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JAL-3829 attempt to fix my changes to follow the Jira issue
author
Arnaldo
<arnaud.gucciardi@gmail.com>
Thu, 1 Apr 2021 13:28:59 +0000
(15:28 +0200)
committer
Arnaldo
<arnaud.gucciardi@gmail.com>
Thu, 1 Apr 2021 13:28:59 +0000
(15:28 +0200)
resources/fts/tdbeacons_data_columns.txt
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src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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diff --git
a/resources/fts/tdbeacons_data_columns.txt
b/resources/fts/tdbeacons_data_columns.txt
index
2eb3d31
..
de50d58
100644
(file)
--- a/
resources/fts/tdbeacons_data_columns.txt
+++ b/
resources/fts/tdbeacons_data_columns.txt
@@
-26,6
+26,7
@@
_group.name
_group.sort_order
g1;Miscellaneous;2
g2;Name;1
_group.sort_order
g1;Miscellaneous;2
g2;Name;1
+g3;Quality;3
#
_data_column.primary_key;id
_data_column.default_response_page_size;100
#
_data_column.primary_key;id
_data_column.default_response_page_size;100
@@
-42,3
+43,5
@@
_data_column.is_searchable
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
+Url;model_url;String;g1;100;150;105;true;true
+Qmean;qmean_avg_local_score;double;g3;100;150;105;true;true
diff --git
a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index
655b960
..
7c06f05
100644
(file)
--- a/
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@
-151,21
+151,19
@@
public class TDBeaconsFTSRestClient extends FTSRestClient
{
jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
}
{
jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
}
- //System.out.println(jsonObj);
Object uniprot_entry = jsonObj.get("uniprot_entry");
Object uniprot_entry = jsonObj.get("uniprot_entry");
- System.out.println(uniprot_entry);
-
Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
- System.out.println("seqLenght :" + seqLength);
+ //System.out.println(uniprot_entry);
+ //System.out.println(jsonObj);
+ //System.out.println("seqLenght :" + seqLength);
- result = new ArrayList<>();
+ //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
List<Object> structures = (List<Object>) jsonObj.get("structures");
List<Object> structures = (List<Object>) jsonObj.get("structures");
- //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
+ result = new ArrayList<>();
int numFound = 0;
int numFound = 0;
- for (Iterator<Object> strucIter = structures.iterator(); strucIter
- .hasNext();)
+ for (Iterator<Object> strucIter = structures.iterator(); strucIter.hasNext();)
{
Map<String, Object> structure = (Map<String, Object>) strucIter.next();
result.add(getFTSData(structure, tdbRestRequest));
{
Map<String, Object> structure = (Map<String, Object>) strucIter.next();
result.add(getFTSData(structure, tdbRestRequest));
@@
-194,9
+192,12
@@
private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
int colCounter = 0;
summaryRowData = new Object[displayFields.size()];
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
int colCounter = 0;
summaryRowData = new Object[displayFields.size()];
+
for (FTSDataColumnI field : displayFields) {
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);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
@@
-219,7
+220,7
@@
private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
: fieldData;
} catch (Exception e)
{
: fieldData;
} catch (Exception e)
{
- e.printStackTrace();
+ //e.printStackTrace();
System.out.println("offending value:" + fieldData);
}
}
System.out.println("offending value:" + fieldData);
}
}
diff --git
a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
index
94b6b63
..
b2884cf
100644
(file)
--- a/
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
+++ b/
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
@@
-277,9
+277,9
@@
public class TDBeaconsFTSRestClientTest
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("id"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
.getDataColumnByNameOrCode("id"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
- .getDataColumnByNameOrCode("uniprot_accession"));
+ .getDataColumnByNameOrCode("model_url"));
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
wantedFields.add(TDBeaconsFTSRestClient.getInstance()
- .getDataColumnByNameOrCode("entry name"));
+ .getDataColumnByNameOrCode("qmean_avg_local_score"));
} catch (Exception e1)
{
e1.printStackTrace();
} catch (Exception e1)
{
e1.printStackTrace();
@@
-289,7
+289,7
@@
public class TDBeaconsFTSRestClientTest
FTSRestRequest request = new FTSRestRequest();
request.setResponseSize(100);
request.setFieldToSearchBy("P");
FTSRestRequest request = new FTSRestRequest();
request.setResponseSize(100);
request.setFieldToSearchBy("P");
- request.setSearchTerm("01308.json");
+ request.setSearchTerm("01318.json");
request.setWantedFields(wantedFields);
System.out.println("request : " + request.getFieldToSearchBy());
//System.out.println(request.toString());
request.setWantedFields(wantedFields);
System.out.println("request : " + request.getFieldToSearchBy());
//System.out.println(request.toString());