From c46069241b7168f45d030ff20b6443da472676c2 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 16 Oct 2009 13:45:33 +0000
Subject: [PATCH] fix feature delete code, needed to access current context,
all the align/block etc copying was not correct, also add delete all features
code.
---
src/zmapView/zmapViewRemoteReceive.c | 360 +++++++++++++++++++--------
1 file changed, 260 insertions(+), 100 deletions(-)
diff --git a/src/zmapView/zmapViewRemoteReceive.c b/src/zmapView/zmapViewRemoteReceive.c
index 9ef196d32..041a607fe 100755
--- a/src/zmapView/zmapViewRemoteReceive.c
+++ b/src/zmapView/zmapViewRemoteReceive.c
@@ -29,9 +29,9 @@
* Exported functions: See zmapView_P.h
*
* HISTORY:
- * Last edited: Sep 11 18:00 2009 (edgrif)
+ * Last edited: Oct 16 14:44 2009 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
- * CVS info: $Id: zmapViewRemoteReceive.c,v 1.32 2009-09-24 12:50:32 edgrif Exp $
+ * CVS info: $Id: zmapViewRemoteReceive.c,v 1.33 2009-10-16 13:45:33 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -101,13 +101,22 @@ typedef struct
/* some operations are "read only" and hence can use the orig_context, others require edits and
* must create an edit_context to do these. */
- ZMapFeatureContext orig_context ;
- ZMapFeatureContext edit_context ;
+ /* Note that only orig_context stays the same throughout processing of a request, other elements
+ * will change if more than one align/block or whatever is specified in the request. */
+ ZMapFeatureContext orig_context ;
+ ZMapFeatureAlignment orig_align;
+ ZMapFeatureBlock orig_block;
+ ZMapFeatureSet orig_feature_set;
+ ZMapFeature orig_feature;
+
+
+ ZMapFeatureContext edit_context ;
ZMapFeatureAlignment align;
ZMapFeatureBlock block;
ZMapFeatureSet feature_set;
ZMapFeature feature;
+
GQuark source_id ;
GList *feature_list;
@@ -175,6 +184,7 @@ static gboolean xml_request_start_cb(gpointer user_data, ZMapXMLElement zmap_ele
static gboolean xml_align_start_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
static gboolean xml_block_start_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
+static gboolean xml_featureset_end_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
static gboolean xml_export_start_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement zmap_element, ZMapXMLParser parser);
@@ -183,6 +193,8 @@ static gboolean xml_return_true_cb(gpointer user_data, ZMapXMLElement zmap_eleme
static void getFeatureNames(ZMapView view, RequestData input_data, ResponseData output_data) ;
static void findUniqueCB(gpointer data, gpointer user_data) ;
static void makeUniqueListCB(gpointer key, gpointer value, gpointer user_data) ;
+static void copyAddFeature(gpointer key, gpointer value, gpointer user_data) ;
+
@@ -211,16 +223,17 @@ static ZMapXMLObjTagFunctionsStruct view_starts_G[] = {
{NULL, NULL}
};
-static ZMapXMLObjTagFunctionsStruct view_ends_G[] = {
- { "zmap", xml_return_true_cb },
- { "request", xml_return_true_cb },
- { "align", xml_return_true_cb },
- { "block", xml_return_true_cb },
- { "featureset", xml_return_true_cb },
- { "feature", xml_return_true_cb },
- { "subfeature", xml_subfeature_end_cb },
- {NULL, NULL}
-};
+static ZMapXMLObjTagFunctionsStruct view_ends_G[] =
+ {
+ { "zmap", xml_return_true_cb },
+ { "request", xml_return_true_cb },
+ { "align", xml_return_true_cb },
+ { "block", xml_return_true_cb },
+ { "featureset", xml_featureset_end_cb },
+ { "feature", xml_return_true_cb },
