From da8c12625f3f168b4fa750e9ce176f1275fb06fc Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 29 Oct 2008 16:11:18 +0000
Subject: [PATCH] fix whole load of stuff that was broken, still more to do.
---
src/zmapServer/file/fileServer.c | 179 ++++++++++++++++++++---------
src/zmapServer/file/fileServer_P.h | 6 +-
2 files changed, 128 insertions(+), 57 deletions(-)
diff --git a/src/zmapServer/file/fileServer.c b/src/zmapServer/file/fileServer.c
index 3dd24a472..814bddb61 100755
--- a/src/zmapServer/file/fileServer.c
+++ b/src/zmapServer/file/fileServer.c
@@ -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 ;
+}
diff --git a/src/zmapServer/file/fileServer_P.h b/src/zmapServer/file/fileServer_P.h
index d328e6b03..68d03d029 100755
--- a/src/zmapServer/file/fileServer_P.h
+++ b/src/zmapServer/file/fileServer_P.h
@@ -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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