From 3bcc18e1aef6eb6c819d4d7aea9f3c9a4c74be04 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 19 Jul 2004 10:13:36 +0000
Subject: [PATCH] try to fix up some cvs funniness, cvs seems to have lost that
I am editting stuff.
---
src/zmapServer/das/README | 68 ++++++++++++++++++++++++++++++++
src/zmapServer/das/dasServer_P.h | 8 +++-
src/zmapServer/das/saxparse.h | 6 +--
src/zmapServer/das/saxparse_P.h | 23 +++++++++--
4 files changed, 97 insertions(+), 8 deletions(-)
diff --git a/src/zmapServer/das/README b/src/zmapServer/das/README
index 208a03847..a05505da4 100755
--- a/src/zmapServer/das/README
+++ b/src/zmapServer/das/README
@@ -19,3 +19,71 @@ For example to get a list of types of data you could issue this request:
http://dev.acedb.org/das/wormbase/1/type
+
+
+
+Some example queries and their replies:
+
+
+http://dev.wormbase.org/das/wormbase/1/feature/processed_transcript:curated/CDS:2L52.1?format=gff
+
+
+<?xml version="1.0" standalone="yes"?>
+
+<FEATURELIST
+ xmlns="http://www.biodas.org/ns/das/2.00"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xml:base="http://dev.wormbase.org/das/wormbase/1/feature/"
+ format="gff">
+II curated processed_transcript 1867 4663 . + . ID=CDS:2L52.1;Note=Zinc+finger%2C+C2H2+type;Note=Zinc+finger%2C+C2H2+type;Gene=WBGene00007063;link=http%3A%2F%2Flocalhost%2Fdb%2Fget%3Fname%3D2L52.1%3Bclass%3DCDS
+II curated coding_exon 1867 1911 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2506 2694 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2738 2888 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2931 3036 . + 2 Parent=CDS:2L52.1
+II curated coding_exon 3406 3552 . + 1 Parent=CDS:2L52.1
+II curated coding_exon 3802 3984 . + 1 Parent=CDS:2L52.1
+II curated coding_exon 4201 4663 . + 1 Parent=CDS:2L52.1
+</FEATURELIST>
+
+
+
+http://dev.wormbase.org/das/wormbase/1/feature/processed_transcript:curated/CDS:2L52.1?format=gff3
+
+<?xml version="1.0" standalone="yes"?>
+
+<FEATURELIST
+ xmlns="http://www.biodas.org/ns/das/2.00"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xml:base="http://dev.wormbase.org/das/wormbase/1/feature/"
+ format="gff3">
+II curated processed_transcript 1867 4663 . + . ID=CDS:2L52.1;Note=Zinc+finger%2C+C2H2+type;Note=Zinc+finger%2C+C2H2+type;Gene=WBGene00007063;link=http%3A%2F%2Flocalhost%2Fdb%2Fget%3Fname%3D2L52.1%3Bclass%3DCDS
+II curated coding_exon 1867 1911 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2506 2694 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2738 2888 . + 0 Parent=CDS:2L52.1
+II curated coding_exon 2931 3036 . + 2 Parent=CDS:2L52.1
+II curated coding_exon 3406 3552 . + 1 Parent=CDS:2L52.1
+II curated coding_exon 3802 3984 . + 1 Parent=CDS:2L52.1
+II curated coding_exon 4201 4663 . + 1 Parent=CDS:2L52.1
+</FEATURELIST>
+
+
+
+
+
+http://dev.wormbase.org/das/wormbase/1/feature/processed_transcript:curated/CDS:B0250.1?format=gff
+
+
+<?xml version="1.0" standalone="yes"?>
+
+<FEATURELIST
+ xmlns="http://www.biodas.org/ns/das/2.00"
+ xmlns:xlink="http://www.w3.org/1999/xlink"
+ xml:base="http://dev.wormbase.org/das/wormbase/1/feature/"
+ format="gff">
+V curated processed_transcript 20477735 20478859 . + . ID=CDS:B0250.1;Note=Ribosomal+Proteins+L2;Note=rpl-2;Note=Ribosomal+Proteins+L2;Note=rpl-2;Confirmed_by=EST;Confirmed_by=EST;Gene=WBGene00004413;link=http%3A%2F%2Flocalhost%2Fdb%2Fget%3Fname%3DB0250.1%3Bclass%3DCDS