+ { "subfeature", xml_subfeature_end_cb },
+ {NULL, NULL}
+ } ;
/* Must match ZMapViewValidXRemoteActions */
static char *actions_G[ZMAPVIEW_REMOTE_UNKNOWN + 1] =
@@ -328,8 +341,10 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
break ;
case ZMAPVIEW_REMOTE_DELETE_FEATURE:
- eraseFeatures(view, &input_data, &output_data) ;
- break ;
+ {
+ eraseFeatures(view, &input_data, &output_data) ;
+ break ;
+ }
case ZMAPVIEW_REMOTE_CREATE_FEATURE:
{
@@ -682,7 +697,7 @@ static void delete_failed_make_message(gpointer list_data, gpointer user_data)
ZMapFeatureAny feature_any = (ZMapFeatureAny)list_data;
ResponseData response_data = (ResponseData)user_data;
- if(feature_any->struct_type == ZMAPFEATURE_STRUCT_INVALID)
+ if (feature_any->struct_type == ZMAPFEATURE_STRUCT_INVALID)
{
response_data->code = ZMAPXREMOTE_CONFLICT; /* possibly the wrong code */
g_string_append_printf(response_data->messages,
@@ -940,7 +955,7 @@ static gboolean xml_align_start_cb(gpointer user_data, ZMapXMLElement set_elemen
ZMapXRemoteParseCommandData xml_data = (ZMapXRemoteParseCommandData)user_data;
RequestData request_data = (RequestData)(xml_data->user_data);
GQuark align_id ;
- char *align_name ;
+ char *align_name = NULL ;
if (xml_data->common.action != ZMAPVIEW_REMOTE_INVALID)
{
@@ -949,27 +964,60 @@ static gboolean xml_align_start_cb(gpointer user_data, ZMapXMLElement set_elemen
align_id = zMapXMLAttributeGetValue(attr) ;
align_name = (char *)g_quark_to_string(align_id) ;
- /* look for align in context. try master and non-master ids */
- if (!(align = zMapFeatureContextGetAlignmentByID(request_data->edit_context,
- zMapFeatureAlignmentCreateID(align_name, TRUE)))
- && !(align = zMapFeatureContextGetAlignmentByID(request_data->edit_context,
- zMapFeatureAlignmentCreateID(align_name, FALSE))))
+ if (!(*align_name))
+ align_name = NULL ;
+ }
+
+ if (align_name)
+ {
+ gboolean master_align ;
+
+ request_data->orig_align = NULL ;
+ if ((request_data->orig_align
+ = zMapFeatureContextGetAlignmentByID(request_data->orig_context,
+ zMapFeatureAlignmentCreateID(align_name, TRUE))))
+ master_align = TRUE ;
+ else if ((request_data->orig_align
+ = zMapFeatureContextGetAlignmentByID(request_data->orig_context,
+ zMapFeatureAlignmentCreateID(align_name, FALSE))))
+ master_align = FALSE ;
+
+ if (!(request_data->orig_align))
{
- /* not there...create... */
- align = zMapFeatureAlignmentCreate(align_name, FALSE) ;
+ /* If we can't find the align it's a serious error and we can't carry on. */
+ char *err_msg ;
+
+ err_msg = g_strdup_printf("Unknown Align \"%s\": not found in original_context", align_name) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
}
+ else
+ {
+ /* look for align in edit context. try master and non-master ids */
+ if (!(align = zMapFeatureContextGetAlignmentByID(request_data->edit_context,
+ zMapFeatureAlignmentCreateID(align_name,
+ master_align))))
+ {
+ /* not there...create... */
+ align = zMapFeatureAlignmentCreate(align_name, FALSE) ;
+ }
- request_data->align = align ;
+ request_data->align = align ;
+ result = TRUE ;
+ }
}
else
{
- request_data->align
- = (ZMapFeatureAlignment)zMapFeatureAnyCopy((ZMapFeatureAny)(request_data->orig_context->master_align)) ;
- }
+ request_data->orig_align = request_data->orig_context->master_align ;
+ request_data->align = (ZMapFeatureAlignment)zMapFeatureAnyCopy((ZMapFeatureAny)(request_data->orig_align)) ;
