/**
* Generic function that loads a given list of BAM files according to
* the values of the other parameters. It starts with creating the
* bam schema and the header tables if these do not exist yet. Then
* it initializes bam_wrapper structs for all bam files and reads the
* headers for all BAM files. If the pairwise storage schema has to
* be used, It then creates a thread for every file that reads all
* alignments for this file.
*
*/
static str
bam_loader(Client cntxt, MalBlkPtr mb, str * filenames, int nr_files,
sht dbschema, sht nr_threads)
{
bam_wrapper *bws = NULL;
MT_Id *reader_threads = NULL;
reader_thread_data *r_thread_data = NULL;
mvc *m = NULL;
sql_schema *s = NULL;
sql_table *files_table = NULL;
lng cur_file_id;
char buf_threads_msg[4096] = "There were reader threads that contained errors:\n";
int threads_msg_len = strlen(buf_threads_msg);
int i, errnr;
str msg = MAL_SUCCEED;
TO_LOG("<bam_loader>: Loader started for %d BAM file%s...\n",
nr_files, (nr_files != 1 ? "s" : ""));
/* Check sanity of input */
if (dbschema != 0 && dbschema != 1) {
msg = createException(MAL, "bam_loader",
"Wrong value for dbschema: '%d' (0=straightforward storage schema, 1=pairwise storage schema)",
dbschema);
goto cleanup;
}
if (nr_threads <= 0) {
nr_threads = 1;
} else if(nr_threads > 4) {
nr_threads = 4;
}
/* Get SQL context */
if ((msg = getSQLContext(cntxt, mb, &m, NULL)) != MAL_SUCCEED) {
/* Here, and in multiple other locations in this code,
* new message is stored in tmp var, since the old msg
* needs to be freed after construction of the new
* msg */
REUSE_EXCEPTION(msg, MAL, "bam_loader",
"Could not retrieve SQLContext: %s", msg);
goto cleanup;
}
/* Start with binding bam schema and the files table */
if ((msg =
bind_bam_schema(m, &s)) != MAL_SUCCEED)
goto cleanup;
if((msg =
bind_table(m, s, "files", &files_table)) != MAL_SUCCEED)
goto cleanup;
/* Get next file id from files table */
TO_LOG("<bam_loader> Retrieving next file id...\n");
if ((msg = next_file_id(m, files_table, &cur_file_id)) != MAL_SUCCEED) {
goto cleanup;
}
/* Init bam_wrapper structs */
if ((bws =
(bam_wrapper *) GDKmalloc(nr_files * sizeof(bam_wrapper))) ==
NULL) {
msg = createException(MAL, "bam_loader", MAL_MALLOC_FAIL);
goto cleanup;
}
/* Enables cleanup to check which bam_wrappers to clear */
memset(bws, 0, nr_files * sizeof(bam_wrapper));
for (i = 0; i < nr_files; ++i) {
int fln = strlen(filenames[i]);
TO_LOG("<bam_loader> 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) {
goto cleanup;
}
}
/* Parse all headers */
for (i = 0; i < nr_files; ++i) {
TO_LOG("<bam_loader> Parsing header for file '%s'...\n",
filenames[i]);
if ((msg = process_header(bws + i)) != MAL_SUCCEED) {
goto cleanup;
}
}
/* If we have to load the BAM data into the pairwise storage
* schema, make sure that all input BAM files are sorted on
* QNAME */
if (dbschema == 1) {
for (i = 0; i < nr_files; ++i) {
TO_LOG("<bam_loader> Checking sortedness for BAM file '%s'...\n", filenames[i]);
if (bws[i].ord != ORDERING_QUERYNAME) {
msg = createException(MAL, "bam_loader",
"Only BAM files that are sorted on queryname can be inserted into the pairwise storage schema; "
"BAM file '%s' has ordering '%s'",
bws[i].file_location,
ordering_str(bws[i].
ord));
goto cleanup;
}
}
}
/* Create alignment storage */
for (i = 0; i < nr_files; ++i) {
TO_LOG("<bam_loader> Creating alignment tables for file '%s'...\n", filenames[i]);
if ((dbschema == 0
&& (msg = create_alignment_storage_0(cntxt,
"bam.create_storage_0",
bws + i)) != MAL_SUCCEED)
|| (dbschema == 1
&& (msg = create_alignment_storage_1(cntxt,
"bam.create_storage_1",
bws + i)) != MAL_SUCCEED)) {
goto cleanup;
}
}
/* Now create threads to read alignment data of different files */
TO_LOG("<bam_loader> Creating reader threads...\n");
if ((reader_threads =
(MT_Id *) GDKmalloc(nr_threads * sizeof(MT_Id))) == NULL) {
msg = createException(MAL, "bam_loader", MAL_MALLOC_FAIL);
goto cleanup;
}
if ((r_thread_data =
create_reader_thread_data(bws, nr_files, nr_threads)) == NULL) {
msg = createException(MAL, "bam_loader", MAL_MALLOC_FAIL);
goto cleanup;
}
for (i = 0; i < nr_threads; ++i) {
if ((errnr =
MT_create_thread(&reader_threads[i],
run_process_bam_alignments,
&r_thread_data[i],
MT_THR_JOINABLE)) != 0) {
msg = createException(MAL, "bam_loader",
"Could not create thread to process alignments (errnr %d)",
errnr);
goto cleanup;
}
}
TO_LOG("<bam_loader> 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
* likely because threads exit once they notice that another
* thread has failed). Therefore, we collect all error
* messages in one big error string
*/
for (i = 0; i < nr_threads; ++i) {
if ((errnr = MT_join_thread(reader_threads[i])) != 0) {
msg = createException(MAL, "bam_loader",
"Could not join alignment processing thread (errnr %d)",
errnr);
goto cleanup;
}
/* Thread finished ok, append its error message, if any */
if (r_thread_data[i].msg != MAL_SUCCEED) {
int step;
if (msg == MAL_SUCCEED) {
/* First encountered thread error,
* indicate this by pointing to error
* buf */
msg = buf_threads_msg;
}
/* snprintf returns -1 on failure; since we
* don't want to fail when snprintf fails, we
* use MAX to make sure we don't add a
* negative amount to threads_msg_len */
step = snprintf(msg + threads_msg_len,
4096 - threads_msg_len, "* %s\n",
r_thread_data[i].msg);
threads_msg_len += MAX(0, step);
GDKfree(r_thread_data[i].msg);
}
}
/* Fail if any thread has failed */
if (msg != MAL_SUCCEED) {
/* Do not use REUSE_EXCEPTION here, since msg was not
* malloced. Instead, just copy buffer contents to
* malloced buffer */
msg = GDKstrdup(msg);
goto cleanup;
}
TO_LOG("<bam_loader> 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) {
goto cleanup;
}
}
cleanup:
if (bws) {
for (i = 0; i < nr_files; ++i) {
if (bws + i)
clear_bam_wrapper(bws + i);
}
GDKfree(bws);
}
if (reader_threads)
GDKfree(reader_threads);
