Merge branch '880-minervanet-error-report-90' into 'master'

Resolve "MINERVANET - Error Report 90"

Closes #880

See merge request minerva/core!875

CHANGELOG

@@ -2,9 +2,11 @@ minerva (14.0.0~alpha.1) unstable; urgency=low
   * Feature removal: support for tomcat7 removed (#828)
   * Small improvement: debian package can be installed on debian:buster (#879)
   * Bug fix: REST API bioEntities:search method didn't limit results to the 
-    submodel id (#880)
-  * Bug fix: Empty Overlay colours were not preserved during export to 
+    submodel id (#860)
+  * Bug fix: Empty Overlay colours were not preserved during export to
     CellDesigner (#714)
+  * Bug fix: some project couldn't be accessed due to problem with migration of 
+    reaction with unknown boolean operator (#880)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 12 Aug 2019 10:00:00 +0200
 

model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java

@@ -119,7 +119,7 @@ public class PolylineData implements Serializable, Drawable {
   public PolylineData(PolylineData param) {
     points = new ArrayList<>();
     for (Point2D point : param.getPoints()) {
-      points.add(new Point2D.Double(point.getX(), point.getY()));
+      addPoint(new Point2D.Double(point.getX(), point.getY()));
     }
     beginAtd = new ArrowTypeData(param.getBeginAtd());
     endAtd = new ArrowTypeData(param.getEndAtd());

persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190527__extract_center_line.sql

@@ -19,7 +19,7 @@ alter table reaction_table add column output_operator integer;
 update reaction_table set reactant = (select id from reaction_node_table where node_type_db='REACTANT_NODE' and reaction_id=reaction_table.id order by id limit 1);
 update reaction_table set product = (select id from reaction_node_table where node_type_db='PRODUCT_NODE' and reaction_id=reaction_table.id order by id limit 1);
 
-update reaction_table set input_operator = (select id from reaction_node_table where node_type_db in ('AND_OPERATOR_NODE', 'ASSOCIATION_OPERATOR_NODE', 'NAND_OPERATOR_NODE', 'OR_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
+update reaction_table set input_operator = (select id from reaction_node_table where node_type_db in ('AND_OPERATOR_NODE', 'ASSOCIATION_OPERATOR_NODE', 'NAND_OPERATOR_NODE', 'OR_OPERATOR_NODE', 'UNKNOWN_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
 update reaction_table set output_operator = (select id from reaction_node_table where node_type_db in ('DISSOCIATION_OPERATOR_NODE', 'SPLIT_OPERATOR_NODE', 'TRUNCATION_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
 
 update reaction_table set start_point = (select one_before_last_point from reaction_node_table, polyline_data_table where reaction_node_table.id = reaction_table.reactant and polyline_data_table.id = line_id);

persist/src/main/resources/db/migration/14.0.0~alpha.1/V14.0.0.20190813__point_coordinates_cannot_be_null.sql

+-- just in case if any point on the map has null coordinates (it should never happen)
+update point_table set point_val = '0.0,0.0' where point_val = null;
+alter table point_table alter column point_val set not null;
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