- zMapFeatureContextAddAlignment(request_data->edit_context, request_data->align, FALSE) ;
+ result = TRUE ;
+ }
- result = TRUE ;
+ if (result)
+ zMapFeatureContextAddAlignment(request_data->edit_context, request_data->align, FALSE) ;
}
return result ;
@@ -983,46 +1031,81 @@ static gboolean xml_block_start_cb(gpointer user_data, ZMapXMLElement set_elemen
ZMapXRemoteParseCommandData xml_data = (ZMapXRemoteParseCommandData)user_data;
RequestData request_data = (RequestData)(xml_data->user_data);
GQuark block_id ;
+ char *block_name = NULL ;
char *block_seq ;
- if(xml_data->common.action != ZMAPVIEW_REMOTE_INVALID)
+ if (xml_data->common.action != ZMAPVIEW_REMOTE_INVALID)
{
if ((attr = zMapXMLElementGetAttributeByName(set_element, "name")))
+ {
+ block_id = zMapXMLAttributeGetValue(attr);
+ block_name = (char *)g_quark_to_string(block_id) ;
+
+ if (!(*block_name))
+ block_name = NULL ;
+ }
+
+ if (block_name)
{
int ref_start, ref_end, non_start, non_end;
ZMapStrand ref_strand, non_strand;
- block_id = zMapXMLAttributeGetValue(attr);
-
- if (zMapFeatureBlockDecodeID(block_id, &ref_start, &ref_end, &ref_strand,
- &non_start, &non_end, &non_strand))
+ if (!zMapFeatureBlockDecodeID(block_id, &ref_start, &ref_end, &ref_strand,
+ &non_start, &non_end, &non_strand))
{
- if (!(block = zMapFeatureAlignmentGetBlockByID(request_data->align, block_id)))
- {
- block_seq = (char *)g_quark_to_string(request_data->align->original_id);
- block = zMapFeatureBlockCreate(block_seq,
- ref_start, ref_end, ref_strand,
- non_start, non_end, non_strand);
- }
+ /* Bad format block name. */
+ char *err_msg ;
+
+ err_msg = g_strdup_printf("Bad Format Block name: \"%s\"", block_name) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
}
else
{
- /* Get the first one! */
- block = zMap_g_hash_table_nth(request_data->align->blocks, 0) ;
- }
+ if (!(request_data->orig_block
+ = zMapFeatureAlignmentGetBlockByID(request_data->orig_align, block_id)))
+ {
+ /* If we can't find the block it's a serious error and we can't carry on. */
+ char *err_msg ;
- request_data->block = block;
+ err_msg = g_strdup_printf("Unknown Block \"%s\": not found in original_context", block_name) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
+ }
+ else
+ {
+ if (!(block = zMapFeatureAlignmentGetBlockByID(request_data->align, block_id)))
+ {
+ block_seq = (char *)g_quark_to_string(request_data->align->original_id);
+ block = zMapFeatureBlockCreate(block_seq,
+ ref_start, ref_end, ref_strand,
+ non_start, non_end, non_strand);
+ }
+ else
+ {
+ /* Get the first one! */
+ block = zMap_g_hash_table_nth(request_data->align->blocks, 0) ;
+ }
+
+ request_data->block = block;
+ result = TRUE ;
+ }
+ }
}
else
{
/* Get the first one! */
- request_data->block
- = (ZMapFeatureBlock)zMapFeatureAnyCopy(zMap_g_hash_table_nth(request_data->orig_context->master_align->blocks, 0)) ;
+ request_data->orig_block = zMap_g_hash_table_nth(request_data->orig_context->master_align->blocks, 0) ;
+ request_data->block = (ZMapFeatureBlock)zMapFeatureAnyCopy((ZMapFeatureAny)(request_data->orig_block)) ;
+ result = TRUE ;
}
- zMapFeatureAlignmentAddBlock(request_data->align, request_data->block);
-
- result = TRUE ;
+ if (result)
+ zMapFeatureAlignmentAddBlock(request_data->align, request_data->block);
}
return result ;
@@ -1041,6 +1124,8 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
if (xml_data->common.action != ZMAPVIEW_REMOTE_INVALID)
{
