Revision 41502
Added by Michele Artini about 8 years ago
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/graph/GraphLoader.java | ||
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7 | 7 |
import java.util.Map; |
8 | 8 |
import java.util.Set; |
9 | 9 |
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10 |
import javax.annotation.Resource; |
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11 |
|
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10 | 12 |
import org.apache.commons.lang.StringUtils; |
13 |
import org.apache.commons.logging.Log; |
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14 |
import org.apache.commons.logging.LogFactory; |
|
11 | 15 |
import org.dom4j.Document; |
12 | 16 |
import org.dom4j.Element; |
13 | 17 |
import org.springframework.beans.factory.annotation.Required; |
14 | 18 |
|
15 | 19 |
import com.google.common.collect.Sets; |
16 | 20 |
|
21 |
import eu.dnetlib.conf.PropertyFetcher; |
|
17 | 22 |
import eu.dnetlib.msro.rmi.MSROException; |
18 | 23 |
import eu.dnetlib.msro.workflows.util.NodeHelper; |
19 | 24 |
|
... | ... | |
24 | 29 |
|
25 | 30 |
private NodeHelper nodeHelper; |
26 | 31 |
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32 |
@Resource(name = "propertyFetcher") |
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33 |
private PropertyFetcher propertyFetcher; |
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34 |
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35 |
private static final Log log = LogFactory.getLog(GraphLoader.class); |
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36 |
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27 | 37 |
public Graph loadGraph(final Document doc, final Map<String, String> globalParams) throws MSROException { |
28 | 38 |
final Graph graph = new Graph(); |
29 | 39 |
|
... | ... | |
67 | 77 |
final String pName = p.valueOf("@name"); |
68 | 78 |
final String pValue = p.valueOf("@value"); |
69 | 79 |
final String pRef = p.valueOf("@ref"); |
80 |
final String pProp = p.valueOf("@property"); |
|
70 | 81 |
|
71 | 82 |
if (StringUtils.isNotBlank(pRef) && StringUtils.isNotBlank(globalParams.get(pRef))) { |
72 | 83 |
params.put(pName, globalParams.get(pRef)); |
73 | 84 |
} else if (StringUtils.isNotBlank(pValue)) { |
74 | 85 |
params.put(pName, pValue); |
86 |
} else if (StringUtils.isNotBlank(pProp)) { |
|
87 |
params.put(pName, resolveProperty(pProp)); |
|
75 | 88 |
} else if (p.selectSingleNode("./MAP") != null) { |
76 | 89 |
|
77 | 90 |
final Map<String, String> map = new HashMap<String, String>(); |
... | ... | |
80 | 93 |
final String eKey = entry.valueOf("@key"); |
81 | 94 |
final String eValue = entry.valueOf("@value"); |
82 | 95 |
final String eRef = entry.valueOf("@ref"); |
96 |
final String eProp = entry.valueOf("@property"); |
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97 |
|
|
83 | 98 |
if (StringUtils.isNotBlank(eRef) && StringUtils.isNotBlank(globalParams.get(eRef))) { |
84 | 99 |
map.put(eKey, globalParams.get(eRef)); |
85 | 100 |
} else if (StringUtils.isNotBlank(eValue)) { |
86 | 101 |
map.put(eKey, eValue); |
102 |
} else if (StringUtils.isNotBlank(eProp)) { |
|
103 |
map.put(eKey, resolveProperty(eProp)); |
|
87 | 104 |
} |
88 | 105 |
} |
89 | 106 |
params.put(pName, map); |
... | ... | |
93 | 110 |
final Element item = (Element) i; |
94 | 111 |
final String iValue = item.valueOf("@value"); |
95 | 112 |
final String iRef = item.valueOf("@ref"); |
113 |
final String iProp = item.valueOf("@property"); |
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114 |
