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[Obo-svn-commit] SF.net SVN: obo: [1670] phenote/trunk
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From: <azu...@us...> - 2008-03-31 16:42:20
|
Revision: 1670
http://obo.svn.sourceforge.net/obo/?rev=1670&view=rev
Author: azurebrd
Date: 2008-03-31 09:42:13 -0700 (Mon, 31 Mar 2008)
Log Message:
-----------
Interaction for phenote works, although person.obo is not loading completely
(e.g. Paul Sternberg and Tuco are missing)
Modified Paths:
--------------
phenote/trunk/conf/worm-interaction.cfg
phenote/trunk/src/java/phenote/dataadapter/worm/WormInteractionAdapter.java
Modified: phenote/trunk/conf/worm-interaction.cfg
===================================================================
--- phenote/trunk/conf/worm-interaction.cfg 2008-03-28 22:25:08 UTC (rev 1669)
+++ phenote/trunk/conf/worm-interaction.cfg 2008-03-31 16:42:13 UTC (rev 1670)
@@ -26,14 +26,16 @@
<field name="Object Name" datatag="Name" warnIfNull="true" enable="true" groups="default"/>
<field name="Effector" datatag="Effector" enable="true" isList="true">
- <ontology name="Effector" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>
+ <!--<ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>-->
+ <ontology name="Effector" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/>
</field>
<field name="tor Variation" datatag="torVariation" enable="true" groups="default"/>
<field name="tor Transgene" datatag="torTransgene" enable="true" groups="default"/>
<field name="tor Remark" datatag="torRemark" enable="true" groups="default"/>
<field name="Effected" datatag="Effector" enable="true" isList="true">
- <ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>
+ <!--<ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>-->
+ <ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/>
</field>
<field name="ted Variation" datatag="tedVariation" enable="true" groups="default"/>
<field name="ted Transgene" datatag="tedTransgene" enable="true" groups="default"/>
@@ -44,19 +46,22 @@
<ontology name="Type" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/interaction_type.obo"/>
</field>
<field name="Phenotype" datatag="Phenotype" enable="true" isList="true">
- <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi?short=short"/>
+ <!--<ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi?short=short"/> -->
+ <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/>
</field>
<field name="RNAi" datatag="RNAi" enable="true" groups="default"/>
<field name="Remark" datatag="Remark" enable="true" groups="default"/>
<field name="Pub" datatag="Pub" enable="true" groups="default">
- <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi?short=5"/>
+ <!--<ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi?short=5"/>-->
+ <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/>
</field>
<field name="Curator" enable="true">
- <ontology name="Curator" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator.obo"/>
+ <ontology name="Curator" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator_interaction.obo"/>
</field>
<field name="Person" datatag="Person" enable="true" groups="default" isList="true">
- <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi?short=5"/>
+ <!--<ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi?short=5"/>-->
+ <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>
</field>
<field name="Other Evidence" datatag="OtherEvidence" enable="true" groups="default"/>
<!-- <constraint className="phenote.dataadapter.worm.WormConstraint"/>-->
Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormInteractionAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormInteractionAdapter.java 2008-03-28 22:25:08 UTC (rev 1669)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormInteractionAdapter.java 2008-03-31 16:42:13 UTC (rev 1670)
@@ -65,42 +65,23 @@
if (joinkey == null) continue;
System.out.println("Delete "+joinkey+" end");
String blank = "";
- String postgres_table = "app_type"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_tempname"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_paper"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_person"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_laboratory"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_intx_desc"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_nbp"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_curator"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_not"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_term"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_phen_remark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_anat_term"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_entity"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_quality"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_suggested"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_lifestage"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_nature"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_func"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_temperature"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_treatment"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_penetrance"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_percent"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_range_start"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_range_end"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
-// postgres_table = "app_quantity_remark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
