diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java index b82f08768c430eb57a03f6a152bc2e8c9fa391bc..a446e1a9bc31c5af39fe16b68d1f1c9934d98ec9 100644 --- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java +++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java @@ -289,7 +289,7 @@ public class ModelAnnotator { try { elementAnnotator.annotateElement(element); } catch (AnnotatorException e) { - logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName() + " annotation problem"); + logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName() + " annotation problem: " + e.getMessage()); } } counter++; diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java index bdfd3764ec5f1ef6319df849a0184e2e2a04d71c..4d69f2e648439e4cae31bec59aeef2aaf6a5e3b6 100644 --- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java +++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java @@ -157,7 +157,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService { ur.setUniprotId(md.getResource()); ur.setSpecies((Species)bioEntity); for (Structure s : structures) { - s.setUniprot(ur); + s.setUniprot(ur); } ur.setStructures(structures); ((Species)bioEntity).getUniprots().add(ur); diff --git a/persist/src/db/11.0.1/fix_db_20170720.sql b/persist/src/db/11.0.1/fix_db_20170720.sql index 71cf63626c3ad465f1682894f40f7fd5a24d6361..396aaa49fa82e2d01796a3174595d577a79eba2e 100644 --- a/persist/src/db/11.0.1/fix_db_20170720.sql +++ b/persist/src/db/11.0.1/fix_db_20170720.sql @@ -44,7 +44,7 @@ CREATE TABLE structure_table iddb integer NOT NULL DEFAULT nextval('structure_table_iddb_seq'::regclass), uniprot_id integer NOT NULL, pdb_id character varying(255) NOT NULL, --should be character(4), but to be on the safe side... - chain_id character varying(1)NOT NULL, + chain_id character varying(255) NOT NULL, --should be char(1), but for example 5T0C has has chains AK and BK struct_start integer, struct_end integer, unp_start integer, diff --git a/persist/src/db/11.0.1/fix_db_20171307.sql b/persist/src/db/11.0.1/fix_db_20171307.sql deleted file mode 100644 index 94523a2c4d08e87d3b5af2767a02ebd675043bea..0000000000000000000000000000000000000000 --- a/persist/src/db/11.0.1/fix_db_20171307.sql +++ /dev/null @@ -1,2 +0,0 @@ -DELETE FROM cache_type WHERE classname = 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator' -INSERT INTO cache_type(validity, classname) VALUES (365, 'lcsb.mapviewer.annotation.services.annotators.PdbAnnotator') \ No newline at end of file diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java index b240a8c2721ef483f6526f5f31158a36ee93c2af..5e9ac8b9f8f0e4e1e4a24acb50d8d0e0ba538c7d 100644 --- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java +++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java @@ -60,7 +60,7 @@ public class ElementRestImplTest extends RestTestFunctions { public void testGetElementsProcessAllColumns() throws Exception { try { ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", true); - List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), ""); + List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "", "", ""); for (Map<String, Object> element : result) { for (String paramName : element.keySet()) { Object val = element.get(paramName); @@ -85,7 +85,7 @@ public class ElementRestImplTest extends RestTestFunctions { try { String proteinType = new GenericProtein("1").getStringType(); ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", false); - List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType); + List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType, "", ""); assertEquals(12, result.size()); } catch (Exception e) { @@ -98,7 +98,7 @@ public class ElementRestImplTest extends RestTestFunctions { public void testGetElementsVisibility() throws Exception { try { ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml"); - List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), ""); + List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "", "", ""); for (Map<String, Object> map : result) { assertTrue(map.get("hierarchyVisibilityLevel") instanceof String); } @@ -174,6 +174,10 @@ public class ElementRestImplTest extends RestTestFunctions { throw e; } } + + private ElementsRestImpl createMockElementRest(String string) throws Exception { + return createMockElementRest(string, false); + } private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception { Model model = super.getModelForFile(string, true);