if (r_thread_data)
destroy_reader_thread_data(r_thread_data);
if (msg != MAL_SUCCEED) {
TO_LOG("<bam_loader> Error on processing BAM files: %s\n",
msg);
}
TO_LOG("<bam_loader>: Loader finished processing %d BAM file%s...\n",
nr_files, (nr_files != 1 ? "s" : ""));
return msg;
}
str
NCDFattach(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
mvc *m = NULL;
sql_schema *sch = NULL;
sql_table *tfiles = NULL, *tdims = NULL, *tvars = NULL, *tvardim = NULL, *tattrs = NULL;
sql_column *col;
str msg = MAL_SUCCEED;
str fname = *(str*)getArgReference(stk, pci, 1);
char buf[BUFSIZ], *s= buf;
oid fid, rid = oid_nil;
sql_trans *tr;
int ncid; /* dataset id */
int ndims, nvars, ngatts, unlimdim;
int didx, vidx, vndims, vnatts, i, aidx, coord_dim_id = -1;
int vdims[NC_MAX_VAR_DIMS];
size_t dlen, alen;
char dname[NC_MAX_NAME+1], vname[NC_MAX_NAME+1], aname[NC_MAX_NAME +1],
abuf[80], *aval;
char **dims = NULL;
nc_type vtype, atype; /* == int */
int retval, avalint;
float avalfl;
double avaldbl;
msg = getSQLContext(cntxt, mb, &m, NULL);
if (msg)
return msg;
tr = m->session->tr;
sch = mvc_bind_schema(m, "sys");
if ( !sch )
return createException(MAL, "netcdf.attach", "Cannot get schema sys\n");
tfiles = mvc_bind_table(m, sch, "netcdf_files");
tdims = mvc_bind_table(m, sch, "netcdf_dims");
tvars = mvc_bind_table(m, sch, "netcdf_vars");
tvardim = mvc_bind_table(m, sch, "netcdf_vardim");
tattrs = mvc_bind_table(m, sch, "netcdf_attrs");
if (tfiles == NULL || tdims == NULL || tvars == NULL ||
tvardim == NULL || tattrs == NULL)
return createException(MAL, "netcdf.attach", "Catalog table missing\n");
/* check if the file is already attached */
col = mvc_bind_column(m, tfiles, "location");
rid = table_funcs.column_find_row(m->session->tr, col, fname, NULL);
if (rid != oid_nil)
return createException(SQL, "netcdf.attach", "File %s is already attached\n", fname);
/* Open NetCDF file */
if ((retval = nc_open(fname, NC_NOWRITE, &ncid)))
return createException(MAL, "netcdf.test", "Cannot open NetCDF \
file %s: %s", fname, nc_strerror(retval));
if ((retval = nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdim)))
return createException(MAL, "netcdf.test", "Cannot read NetCDF \
header: %s", nc_strerror(retval));
/* Insert row into netcdf_files table */
col = mvc_bind_column(m, tfiles, "file_id");
fid = store_funcs.count_col(tr, col, 1) + 1;
snprintf(buf, BUFSIZ, INSFILE, (int)fid, fname);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
/* Read dimensions from NetCDF header and insert a row for each one into netcdf_dims table */
dims = (char **)GDKzalloc(sizeof(char *) * ndims);
for (didx = 0; didx < ndims; didx++){
if ((retval = nc_inq_dim(ncid, didx, dname, &dlen)))
return createException(MAL, "netcdf.attach", "Cannot read dimension %d : %s", didx, nc_strerror(retval));
snprintf(buf, BUFSIZ, INSDIM, didx, (int)fid, dname, (int)dlen);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
dims[didx] = GDKstrdup(dname);
}
/* Read variables and attributes from the header and insert rows in netcdf_vars, netcdf_vardims, and netcdf_attrs tables */
for (vidx = 0; vidx < nvars; vidx++){
if ( (retval = nc_inq_var(ncid, vidx, vname, &vtype, &vndims, vdims, &vnatts)))
return createException(MAL, "netcdf.attach",
"Cannot read variable %d : %s",
vidx, nc_strerror(retval));
/* Check if this is coordinate variable */
if ( (vndims == 1) && ( strcmp(vname, dims[vdims[0]]) == 0 ))
coord_dim_id = vdims[0];
else coord_dim_id = -1;
snprintf(buf, BUFSIZ, INSVAR, vidx, (int)fid, vname, prim_type_name(vtype), vndims, coord_dim_id);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
if ( coord_dim_id < 0 ){
for (i = 0; i < vndims; i++){
snprintf(buf, BUFSIZ, INSVARDIM, vidx, vdims[i], (int)fid, i);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
}
}
if ( vnatts > 0 ) { /* fill in netcdf_attrs table */
for (aidx = 0; aidx < vnatts; aidx++){
if ((retval = nc_inq_attname(ncid,vidx,aidx,aname)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %d of variable %d: %s",
aidx, vidx, nc_strerror(retval));
if ((retval = nc_inq_att(ncid,vidx,aname,&atype,&alen)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %s type and length: %s",
aname, nc_strerror(retval));
switch ( atype ) {
case NC_CHAR:
aval = (char *) GDKzalloc(alen + 1);
if ((retval = nc_get_att_text(ncid,vidx,aname,aval)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %s value: %s",
aname, nc_strerror(retval));
fix_quote(aval, alen);
aval[alen] = '\0';
snprintf(buf, BUFSIZ, INSATTR, vname, aname, "string", aval, (int)fid, "root");
GDKfree(aval);
break;
case NC_INT:
if ((retval = nc_get_att_int(ncid,vidx,aname,&avalint)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %s value: %s",
aname, nc_strerror(retval));
snprintf(abuf,80,"%d",avalint);
snprintf(buf, BUFSIZ, INSATTR, vname, aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
case NC_FLOAT:
if ((retval = nc_get_att_float(ncid,vidx,aname,&avalfl)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %s value: %s",
aname, nc_strerror(retval));
snprintf(abuf,80,"%7.2f",avalfl);
snprintf(buf, BUFSIZ, INSATTR, vname, aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
case NC_DOUBLE:
if ((retval = nc_get_att_double(ncid,vidx,aname,&avaldbl)))
return createException(MAL, "netcdf.attach",
"Cannot read attribute %s value: %s",
aname, nc_strerror(retval));
snprintf(abuf,80,"%7.2e",avaldbl);
snprintf(buf, BUFSIZ, INSATTR, vname, aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
default: continue; /* next attribute */
}
printf("statement: '%s'\n", s);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
} /* attr loop */
}
} /* var loop */
/* Extract global attributes */
for (aidx = 0; aidx < ngatts; aidx++){
if ((retval = nc_inq_attname(ncid,NC_GLOBAL,aidx,aname)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %d: %s",
aidx, nc_strerror(retval));