+V curated 3_UTR 20478811 20478859 . + . Parent=CDS:B0250.1
+V curated 5_UTR 20477735 20477745 . + . Parent=CDS:B0250.1
+V curated coding_exon 20477746 20478025 . + 0 Parent=CDS:B0250.1
+V curated coding_exon 20478252 20478362 . + 2 Parent=CDS:B0250.1
+V curated coding_exon 20478419 20478810 . + 2 Parent=CDS:B0250.1
+</FEATURELIST>
diff --git a/src/zmapServer/das/dasServer_P.h b/src/zmapServer/das/dasServer_P.h
index 47687e434..320d021f9 100755
--- a/src/zmapServer/das/dasServer_P.h
+++ b/src/zmapServer/das/dasServer_P.h
@@ -24,9 +24,9 @@
*
* Description:
* HISTORY:
- * Last edited: Mar 19 10:27 2004 (edgrif)
+ * Last edited: Jul 2 10:40 2004 (edgrif)
* Created: Thu Mar 18 12:02:52 2004 (edgrif)
- * CVS info: $Id: dasServer_P.h,v 1.1 2004-03-22 13:45:20 edgrif Exp $
+ * CVS info: $Id: dasServer_P.h,v 1.2 2004-07-19 10:13:36 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef DAS_SERVER_P_H
@@ -57,6 +57,10 @@ typedef struct _DasServerStruct
char *last_errmsg ; /* The general das msg stuf, could be
curl could be my code. */
+ /* this will not stay like this, it should more properly be a union of types of data that might
+ * be returned.... */
+ void *data ;
+
} DasServerStruct, *DasServer ;
diff --git a/src/zmapServer/das/saxparse.h b/src/zmapServer/das/saxparse.h
index 842099912..7ac418a7f 100755
--- a/src/zmapServer/das/saxparse.h
+++ b/src/zmapServer/das/saxparse.h
@@ -24,9 +24,9 @@
*
* Description:
* HISTORY:
- * Last edited: Mar 18 15:29 2004 (edgrif)
+ * Last edited: Jul 2 09:32 2004 (edgrif)
* Created: Wed Jan 28 16:17:58 2004 (edgrif)
- * CVS info: $Id: saxparse.h,v 1.1 2004-03-22 13:45:20 edgrif Exp $
+ * CVS info: $Id: saxparse.h,v 1.2 2004-07-19 10:13:36 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef SAXPARSE_H
@@ -36,7 +36,7 @@
typedef struct SaxParserStructName *SaxParser ;
-SaxParser saxCreateParser(void) ;
+SaxParser saxCreateParser(void *user_data) ;
gboolean saxParseData(SaxParser parser, void *data, int size) ;
diff --git a/src/zmapServer/das/saxparse_P.h b/src/zmapServer/das/saxparse_P.h
index 3decf168f..013da0d58 100755
--- a/src/zmapServer/das/saxparse_P.h
+++ b/src/zmapServer/das/saxparse_P.h
@@ -24,9 +24,9 @@
*
* Description:
* HISTORY:
- * Last edited: Mar 19 09:30 2004 (edgrif)
+ * Last edited: Jul 2 14:55 2004 (edgrif)
* Created: Wed Jan 28 16:17:58 2004 (edgrif)
- * CVS info: $Id: saxparse_P.h,v 1.1 2004-03-22 13:45:20 edgrif Exp $
+ * CVS info: $Id: saxparse_P.h,v 1.2 2004-07-19 10:13:36 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef SAXPARSE_P_H
@@ -37,13 +37,30 @@
typedef enum {SAXPARSE_NOWHERE, SAXPARSE_STARTDOC,
SAXPARSE_START, SAXPARSE_INSIDE, SAXPARSE_END, SAXPARSE_ENDDOC} SaxParseState ;
+/* For an XML tag holds the element name and attributes, i.e. <element_name attributes>
+ * Used to track which tag we are processing. */
+typedef struct SaxTagStructName
+{
+ char *element_name ;
+
+ char **attributes ;
+} SaxTagStruct, *SaxTag ;
+
+
typedef struct SaxParserStructName
{
XML_Parser p ;
- GQueue *tag_stack ;
+ gboolean debug ;
+
+ GQueue *tag_stack ; /* Stack of SaxTagStruct */
int Depth ;
+
GString *content ;
+
char *last_errmsg ;
+
+ void *user_data ; /* Caller stores any data they need here. */
+
} SaxParserStruct ;
--
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