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package jalview.fts.core; |
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import java.io.BufferedReader; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.io.InputStreamReader; |
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import java.util.ArrayList; |
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import java.util.Collection; |
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import java.util.Objects; |
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import jalview.fts.api.FTSDataColumnI; |
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import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI; |
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import jalview.fts.api.FTSRestClientI; |
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@author |
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| 72.8% |
Uncovered Elements: 64 (235) |
Complexity: 98 |
Complexity Density: 0.65 |
|
43 |
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public abstract class FTSRestClient implements FTSRestClientI |
44 |
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{ |
45 |
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protected Collection<FTSDataColumnI> dataColumns = new ArrayList<>(); |
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protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<>(); |
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protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<>(); |
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protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<>(); |
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protected FTSDataColumnI primaryKeyColumn; |
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private String primaryKeyColumnCode = null; |
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|
57 |
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private int defaultResponsePageSize = 100; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
59 |
17 |
protected FTSRestClient()... |
60 |
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{ |
61 |
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|
62 |
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} |
63 |
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|
|
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| 88.6% |
Uncovered Elements: 5 (44) |
Complexity: 14 |
Complexity Density: 0.5 |
|
64 |
17 |
public void parseDataColumnsConfigFile()... |
65 |
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{ |
66 |
17 |
String fileName = getColumnDataConfigFileName(); |
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|
68 |
17 |
InputStream in = getClass().getResourceAsStream(fileName); |
69 |
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70 |
17 |
try (BufferedReader br = new BufferedReader(new InputStreamReader(in))) |
71 |
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{ |
72 |
17 |
String line; |
73 |
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while ((line = br.readLine()) != null) |
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{ |
75 |
2930 |
final String[] lineData = line.split(";"); |
76 |
2930 |
try |
77 |
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{ |
78 |
2930 |
if (lineData.length == 2) |
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{ |
80 |
51 |
if (lineData[0].equalsIgnoreCase("_data_column.primary_key")) |
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{ |
82 |
17 |
primaryKeyColumnCode = lineData[1]; |
83 |
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} |
84 |
51 |
if (lineData[0].equalsIgnoreCase( |
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"_data_column.default_response_page_size")) |
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{ |
87 |
17 |
defaultResponsePageSize = Integer.valueOf(lineData[1]); |
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} |
89 |
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} |
90 |
2879 |
else if (lineData.length == 3) |
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{ |
92 |
294 |
dataColumnGroups.add(new FTSDataColumnGroupI() |
93 |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
94 |
2165 |
@Override... |
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public String getID() |
96 |
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{ |
97 |
2165 |
return lineData[0]; |
98 |
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} |
99 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
100 |
235 |
@Override... |
101 |
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public String getName() |
102 |
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{ |
103 |
235 |
return lineData[1]; |
104 |
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} |
105 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
106 |
1730 |
@Override... |
107 |
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public int getSortOrder() |
108 |
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{ |
109 |
1730 |
return Integer.valueOf(lineData[2]); |
110 |
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} |