if ((retval = nc_inq_att(ncid,NC_GLOBAL,aname,&atype,&alen)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %s type and length: %s",
aname, nc_strerror(retval));
switch ( atype ) {
case NC_CHAR:
aval = (char *) GDKzalloc(alen + 1);
if ((retval = nc_get_att_text(ncid,NC_GLOBAL,aname,aval)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %s value: %s",
aname, nc_strerror(retval));
fix_quote(aval, alen);
aval[alen] = '\0';
snprintf(buf, BUFSIZ, INSATTR, "GLOBAL", aname, "string", aval, (int)fid, "root");
GDKfree(aval);
break;
case NC_INT:
if ((retval = nc_get_att_int(ncid,NC_GLOBAL,aname,&avalint)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %s of type %s : %s",
aname, prim_type_name(atype), nc_strerror(retval));
snprintf(abuf,80,"%d",avalint);
snprintf(buf, BUFSIZ, INSATTR, "GLOBAL", aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
case NC_FLOAT:
if ((retval = nc_get_att_float(ncid,NC_GLOBAL,aname,&avalfl)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %s of type %s: %s",
aname, prim_type_name(atype), nc_strerror(retval));
snprintf(abuf,80,"%7.2f",avalfl);
snprintf(buf, BUFSIZ, INSATTR, "GLOBAL", aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
case NC_DOUBLE:
if ((retval = nc_get_att_double(ncid,NC_GLOBAL,aname,&avaldbl)))
return createException(MAL, "netcdf.attach",
"Cannot read global attribute %s value: %s",
aname, nc_strerror(retval));
snprintf(abuf,80,"%7.2e",avaldbl);
snprintf(buf, BUFSIZ, INSATTR, "GLOBAL", aname, prim_type_name(atype), abuf, (int)fid, "root");
break;
default: continue; /* next attribute */
}
printf("global: '%s'\n", s);
if ( ( msg = SQLstatementIntern(cntxt, &s, "netcdf.attach", TRUE, FALSE, NULL))
!= MAL_SUCCEED )
goto finish;
} /* global attr loop */
finish:
nc_close(ncid);
if (dims != NULL ){
for (didx = 0; didx < ndims; didx++)
GDKfree(dims[didx]);
GDKfree(dims);
}
return msg;
}
/* import variable given file id and variable name */
str
NCDFimportVariable(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
mvc *m = NULL;
sql_schema *sch = NULL;
sql_table *tfiles = NULL, *arr_table = NULL;
sql_column *col;
str msg = MAL_SUCCEED, vname = *(str*)getArgReference(stk, pci, 2);
str fname = NULL, dimtype = NULL, aname_sys = NULL;
int fid = *(int*)getArgReference(stk, pci, 1);
int varid, vndims, vnatts, i, j, retval;
char buf[BUFSIZ], *s= buf, aname[256], **dname;
oid rid = oid_nil;
int vdims[NC_MAX_VAR_DIMS];
nc_type vtype;
int ncid; /* dataset id */
size_t dlen;
bat vbatid = 0, *dim_bids;
BAT *vbat = NULL, *dimbat;
msg = getSQLContext(cntxt, mb, &m, NULL);
if (msg)
return msg;
sch = mvc_bind_schema(m, "sys");
if ( !sch )
return createException(MAL, "netcdf.importvar", "Cannot get schema sys\n");
tfiles = mvc_bind_table(m, sch, "netcdf_files");
if (tfiles == NULL)
return createException(MAL, "netcdf.importvar", "Catalog table missing\n");
/* get the name of the attached NetCDF file */
col = mvc_bind_column(m, tfiles, "file_id");
if (col == NULL)
return createException(MAL, "netcdf.importvar", "Could not find \"netcdf_files\".\"file_id\"\n");
rid = table_funcs.column_find_row(m->session->tr, col, (void *)&fid, NULL);
if (rid == oid_nil)
return createException(MAL, "netcdf.importvar", "File %d not in the NetCDF vault\n", fid);
col = mvc_bind_column(m, tfiles, "location");
fname = (str)table_funcs.column_find_value(m->session->tr, col, rid);
/* Open NetCDF file */
if ((retval = nc_open(fname, NC_NOWRITE, &ncid)))
return createException(MAL, "netcdf.importvar", "Cannot open NetCDF file %s: %s",
fname, nc_strerror(retval));
/* Get info for variable vname from NetCDF file */
if ( (retval = nc_inq_varid(ncid, vname, &varid)) )
return createException(MAL, "netcdf.importvar",
"Cannot read variable %s: %s",
vname, nc_strerror(retval));
if ( (retval = nc_inq_var(ncid, varid, vname, &vtype, &vndims, vdims, &vnatts)))
return createException(MAL, "netcdf.importvar",
"Cannot read variable %d : %s",
varid, nc_strerror(retval));
/* compose 'create table' statement in the buffer */
dname = (char **) GDKzalloc( sizeof(char *) * vndims);
for (i = 0; i < vndims; i++)
dname[i] = (char *) GDKzalloc(NC_MAX_NAME + 1);
snprintf(aname, 256, "%s%d", vname, fid);
j = snprintf(buf, BUFSIZ,"create table %s.%s( ", sch->base.name, aname);
for (i = 0; i < vndims; i++){
if ((retval = nc_inq_dim(ncid, vdims[i], dname[i], &dlen)))
return createException(MAL, "netcdf.importvar",
"Cannot read dimension %d : %s",
vdims[i], nc_strerror(retval));
if ( dlen <= (int) GDK_bte_max )
dimtype = "TINYINT";
else if ( dlen <= (int) GDK_sht_max )
dimtype = "SMALLINT";
else
dimtype = "INT";
(void)dlen;
j += snprintf(buf + j, BUFSIZ - j, "%s %s, ", dname[i], dimtype);
}
j += snprintf(buf + j, BUFSIZ - j, "value %s);", NCDF2SQL(vtype));
/* execute 'create table ' */
msg = SQLstatementIntern(cntxt, &s, "netcdf.importvar", TRUE, FALSE, NULL);
if (msg != MAL_SUCCEED)
return msg;
/* load variable data */
dim_bids = (bat *)GDKmalloc(sizeof(bat) * vndims);
msg = NCDFloadVar(&dim_bids, &vbatid, ncid, varid, vtype, vndims, vdims);
if ( msg != MAL_SUCCEED )
return msg;
/* associate columns in the table with loaded variable data */
aname_sys = toLower(aname);
arr_table = mvc_bind_table(m, sch, aname_sys);
if (arr_table == NULL)
return createException(MAL, "netcdf.importvar", "netcdf table %s missing\n", aname_sys);
col = mvc_bind_column(m, arr_table, "value");
if (col == NULL)
return createException(MAL, "netcdf.importvar", "Cannot find column %s.value\n", aname_sys);
vbat = BATdescriptor(vbatid);
store_funcs.append_col(m->session->tr, col, vbat, TYPE_bat);
BBPunfix(vbatid);
BBPdecref(vbatid, 1);
vbat = NULL;
/* associate dimension bats */
for (i = 0; i < vndims; i++){
col = mvc_bind_column(m, arr_table, dname[i]);
if (col == NULL)
return createException(MAL, "netcdf.importvar", "Cannot find column %s.%s\n", aname_sys, dname[i]);
dimbat = BATdescriptor(dim_bids[i]);
