/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.fts.core;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Objects;
/**
* Base class providing implementation for common methods defined in
* FTSRestClientI
*
* @author tcnofoegbu
*
* @note implementations MUST be accessed as a singleton.
*/
public abstract class FTSRestClient implements FTSRestClientI
{
protected Collection dataColumns = new ArrayList();
protected Collection dataColumnGroups = new ArrayList();
protected Collection searchableDataColumns = new ArrayList();
protected Collection defaulDisplayedDataColumns = new ArrayList();
protected FTSDataColumnI primaryKeyColumn;
private String primaryKeyColumnCode = null;
private int defaultResponsePageSize = 100;
protected FTSRestClient()
{
}
public void parseDataColumnsConfigFile()
{
String fileName = getColumnDataConfigFileName();
InputStream in = getClass().getResourceAsStream(fileName);
try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
{
String line;
while ((line = br.readLine()) != null)
{
final String[] lineData = line.split(";");
try
{
if (lineData.length == 2)
{
if (lineData[0].equalsIgnoreCase("_data_column.primary_key"))
{
primaryKeyColumnCode = lineData[1];
}
if (lineData[0]
.equalsIgnoreCase("_data_column.default_response_page_size"))
{
defaultResponsePageSize = Integer.valueOf(lineData[1]);
}
}
else if (lineData.length == 3)
{
dataColumnGroups.add(new FTSDataColumnGroupI()
{
@Override
public String getID()
{
return lineData[0];
}
@Override
public String getName()
{
return lineData[1];
}
@Override
public int getSortOrder()
{
return Integer.valueOf(lineData[2]);
}
@Override
public String toString()
{
return lineData[1];
}
@Override
public int hashCode()
{
return Objects.hash(this.getID(), this.getName(),
this.getSortOrder());
}
@Override
public boolean equals(Object otherObject)
{
FTSDataColumnGroupI that = (FTSDataColumnGroupI) otherObject;
return this.getID().equals(that.getID())
&& this.getName().equals(that.getName())
&& this.getSortOrder() == that.getSortOrder();
}
});
}
else if (lineData.length > 6)
{
FTSDataColumnI dataCol = new FTSDataColumnI()
{
@Override
public String toString()
{
return lineData[0];
}
@Override
public String getName()
{
return lineData[0];
}
@Override
public String getCode()
{
return lineData[1].split("\\|")[0];
}
@Override
public String getAltCode()
{
return lineData[1].split("\\|").length > 1 ? lineData[1]
.split("\\|")[1] : getCode();
}
@Override
public DataTypeI getDataType()
{
final String[] dataTypeString = lineData[2].split("\\|");
final String classString = dataTypeString[0].toUpperCase();
return new DataTypeI()
{
@Override
public boolean isFormtted()
{
if (dataTypeString.length > 1
&& dataTypeString[1] != null)
{
switch (dataTypeString[1].toUpperCase())
{
case "T":
case "TRUE":
return true;
case "F":
case "False":
default:
return false;
}
}
return false;
}
@Override
public int getSignificantFigures()
{
if (dataTypeString.length > 2
&& dataTypeString[2] != null)
{
return Integer.valueOf(dataTypeString[2]);
}
return 0;
}
@Override
public Class getDataTypeClass()
{
switch (classString)
{
case "INT":
case "INTEGER":
return Integer.class;
case "DOUBLE":
return Double.class;
case "STRING":
default:
return String.class;
}
}
};
}
@Override
public FTSDataColumnGroupI getGroup()
{
FTSDataColumnGroupI group = null;
try
{
group = getDataColumnGroupById(lineData[3]);
} catch (Exception e)
{
e.printStackTrace();
}
return group;
}
@Override
public int getMinWidth()
{
return Integer.valueOf(lineData[4]);
}
@Override
public int getMaxWidth()
{
return Integer.valueOf(lineData[5]);
}
@Override
public int getPreferredWidth()
{
return Integer.valueOf(lineData[6]);
}
@Override
public boolean isPrimaryKeyColumn()
{
return getName().equalsIgnoreCase(primaryKeyColumnCode)
|| getCode().equalsIgnoreCase(primaryKeyColumnCode);
}
@Override
public boolean isVisibleByDefault()
{
return Boolean.valueOf(lineData[7]);
}
@Override
public boolean isSearchable()
{
return Boolean.valueOf(lineData[8]);
}
@Override
public int hashCode()
{
return Objects.hash(this.getName(), this.getCode(),
this.getGroup());
}
@Override
