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Commit da8c1262 authored by edgrif's avatar edgrif
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fix whole load of stuff that was broken, still more to do.

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src/zmapServer/file/fileServer.c
+ 124
− 55
View file @ da8c1262
......@@ -30,9 +30,9 @@
*
* Exported functions: See ZMap/zmapServerPrototype.h
* HISTORY:
* Last edited: Aug 1 14:06 2008 (edgrif)
* Last edited: Oct 17 14:41 2008 (edgrif)
* Created: Fri Sep 10 18:29:18 2004 (edgrif)
* CVS info: $Id: fileServer.c,v 1.31 2008-09-24 14:57:56 edgrif Exp $
* CVS info: $Id: fileServer.c,v 1.32 2008-10-29 16:11:18 edgrif Exp $
*-------------------------------------------------------------------
*/
......@@ -72,10 +72,11 @@ static gboolean createConnection(void **server_out,
char *version_str, int timeout) ;
static ZMapServerResponseType openConnection(void *server) ;
static ZMapServerResponseType getInfo(void *server, char **database_path) ;
static ZMapServerResponseType getFeatureSetNames(void *server, GList **feature_sets_out, GList **required_styles) ;
static ZMapServerResponseType getStyles(void *server, GData **styles_out) ;
static ZMapServerResponseType haveModes(void *server, gboolean *have_mode) ;
static ZMapServerResponseType getSequences(void *server_in, GList *sequences_inout) ;
static ZMapServerResponseType getFeatureSets(void *server, GList **feature_sets_out, GList **required_styles) ;
static ZMapServerResponseType setContext(void *server, ZMapFeatureContext feature_context) ;
static ZMapServerResponseType getFeatures(void *server_in, ZMapFeatureContext feature_context_out) ;
static ZMapServerResponseType getContextSequence(void *server_in, ZMapFeatureContext feature_context_out) ;
......@@ -90,8 +91,7 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
ZMapFeatureBlock feature_block) ;
static void setLastErrorMsg(FileServer server, GError **gff_file_err_inout) ;
static gboolean getServerInfo(FileServer server, char **database_path_out) ;
......@@ -103,7 +103,8 @@ void fileGetServerFuncs(ZMapServerFuncs file_funcs)
file_funcs->global_init = globalInit ;
file_funcs->create = createConnection ;
file_funcs->open = openConnection ;
file_funcs->feature_set_names = getFeatureSets ;
file_funcs->get_info = getInfo ;
file_funcs->feature_set_names = getFeatureSetNames ;
file_funcs->get_styles = getStyles ;
file_funcs->have_modes = haveModes ;
file_funcs->get_sequence = getSequences ;
......@@ -209,6 +210,26 @@ static ZMapServerResponseType openConnection(void *server_in)
}
static ZMapServerResponseType getInfo(void *server_in, char **database_path)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
FileServer server = (FileServer)server_in ;
if (getServerInfo(server, database_path))
{
result = ZMAP_SERVERRESPONSE_OK ;
}
else
{
result = ZMAP_SERVERRESPONSE_REQFAIL ;
ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, server->file_path,
"Could not get server info because: %s", server->last_err_msg) ;
}
return result ;
}
/* We cannot parse the styles from a gff file, gff simply doesn't have display styles so we
* just return "unsupported", so if this function is called it will alert the caller that
......@@ -222,7 +243,7 @@ static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
zMapAssert(server) ;
server->last_err_msg = g_strdup("Styles cannot be read from a GFF file.") ;
server->last_err_msg = g_strdup("Reading styles from a GFF file is not supported.") ;
ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
......@@ -233,17 +254,15 @@ static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
/* GFF File styles do not include a mode (e.g. transcript etc) so this function
* always returns FALSE.
* always returns unsupported.
*/
static ZMapServerResponseType haveModes(void *server_in, gboolean *have_mode)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
FileServer server = (FileServer)server_in ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
*have_mode = FALSE ;
return result ;
}
......@@ -263,18 +282,37 @@ static ZMapServerResponseType getSequences(void *server_in, GList *sequences_ino
* will alert the caller that something has gone wrong.