store_funcs.append_col(m->session->tr, col, dimbat, TYPE_bat);
BBPunfix(dim_bids[i]); /* phys. ref from BATdescriptor */
BBPdecref(dim_bids[i], 1); /* log. ref. from loadVar */
dimbat = NULL;
}
for (i = 0; i < vndims; i++)
GDKfree(dname[i]);
GDKfree(dname);
GDKfree(dim_bids);
nc_close(ncid);
return msg;
}
str FITSloadTable(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
mvc *m = NULL;
sql_schema *sch;
sql_table *fits_fl, *fits_tbl, *tbl = NULL;
sql_column *col;
sql_subtype tpe;
fitsfile *fptr;
str tname = *(str*)getArgReference(stk, pci, 1);
str fname;
str msg = MAL_SUCCEED;
oid rid = oid_nil, frid = oid_nil;
int status = 0, cnum = 0, fid, hdu, hdutype, i, j, anynull = 0, mtype;
int *tpcode = NULL;
long *rep = NULL, *wid = NULL, rows;
char keywrd[80], **cname, nm[FLEN_VALUE];
ptr nilptr;
msg = getSQLContext(cntxt, mb, &m, NULL);
if (msg)
return msg;
sch = mvc_bind_schema(m, "sys");
fits_tbl = mvc_bind_table(m, sch, "fits_tables");
if (fits_tbl == NULL) {
msg = createException(MAL, "fits.loadtable", "FITS catalog is missing.\n");
return msg;
}
tbl = mvc_bind_table(m, sch, tname);
if (tbl) {
msg = createException(MAL, "fits.loadtable", "Table %s is already created.\n", tname);
return msg;
}
col = mvc_bind_column(m, fits_tbl, "name");
rid = table_funcs.column_find_row(m->session->tr, col, tname, NULL);
if (rid == oid_nil) {
msg = createException(MAL, "fits.loadtable", "Table %s is unknown in FITS catalog. Attach first the containing file\n", tname);
return msg;
}
/* Open FITS file and move to the table HDU */
col = mvc_bind_column(m, fits_tbl, "file_id");
fid = *(int*)table_funcs.column_find_value(m->session->tr, col, rid);
fits_fl = mvc_bind_table(m, sch, "fits_files");
col = mvc_bind_column(m, fits_fl, "id");
frid = table_funcs.column_find_row(m->session->tr, col, (void *)&fid, NULL);
col = mvc_bind_column(m, fits_fl, "name");
fname = (char *)table_funcs.column_find_value(m->session->tr, col, frid);
if (fits_open_file(&fptr, fname, READONLY, &status)) {
msg = createException(MAL, "fits.loadtable", "Missing FITS file %s.\n", fname);
return msg;
}
col = mvc_bind_column(m, fits_tbl, "hdu");
hdu = *(int*)table_funcs.column_find_value(m->session->tr, col, rid);
fits_movabs_hdu(fptr, hdu, &hdutype, &status);
if (hdutype != ASCII_TBL && hdutype != BINARY_TBL) {
msg = createException(MAL, "fits.loadtable", "HDU %d is not a table.\n", hdu);
fits_close_file(fptr, &status);
return msg;
}
/* create a SQL table to hold the FITS table */
/* col = mvc_bind_column(m, fits_tbl, "columns");
cnum = *(int*) table_funcs.column_find_value(m->session->tr, col, rid); */
fits_get_num_cols(fptr, &cnum, &status);
tbl = mvc_create_table(m, sch, tname, tt_table, 0, SQL_PERSIST, 0, cnum);
tpcode = (int *)GDKzalloc(sizeof(int) * cnum);
rep = (long *)GDKzalloc(sizeof(long) * cnum);
wid = (long *)GDKzalloc(sizeof(long) * cnum);
cname = (char **)GDKzalloc(sizeof(char *) * cnum);
for (j = 1; j <= cnum; j++) {
/* fits_get_acolparms(fptr, j, cname, &tbcol, tunit, tform, &tscal, &tzero, tnull, tdisp, &status); */
snprintf(keywrd, 80, "TTYPE%d", j);
fits_read_key(fptr, TSTRING, keywrd, nm, NULL, &status);
if (status) {
snprintf(nm, FLEN_VALUE, "column_%d", j);
status = 0;
}
cname[j - 1] = GDKstrdup(toLower(nm));
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]);
/* mnstr_printf(cntxt->fdout,"#%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);
}
/* data load */
fits_get_num_rows(fptr, &rows, &status);
mnstr_printf(cntxt->fdout,"#Loading %ld rows in table %s\n", rows, tname);
for (j = 1; j <= cnum; j++) {
BAT *tmp = NULL;
int time0 = GDKms();
mtype = fits2mtype(tpcode[j - 1]);
nilptr = ATOMnil(mtype);
col = mvc_bind_column(m, tbl, cname[j - 1]);
tmp = BATnew(TYPE_void, mtype, rows);
if ( tmp == NULL){
GDKfree(tpcode);
GDKfree(rep);
GDKfree(wid);
GDKfree(cname);
throw(MAL,"fits.load", MAL_MALLOC_FAIL);
}
BATseqbase(tmp, 0);
if (rows > (long)REMAP_PAGE_MAXSIZE)
BATmmap(tmp, STORE_MMAP, STORE_MMAP, STORE_MMAP, STORE_MMAP, 0);
if (mtype != TYPE_str) {
fits_read_col(fptr, tpcode[j - 1], j, 1, 1, rows, nilptr, (void *)BUNtloc(bat_iterator(tmp), BUNfirst(tmp)), &anynull, &status);
BATsetcount(tmp, rows);
tmp->tsorted = 0;
tmp->trevsorted = 0;
} else {
/* char *v = GDKzalloc(wid[j-1]);*/
int bsize = 50;
int tm0, tloadtm = 0, tattachtm = 0;
int batch = bsize, k;
char **v = (char **) GDKzalloc(sizeof(char *) * bsize);
for(i = 0; i < bsize; i++)
v[i] = GDKzalloc(wid[j-1]);
for(i = 0; i < rows; i += batch) {
batch = rows - i < bsize ? rows - i: bsize;
tm0 = GDKms();
fits_read_col(fptr, tpcode[j - 1], j, 1 + i, 1, batch, nilptr, (void *)v, &anynull, &status);
tloadtm += GDKms() - tm0;
tm0 = GDKms();
for(k = 0; k < batch ; k++)
BUNappend(tmp, v[k], TRUE);
tattachtm += GDKms() - tm0;
}
for(i = 0; i < bsize ; i++)
GDKfree(v[i]);
GDKfree(v);
mnstr_printf(cntxt->fdout,"#String column load %d ms, BUNappend %d ms\n", tloadtm, tattachtm);
}
if (status) {
char buf[FLEN_ERRMSG + 1];
fits_read_errmsg(buf);
msg = createException(MAL, "fits.loadtable", "Cannot load column %s of %s table: %s.\n", cname[j - 1], tname, buf);
break;
}
mnstr_printf(cntxt->fdout,"#Column %s loaded for %d ms\t", cname[j-1], GDKms() - time0);
store_funcs.append_col(m->session->tr, col, tmp, TYPE_bat);
mnstr_printf(cntxt->fdout,"#Total %d ms\n", GDKms() - time0);
BBPunfix(tmp->batCacheid);
}
GDKfree(tpcode);
GDKfree(rep);
GDKfree(wid);
GDKfree(cname);
fits_close_file(fptr, &status);
return msg;
}
str FITSattach(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
mvc *m = NULL;
sql_trans *tr;
sql_schema *sch;
sql_table *fits_tp, *fits_fl, *fits_tbl, *fits_col, *tbl = NULL;
sql_column *col;
str msg = MAL_SUCCEED;
str fname = *(str*)getArgReference(stk, pci, 1);
fitsfile *fptr; /* pointer to the FITS file */
int status = 0, i, j, hdutype, hdunum = 1, cnum = 0, bitpixnumber = 0;
oid fid, tid, cid, rid = oid_nil;