-// postgres_table = "app_quantity"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_heat_sens"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_heat_degree"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_cold_sens"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_cold_degree"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_mat_effect"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_pat_effect"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_haplo"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_genotype"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_strain"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
- postgres_table = "app_obj_remark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ String postgres_table = "int_name"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_effector"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_torvariation"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_tortransgene"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_torremark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_effected"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_tedvariation"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_tedtransgene"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_tedremark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_type"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_phenotype"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_rnai"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_remark"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_paper"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_curator"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_person"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
+ postgres_table = "int_otherevi"; updateNormalField(c, s, joinkey, postgres_table, postgres_table, blank);
}
} catch (Exception e) {
System.out.println("Could not delete character: " + e);
@@ -112,7 +93,7 @@
try { ps = c.prepareStatement("INSERT INTO "+postgres_table+"_hst VALUES (?, ?)"); ps.setString(1, joinkey); ps.setString(2, value); }
catch (SQLException se) {
System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
+ try { ps.executeUpdate(); }
catch (SQLException se) { System.out.println("We got an exception while executing a history insert in updatePostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); }
String pgisnull = "null";
@@ -123,49 +104,27 @@
try { ps = c.prepareStatement("INSERT INTO "+postgres_table+" VALUES (?, ?)"); ps.setString(1, joinkey); ps.setString(2, value); }
catch (SQLException se) {
System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
+ try { ps.executeUpdate(); }
catch (SQLException se) { System.out.println("We got an exception while executing an insert update in updatePostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); } }
else { // some value in postgres, update it
// System.out.println("UPDATING "+postgres_table+" VALUES "+joinkey+" and "+value+" with postgres_value "+postgres_value+" end");
try { ps = c.prepareStatement("UPDATE "+postgres_table+" SET "+postgres_table+" = ? WHERE joinkey = '"+joinkey+"'"); ps.setString(1, value); }
catch (SQLException se) {
System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
+ try { ps.executeUpdate(); }
catch (SQLException se) { System.out.println("We got an exception while executing a data update in updatePostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); }
- try { ps = c.prepareStatement("UPDATE "+postgres_table+" SET app_timestamp = CURRENT_TIMESTAMP WHERE joinkey = '"+joinkey+"'"); }
+ try { ps = c.prepareStatement("UPDATE "+postgres_table+" SET int_timestamp = CURRENT_TIMESTAMP WHERE joinkey = '"+joinkey+"'"); }
catch (SQLException se) {
System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
+ try { ps.executeUpdate(); }
catch (SQLException se) { System.out.println("We got an exception while executing a timestamp update in updatePostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); } }
} // private void updatePostgresVal(String postgres_table, String joinkey, int colI, String value)
- private void insertPostgresHistVal(Connection c, Statement s, String postgres_table, String joinkey, String value) {
- Integer hasMatch = 0;
- ResultSet rs = null;
- System.out.println("SELECT joinkey FROM "+postgres_table+"_hst WHERE joinkey = '"+joinkey+"' AND "+postgres_table+"_hst = '"+value+"' ");
- try { rs = s.executeQuery("SELECT joinkey FROM "+postgres_table+"_hst WHERE joinkey = '"+joinkey+"' AND "+postgres_table+"_hst = '"+value+"' "); }
- catch (SQLException se) {
- System.out.println("We got an exception while executing our "+postgres_table+" query: that probably means our column SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { if (rs.next()) { hasMatch++; } }
- // get the next highest number joinkey for that character
- catch (SQLException se) {
- System.out.println("We got an exception while getting a insertPostgresHistVal joinkey "+joinkey+" result:this shouldn't happen: we've done something really bad.");
- se.printStackTrace(); System.exit(1); }
- if (hasMatch == 0) {
- PreparedStatement ps = null; // intialize postgres insert
- System.out.println("INSERT INTO "+postgres_table+"_hst VALUES "+joinkey+" and "+value+" end");
- try { ps = c.prepareStatement("INSERT INTO "+postgres_table+"_hst VALUES (?, ?)"); ps.setString(1, joinkey); ps.setString(2, value); }
- catch (SQLException se) {
- System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
- try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
- catch (SQLException se) { System.out.println("We got an exception while executing a history insert in insertPostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); } } }
-
-
private String queryPostgresCharacterNull(Statement s, String postgres_table, String joinkey) {