+ request_data->source_id = 0 ; /* reset needed for remove features. */
+
if ((attr = zMapXMLElementGetAttributeByName(set_element, "name")))
{
ZMapGFFSet set_data ;
@@ -1054,6 +1139,7 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
set_id = zMapFeatureSetCreateID(set_name);
request_data->source_id = set_id ;
+ /* Check to see if we can find this source name in any of the featuresets. */
if (!(set_data = g_hash_table_lookup(request_data->view->source_2_featureset,
GINT_TO_POINTER(set_id))))
{
@@ -1074,6 +1160,10 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
/* Check we can find the _featureset_ id..... */
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* This is surely the wrong test..... */
+
if (result && g_hash_table_lookup(request_data->view->featureset_2_stylelist,
GUINT_TO_POINTER(featureset_id)) == NULL)
{
@@ -1087,82 +1177,124 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
result = FALSE ;
}
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
if (result)
{
- /* Make sure this feature set is a child of the block........ */
- if (!(feature_set = zMapFeatureBlockGetSetByID(request_data->block, featureset_id)))
+ if (!(request_data->orig_feature_set
+ = zMapFeatureBlockGetSetByID(request_data->orig_block, featureset_id)))
{
- feature_set = zMapFeatureSetCreate(featureset_name, NULL);
- zMapFeatureBlockAddFeatureSet(request_data->block, feature_set);
- }
+ /* If we can't find the featureset it's a serious error and we can't carry on. */
+ char *err_msg ;
+ err_msg = g_strdup_printf("Unknown FeatureSet \"%s\": not found in original_block",
+ featureset_name) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
+
+ result = FALSE ;
+ }
+ else
+ {
+ /* Make sure this feature set is a child of the block........ */
+ if (!(feature_set = zMapFeatureBlockGetSetByID(request_data->block, featureset_id)))
+ {
+ feature_set = zMapFeatureSetCreate(featureset_name, NULL);
+ zMapFeatureBlockAddFeatureSet(request_data->block, feature_set);
+ }
- request_data->feature_set = feature_set;
+ request_data->feature_set = feature_set;
- request_data->edit_context->feature_set_names
- = g_list_append(request_data->edit_context->feature_set_names, GINT_TO_POINTER(featureset_id)) ;
+ request_data->edit_context->feature_set_names
+ = g_list_append(request_data->edit_context->feature_set_names, GINT_TO_POINTER(featureset_id)) ;
+ }
}
- }
- else
- {
- /* Get the first one! No one in their right mind should leave this to chance.... */
- request_data->feature_set = zMap_g_hash_table_nth(request_data->block->feature_sets, 0) ;
+ else
+ {
+ /* Get the first one! No one in their right mind should leave this to chance.... */
+ request_data->orig_feature_set = zMap_g_hash_table_nth(request_data->orig_block->feature_sets, 0) ;
+ request_data->feature_set
+ = (ZMapFeatureSet)zMapFeatureAnyCopy((ZMapFeatureAny)(request_data->orig_feature_set)) ;
- result = TRUE ;
+ result = TRUE ;
+ }
}
-
- switch (xml_data->common.action)
+ if (result)
{
- case ZMAPVIEW_REMOTE_LOAD_FEATURES:
- {
- request_data->feature_sets = g_list_append(request_data->feature_sets, GINT_TO_POINTER(set_id)) ;
-
- break;
- }
-
- case ZMAPVIEW_REMOTE_GET_FEATURE_NAMES:
- {
- if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "start")))
+ switch (xml_data->common.action)
+ {
+ case ZMAPVIEW_REMOTE_LOAD_FEATURES:
{
- request_data->start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
- (char **)NULL, 10);
