Changeset: ff8caae13261 for MonetDB
URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ff8caae13261
Modified Files:
sql/backends/monet5/vaults/bam/bam_db_interface.h
sql/backends/monet5/vaults/bam/bam_loader.c
sql/backends/monet5/vaults/bam/bam_wrapper.c
sql/backends/monet5/vaults/fits/fits.c
sql/backends/monet5/vaults/lidar/lidar.c
Branch: tracer
Log Message:
Replaced components in files: lidar, fits, bam_*. Now they belong to separate
category and not in one of the main layers
diffs (truncated from 493 to 300 lines):
diff --git a/sql/backends/monet5/vaults/bam/bam_db_interface.h
b/sql/backends/monet5/vaults/bam/bam_db_interface.h
--- a/sql/backends/monet5/vaults/bam/bam_db_interface.h
+++ b/sql/backends/monet5/vaults/bam/bam_db_interface.h
@@ -38,7 +38,7 @@
}
#endif */
#define RUN_SQL(cntxt, sql, descr, msg) { \
- DEBUG(SQL_BAM, "%s\n", sql); \
+ DEBUG(BAM, "%s\n", sql); \
msg = SQLstatementIntern(cntxt, sql, descr, TRUE, FALSE, NULL); \
}
diff --git a/sql/backends/monet5/vaults/bam/bam_loader.c
b/sql/backends/monet5/vaults/bam/bam_loader.c
--- a/sql/backends/monet5/vaults/bam/bam_loader.c
+++ b/sql/backends/monet5/vaults/bam/bam_loader.c
@@ -119,14 +119,14 @@ run_process_bam_alignments(void *d)
bam_wrapper *bw;
for (;;) {
- DEBUG(SQL_BAM, "<Thread %d> Starting on next file\n",
data->thread_id);
+ DEBUG(BAM, "<Thread %d> Starting on next file\n",
data->thread_id);
/* First, find out on which bam wrapper we have to work */
MT_lock_set(data->reader_lock);
if (*data->cur_file == data->nr_files - 1) {
/* The last file is already (being) processed, this
* thread is done */
MT_lock_unset(data->reader_lock);
- DEBUG(SQL_BAM,
+ DEBUG(BAM,
"<Thread %d> No files left to work on; thread
done\n",
data->thread_id);
return;
@@ -134,7 +134,7 @@ run_process_bam_alignments(void *d)
(*data->cur_file) += 1;
bw = &data->bws[*data->cur_file];
MT_lock_unset(data->reader_lock);
- DEBUG(SQL_BAM,
+ DEBUG(BAM,
"<Thread %d> Processing alignments of file '%s' (file
id " LLFMT ")\n",
data->thread_id, bw->file_location, bw->file_id);
@@ -153,7 +153,7 @@ run_process_bam_alignments(void *d)
return;
}
- DEBUG(SQL_BAM,
+ DEBUG(BAM,
"<Thread %d> All alignments in file '%s' (file id "
LLFMT ") processed!\n",
data->thread_id, bw->file_location, bw->file_id);
}
@@ -187,7 +187,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
int i, errnr;
str msg = MAL_SUCCEED;
- DEBUG(SQL_BAM, "Loader started for %d BAM file%s\n", nr_files,
(nr_files != 1 ? "s" : ""));
+ DEBUG(BAM, "Loader started for %d BAM file%s\n", nr_files, (nr_files !=
1 ? "s" : ""));
/* Check sanity of input */
if (dbschema != 0 && dbschema != 1) {
@@ -222,7 +222,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
goto cleanup;
/* Get next file id from files table */
- DEBUG(SQL_BAM, "Retrieving next file id\n");
+ DEBUG(BAM, "Retrieving next file id\n");
if ((msg = next_file_id(m, files_table, &cur_file_id)) != MAL_SUCCEED) {
goto cleanup;
}
@@ -240,7 +240,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
for (i = 0; i < nr_files; ++i) {
int fln = strlen(filenames[i]);
- DEBUG(SQL_BAM, "Initializing BAM wrapper for file '%s'\n",
filenames[i]);
+ DEBUG(BAM, "Initializing BAM wrapper for file '%s'\n",
filenames[i]);
if ((msg =
init_bam_wrapper(bws + i, (IS_BAM(filenames[i], fln) ?