|
|
96 | 115 |
if (StringUtils.isNotBlank(iRef) && StringUtils.isNotBlank(globalParams.get(iRef))) { |
97 | 116 |
list.add(globalParams.get(iRef)); |
98 | 117 |
} else if (StringUtils.isNotBlank(iValue)) { |
99 | 118 |
list.add(iValue); |
119 |
} else if (StringUtils.isNotBlank(iProp)) { |
|
120 |
list.add(resolveProperty(iProp)); |
|
100 | 121 |
} |
101 | 122 |
} |
102 | 123 |
params.put(pName, list); |
... | ... | |
106 | 127 |
return params; |
107 | 128 |
} |
108 | 129 |
|
130 |
private String resolveProperty(final String propertyName) { |
|
131 |
if (!this.propertyFetcher.getProps().containsKey(propertyName)) { |
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log.warn("unable to find system property: " + propertyName); |
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133 |
} |
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return this.propertyFetcher.getProperty(propertyName); |
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} |
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136 |
|
|
109 | 137 |
private void checkValidity(final Graph graph) throws MSROException { |
110 | 138 |
|
111 | 139 |
final Set<String> nodesFromArcs = new HashSet<String>(); |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/db/ExecuteSqlJobNode.java | ||
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1 | 1 |
package eu.dnetlib.msro.workflows.nodes.db; |
2 | 2 |
|
3 | 3 |
import java.io.IOException; |
4 |
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4 | 5 |
import javax.annotation.Resource; |
5 | 6 |
|
7 |
import org.apache.commons.io.IOUtils; |
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8 |
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6 | 9 |
import eu.dnetlib.enabling.database.rmi.DatabaseService; |
7 | 10 |
import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
8 | 11 |
import eu.dnetlib.msro.workflows.graph.Arc; |
9 | 12 |
import eu.dnetlib.msro.workflows.nodes.AsyncJobNode; |
10 | 13 |
import eu.dnetlib.msro.workflows.procs.Env; |
11 |
import org.apache.commons.io.IOUtils; |
|
12 | 14 |
|
13 | 15 |
public class ExecuteSqlJobNode extends AsyncJobNode { |
14 | 16 |
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15 | 17 |
private String db; |
16 | 18 |
private String dbParam; |
17 |
private String dbProperty; |
|
18 | 19 |
|
19 | 20 |
private String sql; |
20 | 21 |
|
... | ... | |
23 | 24 |
|
24 | 25 |
@Override |
25 | 26 |
protected String execute(final Env env) throws Exception { |
26 |
serviceLocator.getService(DatabaseService.class).updateSQL(findDb(env), fetchSqlAsText(sql));
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27 |
this.serviceLocator.getService(DatabaseService.class).updateSQL(findDb(env), fetchSqlAsText(this.sql));
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27 | 28 |
return Arc.DEFAULT_ARC; |
28 | 29 |
} |
29 | 30 |
|
... | ... | |
32 | 33 |
} |
33 | 34 |
|
34 | 35 |
private String findDb(final Env env) { |
35 |
if (dbParam != null && !dbParam.isEmpty()) { |
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36 |
return env.getAttribute(dbParam, String.class); |
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37 |
} else if (dbProperty != null && !dbProperty.isEmpty()) { |
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38 |
return getPropertyFetcher().getProperty(dbProperty); |
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36 |
if (this.dbParam != null && !this.dbParam.isEmpty()) { |
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37 |
return env.getAttribute(this.dbParam, String.class); |