char tname[BUFSIZ], *tname_low = NULL, *s, bname[BUFSIZ], stmt[BUFSIZ];
long tbcol;
char cname[BUFSIZ], tform[BUFSIZ], tunit[BUFSIZ], tnull[BUFSIZ], tdisp[BUFSIZ];
double tscal, tzero;
char xtensionname[BUFSIZ] = "", stilversion[BUFSIZ] = "";
char stilclass[BUFSIZ] = "", tdate[BUFSIZ] = "", orig[BUFSIZ] = "", comm[BUFSIZ] = "";
msg = getSQLContext(cntxt, mb, &m, NULL);
if (msg)
return msg;
if (fits_open_file(&fptr, fname, READONLY, &status)) {
msg = createException(MAL, "fits.attach", "Missing FITS file %s.\n", fname);
return msg;
}
tr = m->session->tr;
sch = mvc_bind_schema(m, "sys");
fits_fl = mvc_bind_table(m, sch, "fits_files");
if (fits_fl == NULL)
FITSinitCatalog(m);
fits_fl = mvc_bind_table(m, sch, "fits_files");
fits_tbl = mvc_bind_table(m, sch, "fits_tables");
fits_col = mvc_bind_table(m, sch, "fits_columns");
fits_tp = mvc_bind_table(m, sch, "fits_table_properties");
/* check if the file is already attached */
col = mvc_bind_column(m, fits_fl, "name");
rid = table_funcs.column_find_row(m->session->tr, col, fname, NULL);
if (rid != oid_nil) {
fits_close_file(fptr, &status);
msg = createException(SQL, "fits.attach", "File %s already attached\n", fname);
return msg;
}
/* add row in the fits_files catalog table */
col = mvc_bind_column(m, fits_fl, "id");
fid = store_funcs.count_col(tr, col, 1) + 1;
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_fl, "id"), &fid, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_fl, "name"), fname, TYPE_str);
col = mvc_bind_column(m, fits_tbl, "id");
tid = store_funcs.count_col(tr, col, 1) + 1;
if ((s = strrchr(fname, DIR_SEP)) == NULL)
s = fname;
else
s++;
strcpy(bname, s);
s = strrchr(bname, '.');
if (s) *s = 0;
fits_get_num_hdus(fptr, &hdunum, &status);
for (i = 1; i <= hdunum; i++) {
fits_movabs_hdu(fptr, i, &hdutype, &status);
if (hdutype != ASCII_TBL && hdutype != BINARY_TBL)
continue;
/* SQL table name - the name of FITS extention */
fits_read_key(fptr, TSTRING, "EXTNAME", tname, NULL, &status);
if (status) {
snprintf(tname, BUFSIZ, "%s_%d", bname, i);
tname_low = toLower(tname);
status = 0;
}else { /* check table name for existence in the fits catalog */
tname_low = toLower(tname);
col = mvc_bind_column(m, fits_tbl, "name");
rid = table_funcs.column_find_row(m->session->tr, col, tname_low, NULL);
/* or as regular SQL table */
tbl = mvc_bind_table(m, sch, tname_low);
if (rid != oid_nil || tbl) {
snprintf(tname, BUFSIZ, "%s_%d", bname, i);
tname_low = toLower(tname);
}
}
fits_read_key(fptr, TSTRING, "BITPIX", &bitpixnumber, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "DATE-HDU", tdate, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "XTENSION", xtensionname, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "STILVERS", stilversion, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "STILCLAS", stilclass, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "ORIGIN", orig, NULL, &status);
if (status) {
status = 0;
}
fits_read_key(fptr, TSTRING, "COMMENT", comm, NULL, &status);
if (status) {
status = 0;
}
fits_get_num_cols(fptr, &cnum, &status);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "id"), &tid, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "name"), tname_low, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "columns"), &cnum, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "file_id"), &fid, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "hdu"), &i, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "date"), tdate, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "origin"), orig, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tbl, "comment"), comm, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tp, "table_id"), &tid, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tp, "xtension"), xtensionname, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tp, "bitpix"), &bitpixnumber, TYPE_int);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tp, "stilvers"), stilversion, TYPE_str);
store_funcs.append_col(m->session->tr,
mvc_bind_column(m, fits_tp, "stilclas"), stilclass, TYPE_str);
/* read columns description */
s = stmt;
col = mvc_bind_column(m, fits_col, "id");
cid = store_funcs.count_col(tr, col, 1) + 1;
for (j = 1; j <= cnum; j++, cid++) {
fits_get_acolparms(fptr, j, cname, &tbcol, tunit, tform, &tscal, &tzero, tnull, tdisp, &status);
snprintf(stmt, BUFSIZ, FITS_INS_COL, (int)cid, cname, tform, tunit, j, (int)tid);
msg = SQLstatementIntern(cntxt, &s, "fits.attach", TRUE, FALSE);
if (msg != MAL_SUCCEED) {
fits_close_file(fptr, &status);
return msg;
}
}
tid++;
}
fits_close_file(fptr, &status);
return MAL_SUCCEED;
}
str FITSexportTable(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
str msg = MAL_SUCCEED;
str tname = *(str*) getArgReference(stk, pci, 1);
mvc *m = NULL;
sql_trans *tr;
sql_schema *sch;
sql_table *tbl, *column, *tables = NULL;
sql_column *col;
oid rid = oid_nil;
str type, name, *colname, *tform;
fitsfile *fptr;
char filename[BUFSIZ];
long nrows = 0, optimal;
rids * rs;
int tm0, texportboolean=0, texportchar=0, texportstring=0, texportshort=0, texportint=0, texportlong=0, texportfloat=0, texportdouble=0;
int numberrow = 0, cc = 0, status = 0, j = 0, columns, fid, dimension = 0, block = 0;
int boolcols = 0, charcols = 0, strcols = 0, shortcols = 0, intcols = 0, longcols = 0, floatcols = 0, doublecols = 0;
int hdutype;
char charvalue, *readcharrows;
str strvalue; char **readstrrows;
short shortvalue, *readshortrows;
int intvalue, *readintrows;
long longvalue, *readlongrows;
float realvalue, *readfloatrows;
double doublevalue, *readdoublerows;
_Bool boolvalue, *readboolrows;
struct list * set;
msg = getSQLContext(cntxt, mb, &m, NULL);
if (msg)
return msg;
tr = m->session->tr;
sch = mvc_bind_schema(m, "sys");
/* First step: look if the table exists in the database. If the table is not in the database, the export function cannot continue */