BAM : SAM),
filenames[i], cur_file_id++,
dbschema)) != MAL_SUCCEED) {
@@ -250,7 +250,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Parse all headers */
for (i = 0; i < nr_files; ++i) {
- DEBUG(SQL_BAM, "Parsing header for file '%s'\n",
+ DEBUG(BAM, "Parsing header for file '%s'\n",
filenames[i]);
if ((msg = process_header(bws + i)) != MAL_SUCCEED) {
goto cleanup;
@@ -262,7 +262,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
* QNAME */
if (dbschema == 1) {
for (i = 0; i < nr_files; ++i) {
- DEBUG(SQL_BAM, "Checking sortedness for BAM file
'%s'\n", filenames[i]);
+ DEBUG(BAM, "Checking sortedness for BAM file '%s'\n",
filenames[i]);
if (bws[i].ord != ORDERING_QUERYNAME) {
msg = createException(MAL, "bam_loader",
SQLSTATE(BA000) "Only
BAM files that are sorted on queryname can be inserted into the pairwise
storage schema; "
@@ -277,7 +277,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Create alignment storage */
for (i = 0; i < nr_files; ++i) {
- DEBUG(SQL_BAM, "Creating alignment tables for file '%s'\n",
filenames[i]);
+ DEBUG(BAM, "Creating alignment tables for file '%s'\n",
filenames[i]);
if ((dbschema == 0
&& (msg = create_alignment_storage_0(cntxt,
"bam.create_storage_0",
@@ -292,7 +292,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Now create threads to read alignment data of different files */
- DEBUG(SQL_BAM, "Creating reader threads\n");
+ DEBUG(BAM, "Creating reader threads\n");
if ((reader_threads =
(MT_Id *) GDKmalloc(nr_threads * sizeof(MT_Id))) == NULL) {
msg = createException(MAL, "bam_loader", SQLSTATE(HY001)
MAL_MALLOC_FAIL);
@@ -319,7 +319,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
}
}
- DEBUG(SQL_BAM, "Waiting for reader threads to finish\n");
+ DEBUG(BAM, "Waiting for reader threads to finish\n");
/* Wait until all threads finish and collect their
* messages. Though it is not very likely, it could be the
* case that more than 1 thread generates an error message (not
@@ -365,7 +365,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
goto cleanup;
}
- DEBUG(SQL_BAM, "Copying data into DB\n");
+ DEBUG(BAM, "Copying data into DB\n");
/* All threads finished succesfully, copy all data into DB */
for (i = 0; i < nr_files; ++i) {
if ((msg = copy_into_db(cntxt, bws + i)) != MAL_SUCCEED) {
@@ -390,7 +390,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
ERROR(M_ALL, "Error on processing BAM files: %s\n", msg);
}
- DEBUG(SQL_BAM, "Loader finished processing %d BAM file%s\n", nr_files,
(nr_files != 1 ? "s" : ""));
+ DEBUG(BAM, "Loader finished processing %d BAM file%s\n", nr_files,
(nr_files != 1 ? "s" : ""));
return msg;
}
diff --git a/sql/backends/monet5/vaults/bam/bam_wrapper.c
b/sql/backends/monet5/vaults/bam/bam_wrapper.c
--- a/sql/backends/monet5/vaults/bam/bam_wrapper.c
+++ b/sql/backends/monet5/vaults/bam/bam_wrapper.c
@@ -1328,11 +1328,11 @@ check_alignment_buffers(bam_wrapper *bw,
}
if (resized[0])
- DEBUG(SQL_BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
+ DEBUG(BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
if (resized[1])
- DEBUG(SQL_BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
+ DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
if (resized[2])
- DEBUG(SQL_BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
+ DEBUG(BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