111 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
112 |
1 |
@Override... |
113 |
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public String toString() |
114 |
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{ |
115 |
1 |
return lineData[1]; |
116 |
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} |
117 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
118 |
212 |
@Override... |
119 |
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public int hashCode() |
120 |
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{ |
121 |
212 |
return Objects.hash(this.getID(), this.getName(), |
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this.getSortOrder()); |
123 |
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} |
124 |
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|
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
125 |
11 |
@Override... |
126 |
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public boolean equals(Object otherObject) |
127 |
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{ |
128 |
11 |
FTSDataColumnGroupI that = (FTSDataColumnGroupI) otherObject; |
129 |
11 |
return this.getID().equals(that.getID()) |
130 |
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&& this.getName().equals(that.getName()) |
131 |
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&& this.getSortOrder() == that.getSortOrder(); |
132 |
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} |
133 |
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}); |
134 |
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} |
135 |
2585 |
else if (lineData.length > 6) |
136 |
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{ |
137 |
1956 |
FTSDataColumnI dataCol = new FTSDataColumnI() |
138 |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
139 |
51 |
@Override... |
140 |
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public String toString() |
141 |
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{ |
142 |
51 |
return lineData[0]; |
143 |
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} |
144 |
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|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
145 |
1225 |
@Override... |
146 |
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public String getName() |
147 |
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{ |
148 |
1225 |
return lineData[0]; |
149 |
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} |
150 |
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|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
151 |
1938 |
@Override... |
152 |
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public String getCode() |
153 |
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{ |
154 |
1938 |
return lineData[1].split("\\|")[0]; |
155 |
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} |
156 |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
157 |
0 |
@Override... |
158 |
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public String getAltCode() |
159 |
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{ |
160 |
0 |
return lineData[1].split("\\|").length > 1 |
161 |
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? lineData[1].split("\\|")[1] |
162 |
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: getCode(); |
163 |
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} |
164 |
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|
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
165 |
2 |
@Override... |
166 |
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public DataTypeI getDataType() |
167 |
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{ |
168 |
2 |
final String[] dataTypeString = lineData[2].split("\\|"); |
169 |
2 |
final String classString = dataTypeString[0].toUpperCase(); |
170 |
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|
171 |
2 |
return new DataTypeI() |
172 |
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{ |
173 |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 7 |
Complexity Density: 0.7 |
|
174 |
0 |
@Override... |
175 |
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public boolean isFormtted() |
176 |
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{ |
177 |
0 |
if (dataTypeString.length > 1 |
178 |
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&& dataTypeString[1] != null) |
179 |
|
{ |
180 |
0 |
switch (dataTypeString[1].toUpperCase()) |
181 |
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{ |
182 |
0 |
case "T": |
183 |
0 |
case "TRUE": |
184 |
0 |
return true; |
185 |
0 |
case "F": |
186 |
0 |
case "False": |
187 |
0 |
default: |
188 |
0 |
return false; |
189 |
|
} |
190 |
|
} |
191 |
0 |
return false; |
192 |
|
} |
193 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
194 |
0 |
@Override... |
195 |
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public int getSignificantFigures() |
196 |
|
{ |
197 |
0 |
if (dataTypeString.length > 2 |
198 |
|
&& dataTypeString[2] != null) |
199 |
|
{ |
200 |
0 |
return Integer.valueOf(dataTypeString[2]); |
201 |
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} |
202 |
0 |
return 0; |
203 |
|
} |
204 |
|
|
