From 12f593761faaf9a1003bcc6c4e4b6c25bfdcdfaf Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 13 Nov 2006 16:56:52 +0000
Subject: [PATCH] FeatureCvTerm updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4914 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 97 +++++++++++++++----
1 file changed, 76 insertions(+), 21 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 7855330ef..6481b65cb 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -44,6 +44,8 @@ import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
+import org.gmod.schema.pub.PubDbXRef;
+import org.gmod.schema.pub.Pub;
import java.sql.*;
import java.text.SimpleDateFormat;
@@ -103,7 +105,8 @@ public class DatabaseDocument extends Document
// controlled vocabulary
/** controlled_curation controlled vocabulary */
- private static String CONTROLLED_CURATION_TAG_CVNAME = "CC_genedb_controlledcuration";
+ private static String CONTROLLED_CURATION_TAG_CVNAME =
+ "CC_genedb_controlledcuration";
/** product controlled vocabulary */
private static String PRODUCTS_TAG_CVNAME = "genedb_products";
@@ -492,9 +495,11 @@ public class DatabaseDocument extends Document
Hashtable synonym = getAllFeatureSynonyms(dao, null);
Hashtable featureCvTerms = getFeatureCvTermsByFeature(dao);
+ List pubDbXRefs= dao.getPubDbXRef();
+
if(featureCvTerms != null)
- System.out.println("\n\n"+featureCvTerms.size()+"\n\n");
+ System.out.println("\n\n"+featureCvTerms.size()+" "+pubDbXRefs.size()+"\n\n");
// create gff byte stream
for(int i = 0; i < feature_size; i++)
@@ -513,7 +518,7 @@ public class DatabaseDocument extends Document
chadoToGFF(feat, parentFeature.getUniqueName(),
dbxrefs, synonym, featureCvTerms,
- id_store, dao,
+ pubDbXRefs, id_store, dao,
feat.getFeatureLoc(), this_buff);
if( i%10 == 0 || i == feature_size-1)
@@ -580,6 +585,20 @@ public class DatabaseDocument extends Document
return featureCvTerms;
}
+ private static PubDbXRef getPubDbXRef(final List pubDbXRefs,
+ final int pubId)
+ {
+ PubDbXRef pubDbXRef;
+ for(int i=0; i<pubDbXRefs.size(); i++)
+ {
+ pubDbXRef = (PubDbXRef)pubDbXRefs.get(i);
+ if(pubDbXRef.getPub().getPubId() == pubId)
+ return pubDbXRef;
+ }
+
+ return null;
+ }
+
/**
* Use by the gene editor to retrieve the gene and related
* features
@@ -623,7 +642,7 @@ public class DatabaseDocument extends Document
ByteBuffer buff = new ByteBuffer();
- chadoToGFF(feature, null, null, null, null, null, dao,
+ chadoToGFF(feature, null, null, null, null, null, null, dao,
featureloc, buff);
// get children of gene
@@ -644,7 +663,7 @@ public class DatabaseDocument extends Document
FeatureLoc loc = getFeatureLoc(new Vector(
transcript.getFeatureLocsForFeatureId()), src_id);
chadoToGFF(transcript, feature.getUniqueName(), null,
- null, null, id_store, dao, loc, buff);
+ null, null, null, id_store, dao, loc, buff);
// get children of transcript - exons and pp
List transcipt_relations = new Vector(
@@ -664,7 +683,7 @@ public class DatabaseDocument extends Document
loc = getFeatureLoc(
new Vector(child.getFeatureLocsForFeatureId()),src_id);
chadoToGFF(child, transcript.getUniqueName(), null,
- null, null, id_store, dao, loc, buff);
+ null, null, null, id_store, dao, loc, buff);
}
}
@@ -687,6 +706,7 @@ public class DatabaseDocument extends Document
final Hashtable dbxrefs,
final Hashtable synonym,
final Hashtable featureCvTerms,
+ final List pubDbXRefs,
final Hashtable id_store,
final GmodDAO dao,
final FeatureLoc featureloc,
@@ -867,26 +887,49 @@ public class DatabaseDocument extends Document