// see if the postgres value corresponding to a phenote cell has an entry at all (@row) ; returns ``null'' if no row
String default_value = null;
ResultSet rs = null; // intialize postgres query result
- try { rs = s.executeQuery("SELECT * FROM "+postgres_table+" WHERE joinkey = '"+joinkey+"' ORDER BY app_timestamp"); }
+ try { rs = s.executeQuery("SELECT * FROM "+postgres_table+" WHERE joinkey = '"+joinkey+"' ORDER BY int_timestamp"); }
catch (SQLException se) {
System.out.println("We got an exception while executing our "+postgres_table+" joinkey: that probably means our term SQL is invalid"); se.printStackTrace(); System.exit(1); }
try { while (rs.next()) { default_value = rs.getString(2); } } // assign the new term value
@@ -185,7 +144,7 @@
if (postgres_value.equals(pgisnull)) { pg_value = ""; } // pg_value converts postgres null into blank to check against tag value
if (pg_value.equals(tag_value)) {
//System.out.println("table "+postgres_table+" joinkey "+joinkey+" has equal values");
-} else { updatePostgresVal(c, postgres_table, postgres_value, joinkey, tag_value); } // pass the pgisnull string if pg value is null
+ } else { updatePostgresVal(c, postgres_table, postgres_value, joinkey, tag_value); } // pass the pgisnull string if pg value is null
System.out.println( tag_name+" : "+tag_value+" end.");
}
@@ -194,7 +153,8 @@
StringBuilder sb = new StringBuilder(); Integer loopcount = 0;
CharFieldValue list = chr.getValue(chr.getCharFieldForName(tag_name));
List<CharFieldValue> valList = list.getCharFieldValueList();
- for (CharFieldValue kid : valList) { String kidId = kid.getID(); loopcount++; if (loopcount > 1) { sb.append(","); } sb.append("\"").append(kidId).append("\""); }
+// for (CharFieldValue kid : valList) { String kidId = kid.getID(); loopcount++; if (loopcount > 1) { sb.append(","); } sb.append("\"").append(kidId).append("\""); }
+ for (CharFieldValue kid : valList) { String kidId = kid.getID(); loopcount++; if (loopcount > 1) { sb.append("|"); } sb.append(kidId); }
if (sb != null) { String tag_value = sb.toString(); updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value); } }
catch (Exception e) {
System.out.println("Could not get terms from character in updateListField : " + e); e.printStackTrace(); }
@@ -227,36 +187,50 @@
System.out.println("We got an exception while getting a column/term joinkey "+joinkey+" result:this shouldn't happen: we've done something really bad.");
se.printStackTrace(); System.exit(1); } }
//System.out.println("joinkey "+joinkey+" end");
-
chr.setValue("PgdbId",joinkey); // assign the postgres database ID
String postgres_table = "int_name"; String tag_name = "Name"; String tag_value = chr.getValueString(tag_name);
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
- postgres_table = "int_paper"; tag_name = "Pub"; tag_value = "";
- if ( chr.hasValue(tag_name) ) { tag_value = chr.getTerm(tag_name).getID(); }
+ postgres_table = "int_effector"; tag_name = "Effector";
+ updateListField(c, s, joinkey, postgres_table, tag_name, chr);
+ postgres_table = "int_torvariation"; tag_name = "tor Variation"; tag_value = chr.getValueString(tag_name);
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
-System.out.println("paper tag_value "+tag_value+" for postgres");
- postgres_table = "int_person"; tag_name = "Person";
+ postgres_table = "int_tortransgene"; tag_name = "tor Transgene"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_torremark"; tag_name = "tor Remark"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_effected"; tag_name = "Effected";
updateListField(c, s, joinkey, postgres_table, tag_name, chr);
- postgres_table = "int_curator"; tag_name = "Curator"; tag_value = "";
- if ( chr.hasValue(tag_name) ) { tag_value = chr.getTerm(tag_name).getID(); }
+ postgres_table = "int_tedvariation"; tag_name = "ted Variation"; tag_value = chr.getValueString(tag_name);
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_tedtransgene"; tag_name = "ted Transgene"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_tedremark"; tag_name = "ted Remark"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_type"; tag_name = "Interaction Type"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
postgres_table = "int_phenotype"; tag_name = "Phenotype";
updateListField(c, s, joinkey, postgres_table, tag_name, chr);
+ postgres_table = "int_rnai"; tag_name = "RNAi"; tag_value = chr.getValueString(tag_name);
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
postgres_table = "int_remark"; tag_name = "Remark"; tag_value = chr.getValueString(tag_name);
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
- postgres_table = "int_rnai"; tag_name = "RNAi"; tag_value = chr.getValueString(tag_name);
+ postgres_table = "int_paper"; tag_name = "Pub"; tag_value = "";
+ if ( chr.hasValue(tag_name) ) { tag_value = chr.getTerm(tag_name).getID(); }
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+//System.out.println("paper tag_value "+tag_value+" for postgres");
+ postgres_table = "int_curator"; tag_name = "Curator"; tag_value = "";
+ if ( chr.hasValue(tag_name) ) { tag_value = chr.getTerm(tag_name).getID(); }
+ updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
+ postgres_table = "int_person"; tag_name = "Person";
+ updateListField(c, s, joinkey, postgres_table, tag_name, chr);
postgres_table = "int_otherevi"; tag_name = "Other Evidence"; tag_value = chr.getValueString(tag_name);
updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
-
} catch (Exception e) {
System.out.println("Could not get terms from character: " + e);
e.printStackTrace(); // helpful for debugging
}
-
} // for (CharacterI chr : charList.getList())
-
delete(c, s);
} // public void commit(CharacterListI charList)
@@ -342,7 +316,10 @@