tbl = mvc_bind_table(m, sch, tname);
if (tbl == NULL) {
msg = createException (MAL, "fits.exporttable", "Table %s is missing.\n", tname);
return msg;
}
set = (*tbl).columns.set;
columns = list_length(set);
colname = (str *) GDKmalloc(columns * sizeof(str));
tform = (str *) GDKmalloc(columns * sizeof(str));
/* mnstr_printf(GDKout,"Number of columns: %d\n", columns);*/
tables = mvc_bind_table(m, sch, "_tables");
col = mvc_bind_column(m, tables, "name");
rid = table_funcs.column_find_row(m->session->tr, col, tname, NULL);
col = mvc_bind_column(m, tables, "id");
fid = *(int*) table_funcs.column_find_value(m->session->tr, col, rid);
column = mvc_bind_table(m, sch, "_columns");
col = mvc_bind_column(m, column, "table_id");
rs = table_funcs.rids_select(m->session->tr, col, (void *) &fid, (void *) &fid, NULL);
while ((rid = table_funcs.rids_next(rs)) != oid_nil)
{
col = mvc_bind_column(m, column, "name");
name = (char *) table_funcs.column_find_value(m->session->tr, col, rid);
colname[j] = toLower(name);
col = mvc_bind_column(m, column, "type");
type = (char *) table_funcs.column_find_value(m->session->tr, col, rid);
if (strcmp(type,"boolean")==0) tform[j] = "1L";
if (strcmp(type,"char")==0) tform[j] = "1S";
if (strcmp(type,"varchar")==0) tform[j] = "8A";
if (strcmp(type,"smallint")==0) tform[j] = "1I";
if (strcmp(type,"int")==0) tform[j] = "1J";
if (strcmp(type,"bigint")==0) tform[j] = "1K";
if (strcmp(type,"real")==0) tform[j] = "1E";
if (strcmp(type,"double")==0) tform[j] = "1D";
j++;
}
col = mvc_bind_column(m, tbl, colname[0]);
nrows = store_funcs.count_col(tr, col, 1);
snprintf(filename,BUFSIZ,"\n%s.fit",tname);
mnstr_printf(GDKout, "Filename: %s\n", filename);
remove(filename);
status=0;
fits_create_file(&fptr, filename, &status);
fits_create_img(fptr, USHORT_IMG, 0, NULL, &status);
fits_close_file(fptr, &status);
fits_open_file(&fptr, filename, READWRITE, &status);
fits_movabs_hdu(fptr, 1, &hdutype, &status);
fits_create_tbl( fptr, BINARY_TBL, 0, columns, colname, tform, NULL, tname, &status);
for (cc = 0; cc < columns; cc++)
{
char * columntype;
col = mvc_bind_column(m, tbl, colname[cc]);
columntype = col -> type.type->sqlname;
if (strcmp(columntype,"boolean")==0)
{
boolcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readboolrows = (_Bool *) GDKmalloc (sizeof(_Bool) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
boolvalue = *(_Bool*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readboolrows[dimension] = boolvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TLOGICAL, cc+1, (optimal*block)+1, 1, optimal, readboolrows, &status);
texportboolean += GDKms() - tm0;
GDKfree(readboolrows);
readboolrows = (_Bool *) GDKmalloc (sizeof(_Bool) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TLOGICAL, cc+1, (optimal*block)+1, 1, dimension, readboolrows, &status);
texportboolean += GDKms() - tm0;
GDKfree(readboolrows);
}
if (strcmp(columntype,"char")==0)
{
charcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readcharrows = (char *) GDKmalloc (sizeof(char) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
charvalue = *(char*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readcharrows[dimension] = charvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TBYTE, cc+1, (optimal*block)+1, 1, optimal, readcharrows, &status);
texportchar += GDKms() - tm0;
GDKfree(readcharrows);
readcharrows = (char *) GDKmalloc (sizeof(char) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TBYTE, cc+1, (optimal*block)+1, 1, dimension, readcharrows, &status);
texportchar += GDKms() - tm0;
GDKfree(readcharrows);
}
if (strcmp(columntype,"varchar")==0)
{
strcols++; dimension=0; block=0;
fits_get_rowsize(fptr,&optimal,&status);
readstrrows = (char **) GDKmalloc (sizeof(char *) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
strvalue = (char *) table_funcs.column_find_value(m->session->tr, col, numberrow);
readstrrows[dimension] = strvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col_str(fptr, cc+1, (optimal*block)+1, 1, optimal, readstrrows, &status);
texportstring += GDKms() - tm0;
GDKfree(readstrrows);
readstrrows = (char **) GDKmalloc(sizeof(char *) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col_str(fptr, cc+1, (optimal*block)+1, 1, dimension, readstrrows, &status);
texportstring += GDKms() - tm0;
GDKfree(readstrrows);
}
if (strcmp(columntype,"smallint")==0)
{
shortcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readshortrows = (short *) GDKmalloc (sizeof(short) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
shortvalue = *(short*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readshortrows[dimension] = shortvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TSHORT, cc+1, (optimal*block)+1, 1, optimal, readshortrows, &status);
texportshort += GDKms() - tm0;
GDKfree(readshortrows);
readshortrows = (short *) GDKmalloc (sizeof(short) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TSHORT, cc+1, (optimal*block)+1, 1, dimension, readshortrows, &status);
texportshort += GDKms() - tm0;
GDKfree(readshortrows);
}
if (strcmp(columntype,"int")==0)
{
intcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readintrows = (int *) GDKmalloc (sizeof(int) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
intvalue = *(int*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readintrows[dimension] = intvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TINT, cc+1, (optimal*block)+1, 1, optimal, readintrows, &status);
texportint += GDKms() - tm0;
GDKfree(readintrows);
readintrows = (int *) GDKmalloc (sizeof(int) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TINT, cc+1, (optimal*block)+1, 1, dimension, readintrows, &status);
texportint += GDKms() - tm0;
GDKfree(readintrows);
}
if (strcmp(columntype,"bigint")==0)
{
longcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readlongrows = (long *) GDKmalloc (sizeof(long) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
