+struct hash *hash = hashNew(0);
+struct raRecord *rec;
+for (rec = list; rec != NULL; rec = rec->next)
+ {
+ if (rec->key != NULL)
+ hashAdd(hash, rec->key->val, rec);
+ }
+
+/* Scan through doing inheritance. */
+for (rec = list; rec != NULL; rec = rec->next)
+ {
+ struct raRecord *parent;
+ for (parent = findParent(rec, parentField, noInheritField, hash); parent != NULL;
+ parent = findParent(parent, parentField, noInheritField, hash) )
+ {
+ mergeParentRecord(rec, parent, lm);
+ }
+ }
+}
+
+void raSqlQuery(int inCount, char *inNames[], struct lineFile *query, char *mergeField,
+ char *parentField, char *noInheritField, struct lm *lm, FILE *out)
/* raSqlQuery - Do a SQL-like query on a RA file.. */
{
struct raRecord *raList = readRaRecords(inCount, inNames, mergeField, lm);
+if (parentField != NULL)
+ {
+ addMissingKeys(raList, clKey);
+ inheritFromParents(raList, parentField, noInheritField, lm);
+ }
struct rqlStatement *rql = rqlStatementParse(query);
verbose(2, "Got %d records in raFiles\n", slCount(raList));
if (verboseLevel() > 1)
rqlStatementDump(rql, stderr);
@@ -201,12 +294,15 @@
{
optionInit(&argc, argv, options);
if (argc < 2)
usage();
-clMerge = optionVal("merge", NULL);
-clSkipMissing = optionExists("skipMissing");
+clMerge = optionExists("merge");
+clParent = optionExists("parent");
+clParentField = optionVal("parentField", clParentField);
+clKey = optionVal("key", clKey);
clQueryFile = optionVal("queryFile", NULL);
clQuery = optionVal("query", NULL);
+clNoInheritField = optionVal("noInheritField", clNoInheritField);
if (clQueryFile == NULL && clQuery == NULL)
errAbort("Please specify either the query or queryFile option.");
if (clQueryFile != NULL && clQuery != NULL)
errAbort("Please specify just one of the query or queryFile options.");
@@ -215,7 +311,9 @@
query = lineFileOnString("query", TRUE, cloneString(clQuery));
else
query = lineFileOpen(clQueryFile, TRUE);
struct lm *lm = lmInit(0);
-raSqlQuery(argc-1, argv+1, query, clMerge, lm, stdout);
+char *mergeField = (clMerge ? clKey : NULL);
+char *parentField = (clParent ? clParentField : NULL);
+raSqlQuery(argc-1, argv+1, query, mergeField, parentField, clNoInheritField, lm, stdout);
return 0;
}