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39 | 38 |
} else { |
40 |
return db; |
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39 |
return this.db;
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|
41 | 40 |
} |
42 | 41 |
} |
43 | 42 |
|
44 | 43 |
public String getDb() { |
45 |
return db; |
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44 |
return this.db;
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|
46 | 45 |
} |
47 | 46 |
|
48 | 47 |
public void setDb(final String db) { |
... | ... | |
50 | 49 |
} |
51 | 50 |
|
52 | 51 |
public String getDbParam() { |
53 |
return dbParam; |
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52 |
return this.dbParam;
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54 | 53 |
} |
55 | 54 |
|
56 | 55 |
public void setDbParam(final String dbParam) { |
57 | 56 |
this.dbParam = dbParam; |
58 | 57 |
} |
59 | 58 |
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60 |
public String getDbProperty() { |
|
61 |
return dbProperty; |
|
62 |
} |
|
63 |
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|
64 |
public void setDbProperty(final String dbProperty) { |
|
65 |
this.dbProperty = dbProperty; |
|
66 |
} |
|
67 |
|
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68 | 59 |
public String getSql() { |
69 |
return sql; |
|
60 |
return this.sql;
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70 | 61 |
} |
71 | 62 |
|
72 | 63 |
public void setSql(final String sql) { |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/db/QueryDbJobNode.java | ||
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1 | 1 |
package eu.dnetlib.msro.workflows.nodes.db; |
2 | 2 |
|
3 | 3 |
import java.io.IOException; |
4 |
|
|
4 | 5 |
import javax.annotation.Resource; |
5 | 6 |
import javax.xml.ws.wsaddressing.W3CEndpointReference; |
6 | 7 |
|
8 |
import org.apache.commons.io.IOUtils; |
|
9 |
import org.apache.commons.lang.StringUtils; |
|
10 |
|
|
7 | 11 |
import eu.dnetlib.enabling.database.rmi.DatabaseService; |
8 | 12 |
import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
9 | 13 |
import eu.dnetlib.msro.workflows.graph.Arc; |
10 | 14 |
import eu.dnetlib.msro.workflows.nodes.AsyncJobNode; |
11 | 15 |
import eu.dnetlib.msro.workflows.procs.Env; |
12 |
import org.apache.commons.io.IOUtils; |
|
13 |
import org.apache.commons.lang.StringUtils; |
|
14 | 16 |
|
15 | 17 |
public class QueryDbJobNode extends AsyncJobNode { |
16 | 18 |
|
17 | 19 |
private String db; |
18 | 20 |
private String dbParam; |
19 |
private String dbProperty; |
|
20 | 21 |
|
21 | 22 |
private String sql; |
22 | 23 |
private String sqlForSize; |
... | ... | |
28 | 29 |
|
29 | 30 |
@Override |
30 | 31 |
protected String execute(final Env env) throws Exception { |
31 |
final String sqlText = fetchSqlAsText(sql); |
|
32 |
final String sqlText = fetchSqlAsText(this.sql);
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32 | 33 |
|
33 | 34 |
W3CEndpointReference epr = null; |
34 | 35 |
|
35 |
final DatabaseService dbService = serviceLocator.getService(DatabaseService.class); |
|
36 |
final DatabaseService dbService = this.serviceLocator.getService(DatabaseService.class);
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36 | 37 |
|
37 |
if (StringUtils.isNotBlank(xslt)) { |
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38 |
final String xsltText = IOUtils.toString(getClass().getResourceAsStream(xslt)); |
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38 |
if (StringUtils.isNotBlank(this.xslt)) {
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39 |