longvalue = *(long*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readlongrows[dimension] = longvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TLONG, cc+1, (optimal*block)+1, 1, optimal, readlongrows, &status);
texportlong += GDKms() - tm0;
GDKfree(readlongrows);
readlongrows = (long *) GDKmalloc (sizeof(long) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TLONG, cc+1, (optimal*block)+1, 1, dimension, readlongrows, &status);
texportlong += GDKms() - tm0;
GDKfree(readlongrows);
}
if (strcmp(columntype,"real")==0)
{
floatcols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readfloatrows = (float *) GDKmalloc (sizeof(float) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
realvalue = *(float*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readfloatrows[dimension] = realvalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TFLOAT, cc+1, (optimal*block)+1, 1, optimal, readfloatrows, &status);
texportfloat += GDKms() - tm0;
GDKfree(readfloatrows);
readfloatrows = (float *) GDKmalloc (sizeof(float) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TFLOAT, cc+1, (optimal*block)+1, 1, dimension, readfloatrows, &status);
texportfloat += GDKms() - tm0;
GDKfree(readfloatrows);
}
if (strcmp(columntype,"double")==0)
{
doublecols++; dimension = 0; block = 0;
fits_get_rowsize(fptr,&optimal,&status);
readdoublerows = (double *) GDKmalloc (sizeof(double) * optimal);
for (numberrow = 0; numberrow < nrows ; numberrow++)
{
doublevalue = *(double*) table_funcs.column_find_value(m->session->tr, col, numberrow);
readdoublerows[dimension] = doublevalue;
dimension++;
if (dimension == optimal)
{
dimension = 0;
tm0 = GDKms();
fits_write_col(fptr, TDOUBLE, cc+1, (optimal*block)+1, 1, optimal, readdoublerows, &status);
texportdouble += GDKms() - tm0;
GDKfree(readdoublerows);
readdoublerows = (double *) GDKmalloc (sizeof(double) * optimal);
block++;
}
}
tm0 = GDKms();
fits_write_col(fptr, TDOUBLE, cc+1, (optimal*block)+1, 1, optimal, readdoublerows, &status);
texportdouble += GDKms() - tm0;
GDKfree(readdoublerows);
}
}
/* print all the times that were needed to export each one of the columns
mnstr_printf(GDKout, "\n\n");
if (texportboolean > 0) mnstr_printf(GDKout, "%d Boolean\tcolumn(s) exported in %d ms\n", boolcols, texportboolean);
if (texportchar > 0) mnstr_printf(GDKout, "%d Char\t\tcolumn(s) exported in %d ms\n", charcols, texportchar);
if (texportstring > 0) mnstr_printf(GDKout, "%d String\tcolumn(s) exported in %d ms\n", strcols, texportstring);
if (texportshort > 0) mnstr_printf(GDKout, "%d Short\t\tcolumn(s) exported in %d ms\n", shortcols, texportshort);
if (texportint > 0) mnstr_printf(GDKout, "%d Integer\tcolumn(s) exported in %d ms\n", intcols, texportint);
if (texportlong > 0) mnstr_printf(GDKout, "%d Long\t\tcolumn(s) exported in %d ms\n", longcols, texportlong);
if (texportfloat > 0) mnstr_printf(GDKout, "%d Float\t\tcolumn(s) exported in %d ms\n", floatcols, texportfloat);
if (texportdouble > 0) mnstr_printf(GDKout, "%d Double\tcolumn(s) exported in %d ms\n", doublecols, texportdouble);
*/
fits_close_file(fptr, &status);
return msg;
}
static str
SHPimportFile(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci, bool partial) {
mvc *m = NULL;
sql_schema *sch = NULL;
char *sch_name = "sys";
sql_table *shps_table = NULL, *fls_table = NULL, *data_table = NULL;
char *shps_table_name = "shapefiles";
char *fls_table_name = "files";
char *data_table_name = NULL;
sql_column *col;
sql_column **cols;
BAT **colsBAT;
int colsNum = 2; //we will have at least the gid column and a geometry column
int rowsNum = 0; //the number of rows in the shape file that will be imported
//GIntBig rowsNum = 0;
int gidNum = 0;
char *nameToLowerCase = NULL;
str msg = MAL_SUCCEED;
str fname = NULL;
int vid = *(int*)getArgReference(stk, pci, 1);
ptr *p;
wkb *g;
OGRGeometryH geom;
OGREnvelope *mbb;
/* SHP-level descriptor */
OGRFieldDefnH hFieldDefn;
int i=0;
oid irid;
GDALWConnection shp_conn;
GDALWConnection * shp_conn_ptr = NULL;
GDALWSimpleFieldDef * field_definitions;
OGRFeatureH feature;
OGRFeatureDefnH featureDefn;
/* get table columns from shp and create the table */
if((msg = getSQLContext(cntxt, mb, &m, NULL)) != MAL_SUCCEED)
return msg;
if((msg = checkSQLContext(cntxt)) != MAL_SUCCEED)
return msg;
if(!(sch = mvc_bind_schema(m, sch_name)))
return createException(MAL, "shp.import", SQLSTATE(38000) "Schema '%s' missing", sch_name);
/* find the name of the shape file corresponding to the given id */
if(!(fls_table = mvc_bind_table(m, sch, fls_table_name)))
return createException(MAL, "shp.import", SQLSTATE(38000) "Table '%s.%s' missing", sch_name, fls_table_name);
if(!(col = mvc_bind_column(m, fls_table, "id")))
return createException(MAL, "shp.import", SQLSTATE(38000) "Column '%s.%s(id)' missing", sch_name, fls_table_name);
irid = table_funcs.column_find_row(m->session->tr, col, (void *)&vid, NULL);
if (is_oid_nil(irid))
return createException(MAL, "shp.import", SQLSTATE(38000) "Shapefile with id %d not in the %s.%s table\n", vid, sch_name, fls_table_name);
if(!(col = mvc_bind_column(m, fls_table, "path")))
return createException(MAL, "shp.import", SQLSTATE(38000) "Column '%s.%s(path)' missing", sch_name, fls_table_name);
fname = (str)table_funcs.column_find_value(m->session->tr, col, irid);
/* find the name of the table that has been reserved for this shape file */
if(!(shps_table = mvc_bind_table(m, sch, shps_table_name)))
return createException(MAL, "shp.import", SQLSTATE(38000) "Table '%s.%s' missing", sch_name, shps_table_name);
if(!(col = mvc_bind_column(m, shps_table, "fileid")))
return createException(MAL, "shp.import", SQLSTATE(38000) "Column '%s.%s(fileid)' missing", sch_name, shps_table_name);
irid = table_funcs.column_find_row(m->session->tr, col, (void *)&vid, NULL);
if (is_oid_nil(irid))