postgres_table = "int_effector"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
- if (postgres_value == "") { } else { c1.setValue("Effector",postgres_value); } // assign the queried value
+ if (postgres_value == "") { } else {
+ postgres_value = postgres_value.replaceAll("\\|", "\\\",\\\"");
+ postgres_value = "\""+postgres_value+"\"";
+ c1.setValue("Effector",postgres_value); } // assign the queried value
postgres_table = "int_torvariation"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
if (postgres_value == "") { } else { c1.setValue("tor Variation",postgres_value); } // assign the queried value
@@ -355,7 +332,10 @@
postgres_table = "int_effected"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
- if (postgres_value == "") { } else { c1.setValue("Effected",postgres_value); } // assign the queried value
+ if (postgres_value == "") { } else {
+ postgres_value = postgres_value.replaceAll("\\|", "\\\",\\\"");
+ postgres_value = "\""+postgres_value+"\"";
+ c1.setValue("Effected",postgres_value); } // assign the queried value
postgres_table = "int_tedvariation"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
if (postgres_value == "") { } else { c1.setValue("ted Variation",postgres_value); } // assign the queried value
@@ -373,12 +353,15 @@
postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_table = "int_phenotype";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
- String phenotype_match = find("(WBPhenotype[0-9]*)", postgres_value); // Find a WBPhenotype followed by any amount of digits
- if (phenotype_match != null) { postgres_value = phenotype_match; } // query for this, otherwise keep the default value
+// String phenotype_match = find("(WBPhenotype[0-9]*)", postgres_value); // Find a WBPhenotype followed by any amount of digits
+// if (phenotype_match != null) { postgres_value = phenotype_match; } // query for this, otherwise keep the default value
// if (postgres_value == "No postgres value assigned") { } else { c1.setValue("Phenotype",postgres_value); } // assign the queried value
- if (postgres_value == "") { } else { c1.setValue("Phenotype",postgres_value); } // assign the queried value
+ if (postgres_value == "") { } else {
+ postgres_value = postgres_value.replaceAll("\\|", "\\\",\\\"");
+ postgres_value = "\""+postgres_value+"\"";
//System.out.println("set Phenotype to "+postgres_value+" END");
-//
+ c1.setValue("Phenotype",postgres_value); } // assign the queried value
+
postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_table = "int_rnai";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
@@ -396,8 +379,12 @@
//System.out.println("set Pub to "+postgres_value+" END");
postgres_table = "int_person"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
- if (postgres_value == "") { } else { c1.setValue("Person",postgres_value); } // assign the queried value
+ if (postgres_value == "") { } else {
+ postgres_value = postgres_value.replaceAll("\\|", "\\\",\\\"");
+ postgres_value = "\""+postgres_value+"\"";
//System.out.println("set Person to "+postgres_value+" END");
+ c1.setValue("Person",postgres_value); } // assign the queried value
+//System.out.println("set Person to "+postgres_value+" END");
postgres_table = "int_curator"; postgres_value = ""; // postgres_value = "No postgres value assigned";
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
if (postgres_value == "") { } else { c1.setValue("Curator",postgres_value); } // assign the queried value
@@ -406,6 +393,8 @@
postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
if (postgres_value == "") { } else { c1.setValue("Other Evidence",postgres_value); } // assign the queried value
+// WBInteraction0000074
+
charList.add(c1); // add the character to the character list
}
catch (TermNotFoundException e) {
@@ -519,5 +508,27 @@
// return default_value;
// }
+// private void insertPostgresHistVal(Connection c, Statement s, String postgres_table, String joinkey, String value) {
+// Integer hasMatch = 0;
+// ResultSet rs = null;
+// System.out.println("SELECT joinkey FROM "+postgres_table+"_hst WHERE joinkey = '"+joinkey+"' AND "+postgres_table+"_hst = '"+value+"' ");
+// try { rs = s.executeQuery("SELECT joinkey FROM "+postgres_table+"_hst WHERE joinkey = '"+joinkey+"' AND "+postgres_table+"_hst = '"+value+"' "); }
+// catch (SQLException se) {
+// System.out.println("We got an exception while executing our "+postgres_table+" query: that probably means our column SQL is invalid"); se.printStackTrace(); System.exit(1); }
+// try { if (rs.next()) { hasMatch++; } }
+// // get the next highest number joinkey for that character
+// catch (SQLException se) {
+// System.out.println("We got an exception while getting a insertPostgresHistVal joinkey "+joinkey+" result:this shouldn't happen: we've done something really bad.");
+// se.printStackTrace(); System.exit(1); }
+// if (hasMatch == 0) {
+// PreparedStatement ps = null; // intialize postgres insert
+// System.out.println("INSERT INTO "+postgres_table+"_hst VALUES "+joinkey+" and "+value+" end");
+// try { ps = c.prepareStatement("INSERT INTO "+postgres_table+"_hst VALUES (?, ?)"); ps.setString(1, joinkey); ps.setString(2, value); }
+// catch (SQLException se) {
+// System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
+// try { ps.executeUpdate(); } // write to app_tempname, which is not what we really want, but we need to figure out the pubchunk thing to see what we're going to do
+// catch (SQLException se) { System.out.println("We got an exception while executing a history insert in insertPostgresVal table "+postgres_table+" joinkey "+joinkey+" value "+value+" : possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); } } }
+
+
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