final String xsltText = IOUtils.toString(getClass().getResourceAsStream(this.xslt));
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39 | 40 |
|
40 |
if (StringUtils.isBlank(sqlForSize)) { |
|
41 |
if (StringUtils.isBlank(this.sqlForSize)) {
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41 | 42 |
epr = dbService.xsltSearchSQL(findDb(env), sqlText, xsltText); |
42 | 43 |
} else { |
43 |
epr = dbService.alternativeXsltSearchSQL(findDb(env), sqlText, fetchSqlAsText(sqlForSize), xsltText); |
|
44 |
epr = dbService.alternativeXsltSearchSQL(findDb(env), sqlText, fetchSqlAsText(this.sqlForSize), xsltText);
|
|
44 | 45 |
} |
45 | 46 |
} else { |
46 |
if (StringUtils.isBlank(sqlForSize)) { |
|
47 |
if (StringUtils.isBlank(this.sqlForSize)) {
|
|
47 | 48 |
epr = dbService.searchSQL(findDb(env), sqlText); |
48 | 49 |
} else { |
49 |
epr = dbService.alternativeSearchSQL(findDb(env), sqlText, fetchSqlAsText(sqlForSize)); |
|
50 |
epr = dbService.alternativeSearchSQL(findDb(env), sqlText, fetchSqlAsText(this.sqlForSize));
|
|
50 | 51 |
} |
51 | 52 |
} |
52 | 53 |
|
53 |
env.setAttribute(outputEprParam, epr.toString()); |
|
54 |
env.setAttribute(this.outputEprParam, epr.toString());
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54 | 55 |
|
55 | 56 |
return Arc.DEFAULT_ARC; |
56 | 57 |
} |
... | ... | |
60 | 61 |
} |
61 | 62 |
|
62 | 63 |
private String findDb(final Env env) { |
63 |
if (dbParam != null && !dbParam.isEmpty()) { |
|
64 |
return env.getAttribute(dbParam, String.class); |
|
65 |
} else if (dbProperty != null && !dbProperty.isEmpty()) { |
|
66 |
return getPropertyFetcher().getProperty(dbProperty); |
|
64 |
if (this.dbParam != null && !this.dbParam.isEmpty()) { |
|
65 |
return env.getAttribute(this.dbParam, String.class); |
|
67 | 66 |
} else { |
68 |
return db; |
|
67 |
return this.db;
|
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69 | 68 |
} |
70 | 69 |
} |
71 | 70 |
|
72 | 71 |
public String getDb() { |
73 |
return db; |
|
72 |
return this.db;
|
|
74 | 73 |
} |
75 | 74 |
|
76 | 75 |
public void setDb(final String db) { |
... | ... | |
78 | 77 |
} |
79 | 78 |
|
80 | 79 |
public String getDbParam() { |
81 |
return dbParam; |
|
80 |
return this.dbParam;
|
|
82 | 81 |
} |
83 | 82 |
|
84 | 83 |
public void setDbParam(final String dbParam) { |
... | ... | |
86 | 85 |
} |
87 | 86 |
|
88 | 87 |
public String getSql() { |
89 |
return sql; |
|
88 |
return this.sql;
|
|
90 | 89 |
} |
91 | 90 |
|
92 | 91 |
public void setSql(final String sql) { |
... | ... | |
94 | 93 |
} |
95 | 94 |
|
96 | 95 |
public String getXslt() { |
97 |
return xslt; |
|
96 |
return this.xslt;
|
|
98 | 97 |
} |
99 | 98 |
|
100 | 99 |
public void setXslt(final String xslt) { |
... | ... | |
102 | 101 |
} |
103 | 102 |
|
104 | 103 |
public String getOutputEprParam() { |
105 |
return outputEprParam; |
|
104 |
return this.outputEprParam;
|
|
106 | 105 |
} |
107 | 106 |
|
108 | 107 |
public void setOutputEprParam(final String outputEprParam) { |
109 | 108 |
this.outputEprParam = outputEprParam; |
110 | 109 |
} |
111 | 110 |
|
112 |
public String getDbProperty() { |
|
113 |
return dbProperty; |
|
114 |
} |
|
115 |
|
|
116 |
public void setDbProperty(final String dbProperty) { |
|
117 |
this.dbProperty = dbProperty; |
|
118 |
} |
|
119 |
|
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120 | 111 |
public String getSqlForSize() { |
121 |
return sqlForSize; |
|
112 |
return this.sqlForSize;
|
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122 | 113 |
} |
123 | 114 |
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124 | 115 |
