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JAL-3829 more testing wit tdbeacons data columns and FTSclient
arnaud/develop
author
arngucci
<arnaud.gucciardi@gmail.com>
Tue, 6 Apr 2021 13:25:18 +0000
(15:25 +0200)
committer
arngucci
<arnaud.gucciardi@gmail.com>
Tue, 6 Apr 2021 13:25:18 +0000
(15:25 +0200)
resources/fts/tdbeacons_data_columns.txt
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src/jalview/fts/service/pdb/PDBFTSRestClient.java
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src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
patch
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test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
patch
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test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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test/jalview/gui/StructureChooserTest.java
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diff --git
a/resources/fts/tdbeacons_data_columns.txt
b/resources/fts/tdbeacons_data_columns.txt
index
de50d58
..
31d85c6
100644
(file)
--- a/
resources/fts/tdbeacons_data_columns.txt
+++ b/
resources/fts/tdbeacons_data_columns.txt
@@
-28,7
+28,7
@@
g1;Miscellaneous;2
g2;Name;1
g3;Quality;3
#
g2;Name;1
g3;Quality;3
#
-_data_column.primary_key;id
+_data_column.primary_key;model_identifier
_data_column.default_response_page_size;100
#
_data_column.name
_data_column.default_response_page_size;100
#
_data_column.name
@@
-40,6
+40,9
@@
_data_column.max_col_width
_data_column.preferred_col_width
_data_column.is_shown_by_default
_data_column.is_searchable
_data_column.preferred_col_width
_data_column.is_shown_by_default
_data_column.is_searchable
+Sequence;aligned_sequence;String;g1;80;150;85;true;true
+Model id;model_identifier;String;g2;80;150;85;true;true
+Provider;provider;String;g1;80;150;85;true;true
Uniprot Id;id;String;g2;80;150;85;true;true
UniProt Accession;uniprot_accession;String;g2;50;400;95;true;false
Entry Name;entry name;String;g2;100;150;105;true;true
Uniprot Id;id;String;g2;80;150;85;true;true
UniProt Accession;uniprot_accession;String;g2;50;400;95;true;false
Entry Name;entry name;String;g2;100;150;105;true;true
diff --git
a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index
c18ad48
..
dc7fe41
100644
(file)
--- a/
src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/
src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@
-364,8
+364,10
@@
public static String parseJsonExceptionString(String jsonErrorResponse)
for (FTSDataColumnI field : diplayFields)
{
for (FTSDataColumnI field : diplayFields)
{
+ //System.out.println("Field " + field);
String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
: pdbJsonDoc.get(field.getCode()).toString();
String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
: pdbJsonDoc.get(field.getCode()).toString();
+ //System.out.println("Field Data : " + fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
diff --git
a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index
7c06f05
..
9c6f45a
100644
(file)
--- a/
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@
-171,7
+171,7
@@
public class TDBeaconsFTSRestClient extends FTSRestClient
//System.out.println(structure);
}
//System.out.println(structure);
}
- System.out.println("1 : " + structures.get(1));
+ //System.out.println("1 : " + structures.get(1));
searchResult.setNumberOfItemsFound(numFound);
searchResult.setSearchSummary(result);
searchResult.setSequenceLength(seqLength);
searchResult.setNumberOfItemsFound(numFound);
searchResult.setSearchSummary(result);
searchResult.setSequenceLength(seqLength);
@@
-194,10
+194,9
@@
private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
summaryRowData = new Object[displayFields.size()];
for (FTSDataColumnI field : displayFields) {
summaryRowData = new Object[displayFields.size()];
for (FTSDataColumnI field : displayFields) {
- System.out.println("Field " + field);
String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
: tdbJsonStructure.get(field.getCode()).toString();
String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
: tdbJsonStructure.get(field.getCode()).toString();
- System.out.println("Field Data : " + fieldData);
+ System.out.println("Field : " + field + " Data : " + fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
@@
-221,7
+220,7
@@
private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
} catch (Exception e)
{
//e.printStackTrace();
} catch (Exception e)
{
//e.printStackTrace();
- System.out.println("offending value:" + fieldData);
+ System.out.println("offending value:" + fieldData + fieldData);
}
}
}
}
}
}
diff --git
a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
index
bbd45aa
..
