From b4a18a6bce1d1e1b34368b1649399bf83e4b294a Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Thu, 14 Jan 2010 13:34:37 +0000
Subject: [PATCH] add look up of feature style from source data info., add
better error handling for feature create.
---
src/zmapView/zmapViewRemoteReceive.c | 186 +++++++++++++++++----------
1 file changed, 121 insertions(+), 65 deletions(-)
diff --git a/src/zmapView/zmapViewRemoteReceive.c b/src/zmapView/zmapViewRemoteReceive.c
index 0f7e6ed7c..f6e681fb7 100755
--- a/src/zmapView/zmapViewRemoteReceive.c
+++ b/src/zmapView/zmapViewRemoteReceive.c
@@ -29,9 +29,9 @@
* Exported functions: See zmapView_P.h
*
* HISTORY:
- * Last edited: Oct 19 16:00 2009 (edgrif)
+ * Last edited: Jan 14 13:22 2010 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
- * CVS info: $Id: zmapViewRemoteReceive.c,v 1.36 2009-12-15 13:49:10 mh17 Exp $
+ * CVS info: $Id: zmapViewRemoteReceive.c,v 1.37 2010-01-14 13:34:37 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -118,6 +118,8 @@ typedef struct
ZMapFeature feature;
GQuark source_id ;
+ GQuark style_id ;
+ ZMapFeatureTypeStyle style ;
GList *feature_list;
GData *styles;
@@ -156,7 +158,7 @@ typedef struct
static char *view_execute_command(char *command_text, gpointer user_data, int *statusCode);
static char *view_post_execute(char *command_text, gpointer user_data, int *statusCode);
static void delete_failed_make_message(gpointer list_data, gpointer user_data);
-static void drawNewFeatures(ZMapView view, RequestData input_data, ResponseData output_data);
+static gboolean drawNewFeatures(ZMapView view, RequestData input_data, ResponseData output_data);
static void getChildWindowXID(ZMapView view, RequestData input_data, ResponseData output_data);
static void viewDumpContextToFile(ZMapView view, RequestData input_data, ResponseData output_data);
static gboolean sanityCheckContext(ZMapView view, RequestData input_data, ResponseData output_data);
@@ -350,11 +352,20 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
{
if (sanityCheckContext(view, &input_data, &output_data))
{
- drawNewFeatures(view, &input_data, &output_data);
+ ZMapFeatureAny feature ;
- /* slice the input_data into the post_data to make the view_post_execute happy. */
- if(view->xremote_widget && input_data.edit_context)
+ if (!(feature = zMapFeatureContextFindFeatureFromFeature(view->features,
+ input_data.feature)))
{
+ g_string_append_printf(output_data.messages,
+ "Feature \"%s\" already exists in view",
+ g_quark_to_string(input_data.feature->original_id)) ;
+ output_data.code = ZMAPXREMOTE_FAILED ;
+ }
+ else if (drawNewFeatures(view, &input_data, &output_data)
+ && (view->xremote_widget && input_data.edit_context))
+ {
+ /* slice the input_data into the post_data to make the view_post_execute happy. */
PostExecuteData post_data = g_new0(PostExecuteDataStruct, 1);
post_data->action = input.common.action;
@@ -631,39 +642,41 @@ static void eraseFeatures(ZMapView view, RequestData input_data, ResponseData ou
return ;
}
-static void drawNewFeatures(ZMapView view, RequestData input_data, ResponseData output_data)
+static gboolean drawNewFeatures(ZMapView view, RequestData input_data, ResponseData output_data)
{
+ gboolean result = FALSE ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* we shouldn't need to do this..styles should be there and ok..... */
-
- zMapFeatureAnyForceModesToStyles((ZMapFeatureAny)(input_data->edit_context), NULL) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+ if (!(input_data->edit_context = zmapViewMergeInContext(view, input_data->edit_context)))
+ {
+ g_string_append(output_data->messages, "Merge of new feature into View feature context failed") ;
+ output_data->code = ZMAPXREMOTE_FAILED ;
+ }
+ else
+ {
+ zMapFeatureContextExecute((ZMapFeatureAny)(input_data->edit_context),
+ ZMAPFEATURE_STRUCT_FEATURE,
+ delete_from_list,
+ &(input_data->feature_list));
-
- input_data->edit_context = zmapViewMergeInContext(view, input_data->edit_context) ;
-
- zMapFeatureContextExecute((ZMapFeatureAny)(input_data->edit_context),
- ZMAPFEATURE_STRUCT_FEATURE,
- delete_from_list,
- &(input_data->feature_list));
+ zMapFeatureContextExecute((ZMapFeatureAny)(view->features),
+ ZMAPFEATURE_STRUCT_FEATURE,
+ mark_matching_invalid,
+ &(input_data->feature_list));
- zMapFeatureContextExecute((ZMapFeatureAny)(view->features),
- ZMAPFEATURE_STRUCT_FEATURE,
- mark_matching_invalid,
- &(input_data->feature_list));
+ output_data->code = 0;
- output_data->code = 0;
+ if (g_list_length(input_data->feature_list))
+ g_list_foreach(input_data->feature_list, draw_failed_make_message, output_data);
- if(g_list_length(input_data->feature_list))
- g_list_foreach(input_data->feature_list, draw_failed_make_message, output_data);
+ if (output_data->code == 0)
+ output_data->code = ZMAPXREMOTE_OK ;
- if(output_data->code == 0)
- output_data->code = ZMAPXREMOTE_OK;
+ output_data ->handled = TRUE ;
- output_data->handled = TRUE;
+ result = TRUE ;
+ }
- return ;
+ return result ;
}
@@ -813,8 +826,8 @@ static void populate_data_from_view(ZMapView view, RequestData xml_data)
/*
*
* <zmap action="create_feature">
- * <featureset>
- * <feature name="RP6-206I17.6-001" start="3114" end="99885" strand="-" style="Coding">
+ * <featureset name="Coding">
+ * <feature name="RP6-206I17.6-001" start="3114" end="99885" strand="-">