public void setSqlForSize(final String sqlForSize) { |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/ProcessNode.java | ||
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1 | 1 |
package eu.dnetlib.msro.workflows.nodes; |
2 | 2 |
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3 |
import java.util.HashMap; |
|
4 |
import java.util.Map; |
|
5 |
import javax.annotation.Resource; |
|
3 |
import org.springframework.beans.factory.BeanNameAware; |
|
6 | 4 |
|
7 |
import com.google.gson.Gson; |
|
8 |
import eu.dnetlib.conf.PropertyFetcher; |
|
9 |
import eu.dnetlib.msro.workflows.procs.Env; |
|
10 | 5 |
import eu.dnetlib.msro.workflows.procs.Token; |
11 |
import org.apache.commons.lang.StringUtils; |
|
12 |
import org.apache.commons.logging.Log; |
|
13 |
import org.apache.commons.logging.LogFactory; |
|
14 |
import org.springframework.beans.factory.BeanNameAware; |
|
15 | 6 |
|
16 | 7 |
/** |
17 | 8 |
* Created by michele on 19/11/15. |
18 | 9 |
*/ |
19 | 10 |
public abstract class ProcessNode implements BeanNameAware { |
20 | 11 |
|
21 |
private static final Log log = LogFactory.getLog(ProcessNode.class); |
|
22 | 12 |
private String beanName; |
23 | 13 |
|
24 |
@Resource(name = "propertyFetcher") |
|
25 |
private PropertyFetcher propertyFetcher; |
|
26 |
|
|
27 |
/** |
|
28 |
* parameter values injected as json map into subclasses instance beans. |
|
29 |
*/ |
|
30 |
private String jsonParams; |
|
31 |
|
|
32 |
/** |
|
33 |
* parameter values retrieved from the process Env. |
|
34 |
*/ |
|
35 |
private String jsonEnvParams; |
|
36 |
|
|
37 |
/** |
|
38 |
* parameter values retrieved from the system properties. |
|
39 |
*/ |
|
40 |
private String jsonSystemPropertyParams; |
|
41 |
|
|
42 | 14 |
public abstract void execute(final Token token); |
43 | 15 |
|
44 |
protected final Map<String, Object> parseJsonParameters(final Env env) { |
|
45 |
final Map<String, Object> res = new HashMap<String, Object>(); |
|
46 |
|
|
47 |
for (Map.Entry<?, ?> e : asMap(getJsonEnvParams()).entrySet()) { |
|
48 |
final String propertyName = e.getValue().toString(); |
|
49 |
|
|
50 |
if (!getPropertyFetcher().getProps().containsKey(propertyName)) { |
|
51 |
log.warn("unable to find system property: " + propertyName); |
|
52 |
} |
|
53 |
|
|
54 |
final String propertyValue = getPropertyFetcher().getProperty(propertyName); |
|
55 |
res.put(e.getKey().toString(), propertyValue); |
|
56 |
} |
|
57 |
|
|
58 |
for (Map.Entry<?, ?> e : asMap(getJsonEnvParams()).entrySet()) { |
|
59 |
res.put(e.getKey().toString(), env.getAttribute(e.getValue().toString())); |
|
60 |
} |
|
61 |
|
|
62 |
for (Map.Entry<?, ?> e : asMap(getJsonParams()).entrySet()) { |
|
63 |
res.put(e.getKey().toString(), e.getValue()); |
|
64 |
} |
|
65 |
|
|
66 |
return res; |
|
67 |
} |
|
68 |
|
|
69 |
private Map<?, ?> asMap(final String s) { |
|
70 |
return StringUtils.isNotBlank(s) ? new Gson().fromJson(s, Map.class) : new HashMap<String, Object>(); |
|
71 |
} |
|
72 |
|
|
73 | 16 |
public String getBeanName() { |
74 |
return beanName; |
|
17 |
return this.beanName;
|
|
75 | 18 |
} |
76 | 19 |
|
77 | 20 |
@Override |
... | ... | |
79 | 22 |
this.beanName = beanName; |
80 | 23 |
} |
81 | 24 |
|
82 |
public PropertyFetcher getPropertyFetcher() { |
|
83 |
return propertyFetcher; |
|
84 |
} |
|
85 |
|
|
86 |
public void setPropertyFetcher(final PropertyFetcher propertyFetcher) { |
|
87 |
this.propertyFetcher = propertyFetcher; |
|
88 |
} |
|
89 |
|
|
90 |
public String getJsonParams() { |
|
91 |
return jsonParams; |
|
92 |
} |
|
93 |
|
|
94 |