61d2427
100644
(file)
--- a/
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
+++ b/
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
@@
-93,6
+93,8
@@
public class PDBFTSRestClientTest
{
e1.printStackTrace();
}
{
e1.printStackTrace();
}
+ System.out.println("wantedFields >>" + wantedFields);
+
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
@@
-246,6
+248,7
@@
public class PDBFTSRestClientTest
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getNumberOfItemsFound() == 931);
assertTrue(response.getSearchSummary().size() == 14);
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getNumberOfItemsFound() == 931);
assertTrue(response.getSearchSummary().size() == 14);
+ System.out.println("Search summary : " + response.getSearchSummary());
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
diff --git
a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
index
b2884cf
..
b144aa5
100644
(file)
--- a/
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
+++ b/
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
@@
-246,7
+246,7
@@
public class TDBeaconsFTSRestClientTest
try
{
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
try
{
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
- .getDataColumnByNameOrCode("id"));
+ .getDataColumnByNameOrCode("Model id"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("uniprot_accession"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("uniprot_accession"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
@@
-257,10
+257,10
@@
public class TDBeaconsFTSRestClientTest
}
try
{
}
try
{
- assertEquals(1, PDBFTSRestClient.getInstance()
+ assertEquals(1, TDBeaconsFTSRestClient.getInstance()
.getPrimaryKeyColumIndex(wantedFields, true));
.getPrimaryKeyColumIndex(wantedFields, true));
-// assertEquals(4, PDBFTSRestClient.getInstance()
-// .getPrimaryKeyColumIndex(wantedFields, false));
+// assertEquals(3, TDBeaconsFTSRestClient.getInstance()
+// .getPrimaryKeyColumIndex(wantedFields, true));
} catch (Exception e)
{
e.printStackTrace();
} catch (Exception e)
{
e.printStackTrace();
@@
-275,10
+275,12
@@
public class TDBeaconsFTSRestClientTest
try
{
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
try
{
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
- .getDataColumnByNameOrCode("id"));
+ .getDataColumnByNameOrCode("Model id"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("model_url"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("model_url"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+ .getDataColumnByNameOrCode("provider"));
+ wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("qmean_avg_local_score"));
} catch (Exception e1)
{
.getDataColumnByNameOrCode("qmean_avg_local_score"));
} catch (Exception e1)
{
@@
-305,8
+307,8
@@
public class TDBeaconsFTSRestClientTest
return;
}
assertTrue(response.getSearchSummary() != null);
return;
}
assertTrue(response.getSearchSummary() != null);
- assertTrue(response.getNumberOfItemsFound() > 3);
- System.out.println(response.getSearchSummary());
- System.out.println(response.getSearchSummary().size());
+ assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
+ System.out.println("Search summary : \n" + response.getSearchSummary());
+ //System.out.println(response.getSearchSummary().size());
}
}
}
}
diff --git
a/test/jalview/gui/StructureChooserTest.java
b/test/jalview/gui/StructureChooserTest.java
index
073bde8
..
9529d9f
100644
(file)
--- a/
test/jalview/gui/StructureChooserTest.java
+++ b/
test/jalview/gui/StructureChooserTest.java
@@
-83,19
+83,21
@@
public class StructureChooserTest
seq = null;
}
seq = null;
}
+ @SuppressWarnings("deprecation")
@Test(groups = { "Functional" })
public void buildQueryTest()
{
@Test(groups = { "Functional" })
public void buildQueryTest()
{
+ System.out.println("seq >>>> " + seq);
String query = StructureChooser.buildQuery(seq);
assertEquals("pdb_id:1tim", query);
String query = StructureChooser.buildQuery(seq);
assertEquals("pdb_id:1tim", query);
- System.out.println("seq >>>> " + seq);
seq.getAllPDBEntries().clear();
query = StructureChooser.buildQuery(seq);
assertEquals(
"text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
query);
seq.getAllPDBEntries().clear();
query = StructureChooser.buildQuery(seq);
assertEquals(
"text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
query);
- seq.setDBRefs(null);
+ seq.setDBRefs(null);
query = StructureChooser.buildQuery(seq);
query = StructureChooser.buildQuery(seq);
+ System.out.println(query);
assertEquals("text:4kqy", query);
DBRefEntry uniprotDBRef = new DBRefEntry();
assertEquals("text:4kqy", query);
DBRefEntry uniprotDBRef = new DBRefEntry();
@@
-114,6
+116,9
@@
public class StructureChooserTest
dbRef.setAccessionId("XYZ_" + x);
seq.addDBRef(dbRef);
}
dbRef.setAccessionId("XYZ_" + x);
seq.addDBRef(dbRef);
}
+ System.out.println("");
+ System.out.println(seq.getDBRefs());
+ System.out.println(query);
query = StructureChooser.buildQuery(seq);
assertEquals(
"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
query = StructureChooser.buildQuery(seq);
assertEquals(
"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",