* <subfeature ontology="exon" start="3114" end="3505" />
* <subfeature ontology="intron" start="3505" end="9437" />
* <subfeature ontology="exon" start="9437" end="9545" />
@@ -834,8 +847,8 @@ static void populate_data_from_view(ZMapView view, RequestData xml_data)
* </zmap>
*
* <zmap action="delete_feature">
- * <featureset>
- * <feature name="U.2969591-3331416" start="87607" end="87608" strand="+" style="polyA_site" score="0.000"></feature>
+ * <featureset name="polyA_site">
+ * <feature name="U.2969591-3331416" start="87607" end="87608" strand="+"score="0.000"></feature>
* </featureset>
* </zmap>
*
@@ -1184,6 +1197,44 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
result = TRUE ;
}
+ /* We must be able to look up the column and other data for this featureset otherwise we
+ * won't know which column/style etc to use. */
+ if (result)
+ {
+ ZMapGFFSource source_data ;
+
+ if (!(source_data = g_hash_table_lookup(request_data->view->source_2_sourcedata,
+ GINT_TO_POINTER(set_id))))
+ {
+ char *err_msg ;
+
+ err_msg = g_strdup_printf("Source %s not found in view->source_2_sourcedata",
+ g_quark_to_string(set_id)) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
+ }
+ else
+ {
+ request_data->style_id = source_data->style_id ;
+
+ if (!(request_data->style = zMapFindStyle(request_data->view->orig_styles, request_data->style_id)))
+ {
+ char *err_msg ;
+
+ err_msg = g_strdup_printf("Style %s not found in view->orig_styles",
+ g_quark_to_string(request_data->style_id)) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
+ }
+ }
+ }
+
+
+
if (result)
{
@@ -1201,6 +1252,8 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
case ZMAPVIEW_REMOTE_GET_FEATURE_NAMES:
{
+ /* NOTE SURE WHY THIS IS HERE.....should be in the feature handler ?? */
+
if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "start")))
{
request_data->start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
@@ -1291,9 +1344,17 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
RequestData request_data = (RequestData)(xml_data->user_data);
ZMapFeatureAny feature_any;
ZMapStrand strand = ZMAPSTRAND_NONE;
- GQuark feature_name_q = 0, style_q = 0, style_id;
gboolean has_score = FALSE, start_not_found = FALSE, end_not_found = FALSE;
- char *feature_name, *style_name;
+
+ char *feature_name ;
+ GQuark feature_name_q = 0 ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ char *style_name ;
+ GQuark style_q = 0, style_id ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
int start = 0, end = 0, start_phase = ZMAPPHASE_NONE;
double score = 0.0;
@@ -1324,16 +1385,6 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
}
- if (result && (attr = zMapXMLElementGetAttributeByName(feature_element, "style")))
- {
- style_q = zMapXMLAttributeGetValue(attr);
- }
- else
- {
- zMapXMLParserRaiseParsingError(parser, "style is a required attribute for feature.");
- result = FALSE ;
- }
-
if (result && (attr = zMapXMLElementGetAttributeByName(feature_element, "start")))
{
start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
@@ -1411,39 +1462,34 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
if (result && !zMapXMLParserLastErrorMsg(parser))
{
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
ZMapFeatureTypeStyle style ;
style_name = (char *)g_quark_to_string(style_q);
style_id = zMapStyleCreateID(style_name);
- feature_name = (char *)g_quark_to_string(feature_name_q);
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- if (!(style = zMapFindStyle(request_data->view->orig_styles, style_id)))
- {
- char *err_msg ;
- err_msg = g_strdup_printf("Style %s not found in view->orig_styles",
- g_quark_to_string(style_id)) ;
- zMapXMLParserRaiseParsingError(parser, err_msg) ;
- g_free(err_msg) ;
- result = FALSE ;
- }
+
+
+
+ feature_name = (char *)g_quark_to_string(feature_name_q);
if (result
- && (request_data->feature
- = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
- ZMAPSTYLE_MODE_BASIC, style,
- start, end, has_score,
- score, strand, ZMAPPHASE_NONE)))
+ && (request_data->feature = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
+ ZMAPSTYLE_MODE_BASIC,
+ request_data->style,
+ start, end, has_score,
+ score, strand, ZMAPPHASE_NONE)))
{
- request_data->feature->style_id = style_id;
+ request_data->feature->style_id = request_data->style_id ;
zMapFeatureSetAddFeature(request_data->feature_set, request_data->feature);
-
/* We need to get all the source info. in here somehow.... */
zMapFeatureAddText(request_data->feature, request_data->source_id, NULL, NULL) ;
-
if (start_not_found || end_not_found)
{
request_data->feature->type = ZMAPSTYLE_MODE_TRANSCRIPT;
@@ -1782,13 +1828,23 @@ static void reportWindowMark(ZMapView view, RequestData input_data, ResponseData
{
g_string_append_printf(output_data->messages,
"<mark exists=\"true\" start=\"%d\" end=\"%d\" />", start, end) ;
+
+ output_data->code = ZMAPXREMOTE_OK ;
}
else
{
g_string_append(output_data->messages, "<mark exists=\"false\" />") ;
+
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* i'd like to return an error code but this would need sorting out... */
+
+ output_data->code = ZMAPXREMOTE_FAILED;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+ output_data->code = ZMAPXREMOTE_OK ;
}
- output_data->code = ZMAPXREMOTE_OK ;
+
return ;
}
--
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