public boolean equals(Object otherObject)
{
FTSDataColumnI that = (FTSDataColumnI) otherObject;
return this.getCode().equals(that.getCode())
&& this.getName().equals(that.getName())
&& this.getGroup().equals(that.getGroup());
}
};
dataColumns.add(dataCol);
if (dataCol.isSearchable())
{
searchableDataColumns.add(dataCol);
}
if (dataCol.isVisibleByDefault())
{
defaulDisplayedDataColumns.add(dataCol);
}
}
else
{
continue;
}
} catch (Exception e)
{
e.printStackTrace();
}
}
try
{
this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
} catch (Exception e)
{
e.printStackTrace();
}
} catch (IOException e)
{
e.printStackTrace();
}
}
@Override
public int getPrimaryKeyColumIndex(
Collection wantedFields, boolean hasRefSeq)
throws Exception
{
// If a reference sequence is attached then start counting from 1 else
// start from zero
int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
for (FTSDataColumnI field : wantedFields)
{
if (field.isPrimaryKeyColumn())
{
break; // Once PDB Id index is determined exit iteration
}
++pdbFieldIndexCounter;
}
return pdbFieldIndexCounter;
}
@Override
public String getDataColumnsFieldsAsCommaDelimitedString(
Collection dataColumnFields)
{
String result = "";
if (dataColumnFields != null && !dataColumnFields.isEmpty())
{
StringBuilder returnedFields = new StringBuilder();
for (FTSDataColumnI field : dataColumnFields)
{
returnedFields.append(",").append(field.getCode());
}
returnedFields.deleteCharAt(0);
result = returnedFields.toString();
}
return result;
}
@Override
public Collection getAllFTSDataColumns()
{
if (dataColumns == null || dataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
return dataColumns;
}
@Override
public Collection getSearchableDataColumns()
{
if (searchableDataColumns == null || searchableDataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
return searchableDataColumns;
}
@Override
public Collection getAllDefaultDisplayedFTSDataColumns()
{
if (defaulDisplayedDataColumns == null
|| defaulDisplayedDataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
return defaulDisplayedDataColumns;
}
@Override
public FTSDataColumnI getPrimaryKeyColumn()
{
if (defaulDisplayedDataColumns == null
|| defaulDisplayedDataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
return primaryKeyColumn;
}
@Override
public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode)
throws Exception
{
if (dataColumns == null || dataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
for (FTSDataColumnI column : dataColumns)
{
if (column.getName().equalsIgnoreCase(nameOrCode)
|| column.getCode().equalsIgnoreCase(nameOrCode))
{
return column;
}
}
throw new Exception("Couldn't find data column with name : "
+ nameOrCode);
}
@Override
public FTSDataColumnGroupI getDataColumnGroupById(String id)
throws Exception
{
if (dataColumns == null || dataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
for (FTSDataColumnGroupI columnGroup : dataColumnGroups)
{
if (columnGroup.getID().equalsIgnoreCase(id))
{
return columnGroup;
}
}
throw new Exception("Couldn't find data column group with id : " + id);
}
public String getMessageByHTTPStatusCode(int code, String service)
{
String message = "";
switch (code)
{
case 400:
message = MessageManager.getString("exception.bad_request");
break;
case 410:
message = MessageManager.formatMessage(
"exception.fts_rest_service_no_longer_available", service);
break;
case 403:
case 404:
message = MessageManager.getString("exception.resource_not_be_found");
break;
case 408:
case 409:
case 500:
case 501:
case 502:
case 504:
case 505:
message = MessageManager.formatMessage("exception.fts_server_error",
service);
break;
case 503:
message = MessageManager.getString("exception.service_not_available");
break;
default:
break;
}
return message;
}
protected String getResourceFile(String fileName)
{
String result = "";
try
{
result = getClass().getResource(fileName).getFile();
} catch (Exception e)
{
e.printStackTrace();
}
return result;
}
@Override
public int getDefaultResponsePageSize()
{
if (dataColumns == null || dataColumns.isEmpty())
{
parseDataColumnsConfigFile();
}
return defaultResponsePageSize;
}
}