return (alig->cigar != NULL && alig->seq != NULL
&& alig->qual != NULL);
@@ -1357,7 +1357,7 @@ check_qname_buffer(alignment * alig, int
if (tmp == NULL)
return 0;
alig->qname = tmp;
- DEBUG(SQL_BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
+ DEBUG(BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
}
return alig->qname != NULL;
}
@@ -1379,7 +1379,7 @@ check_rname_rnext_buffers(alignment * al
if (tmp == NULL)
return 0;
alig->rnext = tmp;
- DEBUG(SQL_BAM, "Increased size of cigar buffer to: %d
characters\n", alig->rname_size);
+ DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->rname_size);
}
return alig->rname != NULL && alig->rnext != NULL;
}
@@ -1397,7 +1397,7 @@ check_cigar_buffer(alignment * alig, int
if (tmp == NULL)
return 0;
alig->cigar = tmp;
- DEBUG(SQL_BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
+ DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
}
return alig->cigar != NULL;
}
@@ -1418,7 +1418,7 @@ check_seq_qual_buffers(alignment * alig,
if (tmp == NULL)
return 0;
alig->qual = tmp;
- DEBUG(SQL_BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
+ DEBUG(BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
}
return alig->seq != NULL && alig->qual != NULL;
}
@@ -1435,7 +1435,7 @@ check_aux_buffer(alignment * alig, int c
if (tmp == NULL)
return 0;
alig->aux = tmp;
- DEBUG(SQL_BAM, "Increased size of aux buffer to: %d
characters\n", alig->aux_size);
+ DEBUG(BAM, "Increased size of aux buffer to: %d characters\n",
alig->aux_size);
}
return alig->aux != NULL;
}
@@ -2318,7 +2318,7 @@ process_alignments(bam_wrapper * bw, bit
}
}
nr_aligs = new_nr_aligs;
- DEBUG(SQL_BAM, "<bam_loader> Increased
size of alignment buffer to: %d alignments\n", nr_aligs);
+ DEBUG(BAM, "<bam_loader> Increased size
of alignment buffer to: %d alignments\n", nr_aligs);
}
}
}
diff --git a/sql/backends/monet5/vaults/fits/fits.c
b/sql/backends/monet5/vaults/fits/fits.c
--- a/sql/backends/monet5/vaults/fits/fits.c
+++ b/sql/backends/monet5/vaults/fits/fits.c
@@ -227,7 +227,7 @@ str FITSexportTable(Client cntxt, MalBlk
throw(MAL, "fits.exporttable", SQLSTATE(HY001) MAL_MALLOC_FAIL);
}
- DEBUG(SQL_FITS, "Number of columns: %d\n", columns);
+ DEBUG(FITS, "Number of columns: %d\n", columns);
tables = mvc_bind_table(m, sch, "_tables");
col = mvc_bind_column(m, tables, "name");
@@ -545,14 +545,14 @@ str FITSexportTable(Client cntxt, MalBlk
// print all the times that were needed to export each one of the
columns
- if (texportboolean > 0) DEBUG(SQL_FITS, "%d Boolean\tcolumn(s)
exported in %d ms\n", boolcols, texportboolean);
- if (texportchar > 0) DEBUG(SQL_FITS, "%d Char\t\tcolumn(s)
exported in %d ms\n", charcols, texportchar);
- if (texportstring > 0) DEBUG(SQL_FITS, "%d String\tcolumn(s)
exported in %d ms\n", strcols, texportstring);
- if (texportshort > 0) DEBUG(SQL_FITS, "%d Short\t\tcolumn(s)
exported in %d ms\n", shortcols, texportshort);
- if (texportint > 0) DEBUG(SQL_FITS, "%d
Integer\tcolumn(s) exported in %d ms\n", intcols, texportint);
- if (texportlng > 0) DEBUG(SQL_FITS, "%d
Long\t\tcolumn(s) exported in %d ms\n", lngcols, texportlng);
- if (texportfloat > 0) DEBUG(SQL_FITS, "%d Float\t\tcolumn(s)
exported in %d ms\n", floatcols, texportfloat);
- if (texportdouble > 0) DEBUG(SQL_FITS, "%d Double\tcolumn(s)
exported in %d ms\n", doublecols, texportdouble);