public void setJsonParams(final String jsonParams) { |
|
95 |
this.jsonParams = jsonParams; |
|
96 |
} |
|
97 |
|
|
98 |
public String getJsonEnvParams() { |
|
99 |
return jsonEnvParams; |
|
100 |
} |
|
101 |
|
|
102 |
public void setJsonEnvParams(final String jsonEnvParams) { |
|
103 |
this.jsonEnvParams = jsonEnvParams; |
|
104 |
} |
|
105 |
|
|
106 |
public String getJsonSystemPropertyParams() { |
|
107 |
return jsonSystemPropertyParams; |
|
108 |
} |
|
109 |
|
|
110 |
public void setJsonSystemPropertyParams(final String jsonSystemPropertyParams) { |
|
111 |
this.jsonSystemPropertyParams = jsonSystemPropertyParams; |
|
112 |
} |
|
113 |
|
|
114 | 25 |
@Override |
115 | 26 |
public String toString() { |
116 |
return String.format("[node beanName=%s]", beanName); |
|
27 |
return String.format("[node beanName=%s]", this.beanName);
|
|
117 | 28 |
} |
118 | 29 |
} |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/transform/ApplyXsltJobNode.java | ||
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2 | 2 |
|
3 | 3 |
import java.util.HashMap; |
4 | 4 |
import java.util.Map; |
5 |
|
|
5 | 6 |
import javax.xml.ws.wsaddressing.W3CEndpointReference; |
6 | 7 |
|
8 |
import org.springframework.beans.factory.annotation.Required; |
|
9 |
import org.springframework.core.io.ClassPathResource; |
|
10 |
|
|
7 | 11 |
import eu.dnetlib.enabling.resultset.XSLTMappedResultSetFactory; |
8 | 12 |
import eu.dnetlib.enabling.resultset.client.utils.EPRUtils; |
9 | 13 |
import eu.dnetlib.msro.rmi.MSROException; |
10 | 14 |
import eu.dnetlib.msro.workflows.graph.Arc; |
11 | 15 |
import eu.dnetlib.msro.workflows.nodes.SimpleJobNode; |
12 | 16 |
import eu.dnetlib.msro.workflows.procs.Env; |
13 |
import org.springframework.beans.factory.annotation.Required; |
|
14 |
import org.springframework.core.io.ClassPathResource; |
|
15 | 17 |
|
16 | 18 |
public class ApplyXsltJobNode extends SimpleJobNode { |
17 | 19 |
|
18 | 20 |
private String inputEprParam; |
19 | 21 |
private String outputEprParam; |
20 | 22 |
private String xsltClasspath; |
23 |
private Map<String, String> xsltParams; |
|
21 | 24 |
|
22 | 25 |
private XSLTMappedResultSetFactory xsltMappedResultSetFactory; |
23 | 26 |
|
24 | 27 |
@Override |
25 | 28 |
protected String execute(final Env env) throws Exception { |
26 |
final String inputEpr = env.getAttribute(inputEprParam, String.class); |
|
27 |
if ((inputEpr == null) || inputEpr.isEmpty()) throw new MSROException("InputEprParam (" + inputEprParam + ") not found in ENV");
|
|
29 |
final String inputEpr = env.getAttribute(this.inputEprParam, String.class);
|
|
30 |
if ((inputEpr == null) || inputEpr.isEmpty()) { throw new MSROException("InputEprParam (" + this.inputEprParam + ") not found in ENV"); }
|
|
28 | 31 |
|
29 |
final Map<String, String> xsltParams = new HashMap<String, String>();
|
|
32 |
final Map<String, String> params = new HashMap<String, String>();
|
|
30 | 33 |
|
31 |
for (Map.Entry<String, Object> e : env.getAttributes().entrySet()) {
|
|
32 |
xsltParams.put(e.getKey().replaceAll(":", "_"), e.getValue().toString());
|
|
34 |
if (this.xsltParams != null) {
|
|
35 |
params.putAll(this.xsltParams);
|
|
33 | 36 |
} |
34 | 37 |
|
35 |
for (Map.Entry<String, Object> e : parseJsonParameters(env).entrySet()) {
|
|
36 |
xsltParams.put(e.getKey(), e.getValue().toString());
|
|
38 |
for (final Map.Entry<String, Object> e : env.getAttributes().entrySet()) {
|
|
39 |
params.put(e.getKey().replaceAll(":", "_"), e.getValue().toString());
|
|
37 | 40 |
} |
38 | 41 |
|
39 |
final W3CEndpointReference epr = xsltMappedResultSetFactory.createMappedResultSet(new EPRUtils().getEpr(inputEpr), |