|
|
| 55.6% |
Uncovered Elements: 4 (9) |
Complexity: 5 |
Complexity Density: 0.56 |
|
205 |
2 |
@Override... |
206 |
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public Class getDataTypeClass() |
207 |
|
{ |
208 |
2 |
switch (classString) |
209 |
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{ |
210 |
1 |
case "INT": |
211 |
0 |
case "INTEGER": |
212 |
1 |
return Integer.class; |
213 |
0 |
case "DOUBLE": |
214 |
0 |
return Double.class; |
215 |
1 |
case "STRING": |
216 |
0 |
default: |
217 |
1 |
return String.class; |
218 |
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} |
219 |
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} |
220 |
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}; |
221 |
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|
222 |
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} |
223 |
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|
|
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| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.4 |
|
224 |
400 |
@Override... |
225 |
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public FTSDataColumnGroupI getGroup() |
226 |
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{ |
227 |
400 |
FTSDataColumnGroupI group = null; |
228 |
400 |
try |
229 |
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{ |
230 |
400 |
group = getDataColumnGroupById(lineData[3]); |
231 |
|
} catch (Exception e) |
232 |
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{ |
233 |
0 |
e.printStackTrace(); |
234 |
|
} |
235 |
400 |
return group; |
236 |
|
} |
237 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
238 |
1 |
@Override... |
239 |
|
public int getMinWidth() |
240 |
|
{ |
241 |
1 |
return Integer.valueOf(lineData[4]); |
242 |
|
} |
243 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
244 |
1 |
@Override... |
245 |
|
public int getMaxWidth() |
246 |
|
{ |
247 |
1 |
return Integer.valueOf(lineData[5]); |
248 |
|
} |
249 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
250 |
1 |
@Override... |
251 |
|
public int getPreferredWidth() |
252 |
|
{ |
253 |
1 |
return Integer.valueOf(lineData[6]); |
254 |
|
} |
255 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
256 |
12 |
@Override... |
257 |
|
public boolean isPrimaryKeyColumn() |
258 |
|
{ |
259 |
12 |
return getName().equalsIgnoreCase(primaryKeyColumnCode) |
260 |
|
|| getCode().equalsIgnoreCase(primaryKeyColumnCode); |
261 |
|
} |
262 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
263 |
1956 |
@Override... |
264 |
|
public boolean isVisibleByDefault() |
265 |
|
{ |
266 |
1956 |
return Boolean.valueOf(lineData[7]); |
267 |
|
} |
268 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
269 |
1956 |
@Override... |
270 |
|
public boolean isSearchable() |
271 |
|
{ |
272 |
1956 |
return Boolean.valueOf(lineData[8]); |
273 |
|
} |
274 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
275 |
212 |
@Override... |
276 |
|
public int hashCode() |
277 |
|
{ |
278 |
212 |
return Objects.hash(this.getName(), this.getCode(), |
279 |
|
this.getGroup()); |
280 |
|
} |
281 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
282 |
655 |
@Override... |
283 |
|
public boolean equals(Object otherObject) |
284 |
|
{ |
285 |
655 |
FTSDataColumnI that = (FTSDataColumnI) otherObject; |
286 |
655 |
return otherObject == null ? false |
287 |
|
: this.getCode().equals(that.getCode()) |
288 |
|
&& this.getName().equals(that.getName()) |
289 |
|
&& this.getGroup().equals(that.getGroup()); |
290 |
|
} |
291 |
|
|
292 |
|
}; |
293 |
1956 |
dataColumns.add(dataCol); |
294 |
|
|
295 |
1956 |
if (dataCol.isSearchable()) |
296 |
|
{ |
297 |
361 |
searchableDataColumns.add(dataCol); |
298 |
|
} |
299 |
|
|
300 |
1956 |
if (dataCol.isVisibleByDefault()) |
301 |
|
{ |
302 |
116 |
defaulDisplayedDataColumns.add(dataCol); |
303 |
|
} |
304 |
|
|
305 |
|
} |
306 |
|
else |
307 |
|
{ |
308 |
629 |
continue; |
309 |
|
} |
310 |
|
} catch (Exception e) |
311 |
|
{ |
312 |
0 |
e.printStackTrace(); |
313 |
|
} |
314 |
|
} |
315 |
17 |
try |
316 |
|
{ |
317 |
17 |
this.primaryKeyColumn = getDataColumnByNameOrCode( |
318 |
|
primaryKeyColumnCode); |
319 |
|
} catch (Exception e) |
320 |
|
{ |
321 |
0 |
e.printStackTrace(); |
322 |
|
} |
323 |
|
} catch (IOException e) |
324 |
|
{ |
325 |
0 |
e.printStackTrace(); |
326 |
|
} |
327 |
|
} |
328 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
329 |
4 |
@Override... |
330 |
|
public int getPrimaryKeyColumIndex( |
331 |
|
Collection<FTSDataColumnI> wantedFields, boolean hasRefSeq) |
332 |
|
throws Exception |
333 |
|
{ |
334 |
|
|
335 |
|
|
336 |
|
|
337 |
4 |
int pdbFieldIndexCounter = hasRefSeq ? 1 : 0; |
338 |
|
|
339 |
4 |
for (FTSDataColumnI field : wantedFields) |
340 |
|
{ |
341 |
12 |
if (field.isPrimaryKeyColumn()) |
342 |
|
{ |
343 |
4 |
break; |
344 |
|
} |
345 |
8 |
++pdbFieldIndexCounter; |
346 |
|
} |
347 |
4 |
return pdbFieldIndexCounter; |
348 |
|
} |
349 |
|
|
|
|
| 90% |
Uncovered Elements: 1 (10) |
Complexity: 3 |
Complexity Density: 0.38 |
|
350 |
3 |
@Override... |
351 |
|
public String getDataColumnsFieldsAsCommaDelimitedString( |
352 |
|
Collection<FTSDataColumnI> dataColumnFields) |
353 |
|
{ |