+ if (texportboolean > 0) DEBUG(FITS, "%d Boolean\tcolumn(s)
exported in %d ms\n", boolcols, texportboolean);
+ if (texportchar > 0) DEBUG(FITS, "%d Char\t\tcolumn(s)
exported in %d ms\n", charcols, texportchar);
+ if (texportstring > 0) DEBUG(FITS, "%d String\tcolumn(s)
exported in %d ms\n", strcols, texportstring);
+ if (texportshort > 0) DEBUG(FITS, "%d Short\t\tcolumn(s)
exported in %d ms\n", shortcols, texportshort);
+ if (texportint > 0) DEBUG(FITS, "%d
Integer\tcolumn(s) exported in %d ms\n", intcols, texportint);
+ if (texportlng > 0) DEBUG(FITS, "%d
Long\t\tcolumn(s) exported in %d ms\n", lngcols, texportlng);
+ if (texportfloat > 0) DEBUG(FITS, "%d Float\t\tcolumn(s)
exported in %d ms\n", floatcols, texportfloat);
+ if (texportdouble > 0) DEBUG(FITS, "%d Double\tcolumn(s)
exported in %d ms\n", doublecols, texportdouble);
fits_close_file(fptr, &status);
@@ -590,7 +590,7 @@ str FITSdir(Client cntxt, MalBlkPtr mb,
fits_open_file(&fptr, fname, READONLY, &status);
if (status == 0) {
snprintf(stmt, BUFSIZ, ATTACHDIR, fname);
- DEBUG(SQL_FITS, "Executing: %s\n", s);
+ DEBUG(FITS, "Executing: %s\n", s);
msg = SQLstatementIntern(cntxt, &s,
"fits.listofdir", TRUE, FALSE, NULL);
fits_close_file(fptr, &status);
}
@@ -623,7 +623,7 @@ str FITSdirpat(Client cntxt, MalBlkPtr m
snprintf(fulldirectory, BUFSIZ, "%s%s", dir, pat);
glob(fulldirectory, GLOB_DOOFFS, NULL, &globbuf);
- DEBUG(SQL_FITS, "Fulldir: %s - Size: %lu\n", fulldirectory,
globbuf.gl_pathc);
+ DEBUG(FITS, "Fulldir: %s - Size: %lu\n", fulldirectory,
globbuf.gl_pathc);
if (globbuf.gl_pathc == 0)
throw(MAL, "fits.listdirpat", SQLSTATE(FI000) "Couldn't open
the directory or there are no files that match the pattern");
@@ -643,7 +643,7 @@ str FITSdirpat(Client cntxt, MalBlkPtr m
if (status == 0) {
snprintf(stmt, BUFSIZ, ATTACHDIR, filename);
GDKfree(filename);
- DEBUG(SQL_FITS, "Executing: %s\n", s);
+ DEBUG(FITS, "Executing: %s\n", s);
msg = SQLstatementIntern(cntxt, &s,
"fits.listofdirpat", TRUE, FALSE, NULL);
fits_close_file(fptr, &status);
@@ -961,7 +961,7 @@ str FITSloadTable(Client cntxt, MalBlkPt
fits_get_coltype(fptr, j, &tpcode[j - 1], &rep[j - 1], &wid[j -
1], &status);
fits2subtype(&tpe, tpcode[j - 1], rep[j - 1], wid[j - 1]);
- DEBUG(SQL_FITS, "%d %ld %ld - M: %s\n", tpcode[j-1], rep[j-1],
wid[j-1], tpe.type->sqlname);
+ DEBUG(FITS, "%d %ld %ld - M: %s\n", tpcode[j-1], rep[j-1],
wid[j-1], tpe.type->sqlname);
mvc_create_column(m, tbl, cname[j - 1], &tpe);
}
diff --git a/sql/backends/monet5/vaults/lidar/lidar.c
b/sql/backends/monet5/vaults/lidar/lidar.c
--- a/sql/backends/monet5/vaults/lidar/lidar.c
+++ b/sql/backends/monet5/vaults/lidar/lidar.c
@@ -71,93 +71,93 @@ void print_lidar_header(LASHeaderH heade
major = LASHeader_GetVersionMajor(header);
minor = LASHeader_GetVersionMinor(header);
- DEBUG(SQL_LIDAR,
"---------------------------------------------------------\n");
- DEBUG(SQL_LIDAR, " Header Summary\n");
- DEBUG(SQL_LIDAR,
"---------------------------------------------------------\n");
+ DEBUG(LIDAR,
"---------------------------------------------------------\n");
+ DEBUG(LIDAR, " Header Summary\n");
+ DEBUG(LIDAR,
"---------------------------------------------------------\n");
- DEBUG(SQL_LIDAR, " File Name: %s\n", file_name);
+ DEBUG(LIDAR, " File Name: %s\n", file_name);
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