if(cvterm.getCv().getName().equals(CONTROLLED_CURATION_TAG_CVNAME))
{
- int cvtermId = feature_cvterm.getCvTerm().getCvTermId();
- String cvName = getCvTerm(cvtermId, dao).getCv().getName();
+ //int cvtermId = feature_cvterm.getCvTerm().getCvTermId();
+ //String cvName = getCvTerm(cvtermId, dao).getCv().getName();
+ //this_buff.append("cv="+cvName+"%3B");
+ //this_buff.append("db_xref="+dbXRef.getDb().getName() + ":"
+ // + dbXRef.getAccession() + "%3B");
this_buff.append("controlled_curation=");
this_buff.append("term="+feature_cvterm.getCvTerm().getName()+"%3B");
- this_buff.append("cv="+cvName+"%3B");
- this_buff.append("db_xref="+dbXRef.getDb().getName() + ":"
- + dbXRef.getAccession() + "%3B");
+ // PMID
+ if(feature_cvterm.getPub().getUniqueName() != null &&
+ !feature_cvterm.getPub().getUniqueName().equals("NULL"))
+ {
+ Pub pub = feature_cvterm.getPub();
+ PubDbXRef pubDbXRef = getPubDbXRef(pubDbXRefs,
+ pub.getPubId());
+
+ if(pubDbXRef == null ||
+ !pub.getUniqueName().endsWith(pubDbXRef.getDbXRef().getAccession()))
+ {
+ JOptionPane.showMessageDialog(null, "Cannot find pub_dbxref for:\n"+
+ feature_cvterm.getPub().getUniqueName(),
+ "Database Error",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ this_buff.append("db_xref="+
+ pub.getUniqueName()+ "%3B");
+ }
- List feature_cvtermprops = (List)feature_cvterm.getFeatureCvTermProps();
- for(int i=0; i<feature_cvtermprops.size(); i++)
+ List feature_cvtermprops = (List) feature_cvterm.getFeatureCvTermProps();
+ for(int i = 0; i < feature_cvtermprops.size(); i++)
{
- FeatureCvTermProp feature_cvtermprop = (FeatureCvTermProp)feature_cvtermprops.get(i);
- this_buff.append(getCvtermName(feature_cvtermprop.getCvTerm().getCvTermId(), dao));
+ FeatureCvTermProp feature_cvtermprop =
+ (FeatureCvTermProp)feature_cvtermprops.get(i);
+ this_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
+ .getCvTermId(), dao));
this_buff.append("=");
this_buff.append(feature_cvtermprop.getValue());
- if(i<feature_cvtermprops.size())
+ if(i < feature_cvtermprops.size())
this_buff.append("%3B");
}
+
this_buff.append(";");
}
else if(cvterm.getCv().getName().equals(PRODUCTS_TAG_CVNAME))
@@ -916,16 +959,21 @@ public class DatabaseDocument extends Document
this_buff.append("db_xref="+dbXRef.getDb().getName() + ":"
+ dbXRef.getAccession() + "%3B");
- List feature_cvtermprops = (List)feature_cvterm.getFeatureCvTermProps();
- for(int i=0; i<feature_cvtermprops.size(); i++)
+
+ List feature_cvtermprops = (List)feature_cvterm
+ .getFeatureCvTermProps();
+ for(int i = 0; i < feature_cvtermprops.size(); i++)
{
- FeatureCvTermProp feature_cvtermprop = (FeatureCvTermProp)feature_cvtermprops.get(i);
- this_buff.append(getCvtermName(feature_cvtermprop.getCvTerm().getCvTermId(), dao));
+ FeatureCvTermProp feature_cvtermprop =
+ (FeatureCvTermProp)feature_cvtermprops.get(i);
+ this_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
+ .getCvTermId(), dao));
this_buff.append("=");
this_buff.append(feature_cvtermprop.getValue());
- if(i<feature_cvtermprops.size())
+ if(i < feature_cvtermprops.size())
this_buff.append("%3B");
}
+
this_buff.append(";");
}
}
@@ -1165,6 +1213,13 @@ public class DatabaseDocument extends Document
GmodDAO dao = null;
dao = getDAO();
schema_list = dao.getOrganisms();
+
+
+/* Organism o = new Organism();
+ o.setCommonName("web");
+ schema_list.add(o);*/
+
+
Iterator it = schema_list.iterator();
db = new Hashtable();
--
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