354 |
3 |
String result = ""; |
355 |
3 |
if (dataColumnFields != null && !dataColumnFields.isEmpty()) |
356 |
|
{ |
357 |
3 |
StringBuilder returnedFields = new StringBuilder(); |
358 |
3 |
for (FTSDataColumnI field : dataColumnFields) |
359 |
|
{ |
360 |
16 |
returnedFields.append(",").append(field.getCode()); |
361 |
|
} |
362 |
3 |
returnedFields.deleteCharAt(0); |
363 |
3 |
result = returnedFields.toString(); |
364 |
|
} |
365 |
3 |
return result; |
366 |
|
} |
367 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
368 |
3 |
@Override... |
369 |
|
public Collection<FTSDataColumnI> getAllFTSDataColumns() |
370 |
|
{ |
371 |
3 |
if (dataColumns == null || dataColumns.isEmpty()) |
372 |
|
{ |
373 |
1 |
parseDataColumnsConfigFile(); |
374 |
|
} |
375 |
3 |
return dataColumns; |
376 |
|
} |
377 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
378 |
4 |
@Override... |
379 |
|
public Collection<FTSDataColumnI> getSearchableDataColumns() |
380 |
|
{ |
381 |
4 |
if (searchableDataColumns == null || searchableDataColumns.isEmpty()) |
382 |
|
{ |
383 |
2 |
parseDataColumnsConfigFile(); |
384 |
|
} |
385 |
4 |
return searchableDataColumns; |
386 |
|
} |
387 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
388 |
89 |
@Override... |
389 |
|
public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns() |
390 |
|
{ |
391 |
89 |
if (defaulDisplayedDataColumns == null |
392 |
|
|| defaulDisplayedDataColumns.isEmpty()) |
393 |
|
{ |
394 |
4 |
parseDataColumnsConfigFile(); |
395 |
|
} |
396 |
89 |
return defaulDisplayedDataColumns; |
397 |
|
} |
398 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
399 |
3 |
@Override... |
400 |
|
public FTSDataColumnI getPrimaryKeyColumn() |
401 |
|
{ |
402 |
3 |
if (defaulDisplayedDataColumns == null |
403 |
|
|| defaulDisplayedDataColumns.isEmpty()) |
404 |
|
{ |
405 |
1 |
parseDataColumnsConfigFile(); |
406 |
|
} |
407 |
3 |
return primaryKeyColumn; |
408 |
|
} |
409 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 5 |
Complexity Density: 0.83 |
|
410 |
36 |
@Override... |
411 |
|
public FTSDataColumnI getDataColumnByNameOrCode(String nameOrCode) |
412 |
|
throws Exception |
413 |
|
{ |
414 |
36 |
if (dataColumns == null || dataColumns.isEmpty()) |
415 |
|
{ |
416 |
7 |
parseDataColumnsConfigFile(); |
417 |
|
} |
418 |
36 |
for (FTSDataColumnI column : dataColumns) |
419 |
|
{ |
420 |
398 |
if (column.getName().equalsIgnoreCase(nameOrCode) |
421 |
|
|| column.getCode().equalsIgnoreCase(nameOrCode)) |
422 |
|
{ |
423 |
34 |
return column; |
424 |
|
} |
425 |
|
} |
426 |
2 |
throw new Exception( |
427 |
|
"Couldn't find data column with name : " + nameOrCode); |
428 |
|
} |
429 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
430 |
404 |
@Override... |
431 |
|
public FTSDataColumnGroupI getDataColumnGroupById(String id) |
432 |
|
throws Exception |
433 |
|
{ |
434 |
404 |
if (dataColumns == null || dataColumns.isEmpty()) |
435 |
|
{ |
436 |
1 |
parseDataColumnsConfigFile(); |
437 |
|
} |
438 |
404 |
for (FTSDataColumnGroupI columnGroup : dataColumnGroups) |
439 |
|
{ |
440 |
1931 |
if (columnGroup.getID().equalsIgnoreCase(id)) |
441 |
|
{ |
442 |
402 |
return columnGroup; |
443 |
|
} |
444 |
|
} |
445 |
2 |
throw new Exception("Couldn't find data column group with id : " + id); |
446 |
|
} |
447 |
|
|
|
|
| 0% |
Uncovered Elements: 27 (27) |
Complexity: 13 |
Complexity Density: 0.48 |
|
448 |
0 |
public static String getMessageByHTTPStatusCode(int code, String service)... |
449 |
|
{ |
450 |
0 |
String message = ""; |
451 |
0 |
switch (code) |
452 |
|
{ |
453 |
0 |
case 400: |
454 |
0 |
message = "Bad request. There is a problem with your input."; |
455 |
0 |
break; |
456 |
|
|
457 |
0 |
case 410: |
458 |
0 |
message = service + " rest services no longer available!"; |
459 |
0 |
break; |
460 |
0 |
case 403: |
461 |
0 |
case 404: |
462 |
0 |
message = "The requested resource could not be found"; |
463 |
0 |
break; |
464 |
0 |
case 408: |
465 |
0 |
case 409: |
466 |
0 |
case 500: |
467 |
0 |
case 501: |
468 |
0 |
case 502: |
469 |
0 |
case 504: |
470 |
0 |
case 505: |
471 |
0 |
message = "There seems to be an error from the " + service |
472 |
|
+ " server"; |
473 |
0 |
break; |
474 |
0 |
case 503: |
475 |
0 |
message = "Service not available. The server is being updated, try again later."; |
476 |
0 |
break; |
477 |
0 |
default: |
478 |
0 |
break; |
479 |
|
} |
480 |
0 |
return String.valueOf(code) + " " + message; |
481 |
|
} |
482 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.4 |
|
483 |
1 |
protected String getResourceFile(String fileName)... |
484 |
|
{ |
485 |
1 |
String result = ""; |
486 |
1 |
try |
487 |
|
{ |
488 |
1 |
result = getClass().getResource(fileName).getFile(); |
489 |
|
} catch (Exception e) |
490 |
|
{ |
491 |
0 |
e.printStackTrace(); |
492 |
|
} |
493 |
1 |
return result; |
494 |
|
|
495 |
|
} |
496 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
497 |
2 |
@Override... |
498 |
|
public int getDefaultResponsePageSize() |
499 |
|
{ |
500 |
2 |
if (dataColumns == null || dataColumns.isEmpty()) |
501 |
|
{ |
502 |
1 |
parseDataColumnsConfigFile(); |
503 |
|
} |
504 |
2 |
return defaultResponsePageSize; |
505 |
|
} |
506 |
|
|
507 |
|
} |