+ request_data->feature_sets = g_list_append(request_data->feature_sets, GINT_TO_POINTER(set_id)) ;
+
+ break;
}
- else
+
+ case ZMAPVIEW_REMOTE_GET_FEATURE_NAMES:
{
- zMapXMLParserRaiseParsingError(parser, "start is a required attribute for feature.");
- result = FALSE ;
- }
+ if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "start")))
+ {
+ request_data->start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ (char **)NULL, 10);
+ }
+ else
+ {
+ zMapXMLParserRaiseParsingError(parser, "start is a required attribute for feature.");
+ result = FALSE ;
+ }
- if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "end")))
- {
- request_data->end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
- (char **)NULL, 10);
- }
- else
- {
- zMapXMLParserRaiseParsingError(parser, "end is a required attribute for feature.");
- result = FALSE ;
- }
-
- break;
- }
-
+ if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "end")))
+ {
+ request_data->end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ (char **)NULL, 10);
+ }
+ else
+ {
+ zMapXMLParserRaiseParsingError(parser, "end is a required attribute for feature.");
+ result = FALSE ;
+ }
+ break;
+ }
- default:
- break ;
+ default:
+ break ;
+ }
}
+ }
+ return result ;
+}
+static gboolean xml_featureset_end_cb(gpointer user_data, ZMapXMLElement set_element,
+ ZMapXMLParser parser)
+{
+ gboolean result = FALSE ;
+ ZMapXRemoteParseCommandData xml_data = (ZMapXRemoteParseCommandData)user_data;
+ RequestData request_data = (RequestData)(xml_data->user_data);
+ if (xml_data->common.action != ZMAPVIEW_REMOTE_INVALID)
+ {
+ /* Only do stuff if a feature set was found and has features. */
+ if (request_data->feature_set && request_data->feature_set->features)
+ {
+ /* If deleting and no feature was specified then delete them all. NOTE that if
+ * a source name was given then only features from _that_ source are deleted, not
+ * all features in the column. */
+ if (xml_data->common.action == ZMAPVIEW_REMOTE_DELETE_FEATURE && !(request_data->feature_list))
+ {
+ g_hash_table_foreach(request_data->orig_feature_set->features,
+ copyAddFeature, request_data) ;
+ }
+ }
}
return result ;
}
+
static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_element,
ZMapXMLParser parser)
{
@@ -1789,3 +1921,31 @@ static void makeUniqueListCB(gpointer key, gpointer value, gpointer user_data)
}
+
+/* A GHFunc() to copy a feature and add it to the supplied list. */
+static void copyAddFeature(gpointer key, gpointer value, gpointer user_data)
+{
+ ZMapFeature feature = (ZMapFeature)value ;
+ RequestData request_data = (RequestData)user_data ;
+ ZMapFeatureAny feature_any ;
+
+ /* Only add to this list if there is no source name or the feature and source
+ * names match, caller will have given a source name. */
+ if (!(request_data->source_id) || feature->source_id == request_data->source_id)
+ {
+ /* THIS DOESN'T DO A DEEP ENOUGH COPY, WE FAIL LATER FOR SOME ACTIONS
+ * BECAUSE STUFF LIKE THE HOMOL DATA IS NOT COPIED SO WE CAN'T FIND
+ * THE FEATURE IN THE HASH. */
+ if ((feature_any = zMapFeatureAnyCopy((ZMapFeatureAny)feature)))
+ {
+ ZMapFeatureAny feature_copy ;
+
+ zMapFeatureSetAddFeature(request_data->feature_set, (ZMapFeature)feature_any) ;
+
+ feature_copy = zMapFeatureAnyCopy(feature_any) ;
+ request_data->feature_list = g_list_append(request_data->feature_list, feature_copy) ;
+ }
+ }
+
+ return ;
+}
--
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