return createException(MAL, "shp.import", SQLSTATE(38000) "Shapefile with id %d not in the Shapefile catalog\n", vid);
if(!(col = mvc_bind_column(m, shps_table, "datatable")))
return createException(MAL, "shp.import", SQLSTATE(38000) "Column '%s.%s(datatable)' missing", sch_name, shps_table_name);
data_table_name = (str)table_funcs.column_find_value(m->session->tr, col, irid);
/* add the data on the file to the table */
if(!(shp_conn_ptr = GDALWConnect((char *) fname)))
return createException(MAL, "shp.import", SQLSTATE(38000) "Missing shape file %s\n", fname);
shp_conn = *shp_conn_ptr;
/*count the number of lines in the shape file */
if ((rowsNum = OGR_L_GetFeatureCount(shp_conn.layer, false)) == -1) {
if ((rowsNum = OGR_L_GetFeatureCount(shp_conn.layer, true)) == -1) {
OGR_L_ResetReading(shp_conn.layer);
rowsNum = 0;
while ((feature = OGR_L_GetNextFeature(shp_conn.layer)) != NULL ) {
rowsNum++;
OGR_F_Destroy(feature);
}
}
}
/* calculate the mbb of the query geometry */
if (partial) {
p = (ptr*)getArgReference(stk, pci, 2);
g = (wkb*)*p;
geom = OGR_G_CreateGeometry(wkbPolygon);
if (OGR_G_ImportFromWkb(geom, (unsigned char*)g->data, g->len) != OGRERR_NONE) {
msg = createException(MAL, "shp.import", SQLSTATE(38000) "Could not intantiate the query polygon.");
OGR_F_Destroy(geom);
goto final;
}
if (!(mbb = (OGREnvelope*)GDKmalloc(sizeof(OGREnvelope)))) {
msg = createException(MAL, "shp.import", SQLSTATE(HY001) MAL_MALLOC_FAIL);
OGR_F_Destroy(geom);
goto final;
}
/* attach a single shp file given its name, fill in shp catalog tables */
str
SHPattach(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
mvc *m = NULL;
sql_schema *sch = NULL;
sql_table *fls = NULL, *shps = NULL, *shps_dbf = NULL;
sql_column *col;
str msg = MAL_SUCCEED;
str fname = *(str*)getArgReference(stk, pci, 1);
/* SHP-level descriptor */
char buf[BUFSIZ], temp_buf[BUFSIZ], *s=buf;
int i=0, shpid = 0;
oid fid, rid = oid_nil;
GDALWConnection shp_conn;
GDALWConnection * shp_conn_ptr = NULL;
GDALWSimpleFieldDef * field_definitions;
GDALWSpatialInfo spatial_info;
char *nameToLowerCase = NULL;
if((msg = getSQLContext(cntxt, mb, &m, NULL)) != MAL_SUCCEED)
return msg;
if((msg = checkSQLContext(cntxt)) != MAL_SUCCEED)
return msg;
if(!(sch = mvc_bind_schema(m, "sys")))
return createException(MAL, "shp.attach", SQLSTATE(38000) "Schema sys missing\n");
fls = mvc_bind_table(m, sch, "files");
shps = mvc_bind_table(m, sch, "shapefiles");
shps_dbf = mvc_bind_table(m, sch, "shapefiles_dbf");
if (fls == NULL || shps == NULL || shps_dbf == NULL )
return createException(MAL, "shp.attach", SQLSTATE(38000) "Catalog table missing\n");
if ((shp_conn_ptr = GDALWConnect((char *) fname)) == NULL) {
return createException(MAL, "shp.attach", SQLSTATE(38000) "Missing shape file %s\n", fname);
}
shp_conn = *shp_conn_ptr;
/* check if the file is already attached */
col = mvc_bind_column(m, fls, "path");
rid = table_funcs.column_find_row(m->session->tr, col, fname, NULL);
if (!is_oid_nil(rid)) {
GDALWClose(shp_conn_ptr);
return createException(MAL, "shp.attach", SQLSTATE(38000) "File %s already attached\n", fname);
}
/* add row in the files(id, path) catalog table */
col = mvc_bind_column(m, fls, "id");
fid = store_funcs.count_col(m->session->tr, col, 1) + 1;
snprintf(buf, BUFSIZ, INSFILE, (int)fid, fname);
if ( ( msg = SQLstatementIntern(cntxt, &s,"shp.attach",TRUE,FALSE,NULL)) != MAL_SUCCEED)
goto finish;
/*if (shp_conn.layer == NULL || shp_conn.source == NULL || shp_conn.handler == NULL || shp_conn.driver == NULL) {
msg = createException(MAL, "shp.attach", SQLSTATE(38000) "lol-1\n");
return msg;
}*/
/* add row in the shapefiles catalog table (e.g. the name of the table that will store tha data of the shapefile) */
spatial_info = GDALWGetSpatialInfo(shp_conn);
col = mvc_bind_column(m, shps, "shapefileid");
shpid = store_funcs.count_col(m->session->tr, col, 1) + 1;
nameToLowerCase = toLower(shp_conn.layername);
snprintf(buf, BUFSIZ, INSSHP, shpid, (int)fid, spatial_info.epsg, nameToLowerCase);
GDKfree(nameToLowerCase);
if ( ( msg = SQLstatementIntern(cntxt, &s,"shp.attach",TRUE,FALSE,NULL)) != MAL_SUCCEED)
goto finish;
/* add information about the fields of the shape file
* one row for each field with info (shapefile_id, field_name, field_type) */
field_definitions = GDALWGetSimpleFieldDefinitions(shp_conn);
if (field_definitions == NULL) {
GDALWClose(&shp_conn);
return createException(MAL, "shp.attach", SQLSTATE(HY001) MAL_MALLOC_FAIL);
}
for (i=0 ; i<shp_conn.numFieldDefinitions ; i++) {
snprintf(buf, BUFSIZ, INSSHPDBF, shpid, field_definitions[i].fieldName, field_definitions[i].fieldType);
if ( ( msg = SQLstatementIntern(cntxt, &s,"shp.attach",TRUE,FALSE,NULL)) != MAL_SUCCEED)
goto fin;
}
/* create the table that will store the data of the shape file */
temp_buf[0]='\0';
for (i=0 ; i<shp_conn.numFieldDefinitions ; i++) {
nameToLowerCase = toLower(field_definitions[i].fieldName);
if (strcmp(field_definitions[i].fieldType, "Integer") == 0) {
sprintf(temp_buf + strlen(temp_buf), "\"%s\" INT, ", nameToLowerCase);
} else if (strcmp(field_definitions[i].fieldType, "Real") == 0) {
sprintf(temp_buf + strlen(temp_buf), "\"%s\" FLOAT, ", nameToLowerCase);
#if 0
} else if (strcmp(field_definitions[i].fieldType, "Date") == 0) {
sprintf(temp_buf + strlen(temp_buf), "\"%s\" STRING, ", nameToLowerCase);
#endif
} else
sprintf(temp_buf + strlen(temp_buf), "\"%s\" STRING, ", nameToLowerCase);
GDKfree(nameToLowerCase);
}
sprintf(temp_buf + strlen(temp_buf), "geom GEOMETRY ");
snprintf(buf, BUFSIZ, CRTTBL, shp_conn.layername, temp_buf);
if ( ( msg = SQLstatementIntern(cntxt, &s,"shp.import",TRUE,FALSE,NULL)) != MAL_SUCCEED)
goto fin;
fin:
free(field_definitions);
finish:
/* if (msg != MAL_SUCCEED){
snprintf(buf, BUFSIZ,"ROLLBACK;");
SQLstatementIntern(cntxt,&s,"geotiff.attach",TRUE,FALSE));
}*/
GDALWClose(&shp_conn);
return msg;
}