*
* */
static ZMapServerResponseType getFeatureSets(void *server_in, GList **feature_sets_out, GList **required_styles)
static ZMapServerResponseType getFeatureSetNames(void *server_in,
GList **feature_sets_inout, GList **required_styles_out)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
FileServer server = (FileServer)server_in ;
GList *feature_sets = NULL ;
zMapAssert(server) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
server->last_err_msg = g_strdup("Feature Sets cannot be read from a GFF file.") ;
ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
/* We should check feature_sets_in against those found in file.....the below is a total hack... */
feature_sets = g_list_append(feature_sets, GINT_TO_POINTER(g_quark_from_string("utr"))) ;
feature_sets = g_list_append(feature_sets, GINT_TO_POINTER(g_quark_from_string("coding_transcript"))) ;
result = ZMAP_SERVERRESPONSE_OK ;
*feature_sets_inout = feature_sets ;
*required_styles_out = g_list_copy(feature_sets) ;
return result ;
}
......@@ -309,7 +347,7 @@ static ZMapServerResponseType getFeatures(void *server_in, ZMapFeatureContext fe
gsize terminator_pos = 0 ;
GError *gff_file_err = NULL ;
ZMapGFFHeader header ;
GError *error = NULL ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
{
......@@ -335,66 +373,84 @@ static ZMapServerResponseType getFeatures(void *server_in, ZMapFeatureContext fe
get_features.gff_line = g_string_sized_new(2000) ; /* Probably not many lines will be >
2k chars. */
/* Read the header, needed for feature coord range. */
while ((status = g_io_channel_read_line_string(server->gff_file, get_features.gff_line,
&terminator_pos,
&gff_file_err)) == G_IO_STATUS_NORMAL)
{
*(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
gboolean done_header = FALSE ;
*(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
if (!zMapGFFParseHeader(get_features.parser, get_features.gff_line->str))
if (zMapGFFParseHeader(get_features.parser, get_features.gff_line->str, &done_header))
{
GError *error = zMapGFFGetError(get_features.parser) ;
if (!error && (header = zMapGFFGetHeader(get_features.parser)))
{
/* Header finished..ugh poor interface.... */
break ;
}
if (!error)
{
server->last_err_msg =
g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str) ;
ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
}
if (done_header)
break ;
else
get_features.gff_line = g_string_truncate(get_features.gff_line, 0) ;
/* Reset line to empty. */
}
else
{
if (!done_header)
{
/* If the error was serious we stop processing and return the error,
* otherwise we just log the error. */
if (zMapGFFTerminated(get_features.parser))
error = zMapGFFGetError(get_features.parser) ;
if (!error)
{
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
server->last_err_msg = g_strdup_printf("%s", error->message) ;
/* SHOULD ABORT HERE.... */
server->last_err_msg =
g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str) ;
ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
}
else
{
ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, server->file_path,
"%s", error->message) ;
/* If the error was serious we stop processing and return the error,
* otherwise we just log the error. */
if (zMapGFFTerminated(get_features.parser))
{
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
server->last_err_msg = g_strdup_printf("%s", error->message) ;
}
else
{
server->last_err_msg =
g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str) ;
ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
}
}
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
}
break ;
}
get_features.gff_line = g_string_truncate(get_features.gff_line, 0) ;
/* Reset line to empty. */
}
if (get_features.result == ZMAP_SERVERRESPONSE_OK)
{
header = zMapGFFGetHeader(get_features.parser) ;
addMapping(feature_context, header) ;
addMapping(feature_context, header) ;
zMapGFFFreeHeader(header) ;
zMapGFFFreeHeader(header) ;
/* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
* we would have to parse and reparse the file....can be done but not needed this second. */
g_hash_table_foreach(feature_context->alignments, eachAlignment, (gpointer)&get_features) ;
/* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
* we would have to parse and reparse the file....can be done but not needed this second. */
g_hash_table_foreach(feature_context->alignments, eachAlignment, (gpointer)&get_features) ;
{
GError *error = NULL ;
zMapFeatureDumpStdOutFeatures(feature_context, &error) ;
}
}
/* Clear up. */
......@@ -579,7 +635,7 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
gsize terminator_pos = 0 ;
gboolean free_on_destroy = FALSE ;
GError *gff_file_err = NULL ;
gboolean first ;
/* Tempting to check that block is inside features_start/end, but it may be a different
* sequence....we don't really deal with this... */
......@@ -591,11 +647,13 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
feature_block->block_to_sequence.q1,
feature_block->block_to_sequence.q2) ;
while ((status = g_io_channel_read_line_string(server->gff_file, gff_line, &terminator_pos,
&gff_file_err)) == G_IO_STATUS_NORMAL)
first = TRUE ;
do
{
*(gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
if (first)
first = FALSE ;
else
*(gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
if (!zMapGFFParseLine(parser, gff_line->str))
......@@ -630,7 +688,9 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
}
gff_line = g_string_truncate(gff_line, 0) ; /* Reset line to empty. */
}
} while ((status = g_io_channel_read_line_string(server->gff_file, gff_line, &terminator_pos,
&gff_file_err)) == G_IO_STATUS_NORMAL) ;
/* If we reached the end of the file then all is fine, so return features... */
......@@ -660,3 +720,12 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
}
static gboolean getServerInfo(FileServer server, char **database_path_out)
{
gboolean result = FALSE ;
result = TRUE ;
*database_path_out = g_strdup(server->file_path) ;
return result ;
}
src/zmapServer/file/fileServer_P.h
+ 4
− 2
View file @ da8c1262
......@@ -26,9 +26,9 @@
* of the server code.
*
* HISTORY:
* Last edited: Jul 26 09:03 2005 (edgrif)
* Last edited: Oct 14 14:59 2008 (edgrif)
* Created: Fri Sep 10 18:42:18 2004 (edgrif)
* CVS info: $Id: fileServer_P.h,v 1.5 2006-11-08 09:24:31 edgrif Exp $
* CVS info: $Id: fileServer_P.h,v 1.6 2008-10-29 16:11:18 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef FILE_SERVER_P_H
......@@ -46,6 +46,8 @@ typedef struct _FileServerStruct
gchar *file_path ;
GIOChannel* gff_file ;
char *styles_file ;
gboolean error ; /* TRUE if any error occurred. */
char *last_err_msg ;
......
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