|
40 |
(new ClassPathResource(xsltClasspath)), xsltParams);
|
|
42 |
final W3CEndpointReference epr = this.xsltMappedResultSetFactory.createMappedResultSet(new EPRUtils().getEpr(inputEpr),
|
|
43 |
(new ClassPathResource(this.xsltClasspath)), params);
|
|
41 | 44 |
|
42 |
env.setAttribute(outputEprParam, epr.toString()); |
|
45 |
env.setAttribute(this.outputEprParam, epr.toString());
|
|
43 | 46 |
|
44 | 47 |
return Arc.DEFAULT_ARC; |
45 | 48 |
} |
46 | 49 |
|
47 | 50 |
public String getInputEprParam() { |
48 |
return inputEprParam; |
|
51 |
return this.inputEprParam;
|
|
49 | 52 |
} |
50 | 53 |
|
51 | 54 |
public void setInputEprParam(final String inputEprParam) { |
... | ... | |
53 | 56 |
} |
54 | 57 |
|
55 | 58 |
public String getOutputEprParam() { |
56 |
return outputEprParam; |
|
59 |
return this.outputEprParam;
|
|
57 | 60 |
} |
58 | 61 |
|
59 | 62 |
public void setOutputEprParam(final String outputEprParam) { |
... | ... | |
61 | 64 |
} |
62 | 65 |
|
63 | 66 |
public String getXsltClasspath() { |
64 |
return xsltClasspath; |
|
67 |
return this.xsltClasspath;
|
|
65 | 68 |
} |
66 | 69 |
|
67 | 70 |
public void setXsltClasspath(final String xsltClasspath) { |
... | ... | |
69 | 72 |
} |
70 | 73 |
|
71 | 74 |
public XSLTMappedResultSetFactory getXsltMappedResultSetFactory() { |
72 |
return xsltMappedResultSetFactory; |
|
75 |
return this.xsltMappedResultSetFactory;
|
|
73 | 76 |
} |
74 | 77 |
|
75 | 78 |
@Required |
... | ... | |
77 | 80 |
this.xsltMappedResultSetFactory = xsltMappedResultSetFactory; |
78 | 81 |
} |
79 | 82 |
|
83 |
public Map<String, String> getXsltParams() { |
|
84 |
return this.xsltParams; |
|
85 |
} |
|
86 |
|
|
87 |
public void setXsltParams(final Map<String, String> xsltParams) { |
|
88 |
this.xsltParams = xsltParams; |
|
89 |
} |
|
90 |
|
|
80 | 91 |
} |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/transform/GroovyJobNode.java | ||
---|---|---|
2 | 2 |
|
3 | 3 |
import java.io.IOException; |
4 | 4 |
import java.util.Map; |
5 |
|
|
5 | 6 |
import javax.annotation.Resource; |
6 | 7 |
import javax.xml.ws.wsaddressing.W3CEndpointReference; |
7 | 8 |
|
9 |
import org.apache.commons.logging.Log; |
|
10 |
import org.apache.commons.logging.LogFactory; |
|
11 |
import org.springframework.beans.factory.annotation.Required; |
|
12 |
|
|
8 | 13 |
import com.google.common.collect.Maps; |
14 |
|
|
9 | 15 |
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; |
10 | 16 |
import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
11 | 17 |
import eu.dnetlib.enabling.resultset.MappedResultSetFactory; |
... | ... | |
16 | 22 |
import eu.dnetlib.msro.workflows.procs.Env; |
17 | 23 |
import groovy.lang.GroovyShell; |
18 | 24 |
import groovy.util.GroovyScriptEngine; |
19 |
import org.apache.commons.logging.Log; |
|
20 |
import org.apache.commons.logging.LogFactory; |
|
21 |
import org.springframework.beans.factory.annotation.Required; |
|
22 | 25 |
|
23 | 26 |
public class GroovyJobNode extends SimpleJobNode { |
24 | 27 |
|
... | ... | |
33 | 36 |
private String inputEprParam; |
34 | 37 |
private String outputEprParam; |
35 | 38 |
private String transformationRuleId; |
36 |
// private String groovyParams;
|
|
39 |
private Map<String, String> groovyParams;
|
|
37 | 40 |
|
38 | 41 |
@Resource |
39 | 42 |
private UniqueServiceLocator serviceLocator; |
40 | 43 |
|
41 | 44 |
private Map<String, String> retrieveGroovyParameter() { |
42 |
Map<String, String> out = Maps.newHashMap(); |
|
45 |
final Map<String, String> out = Maps.newHashMap();
|
|
43 | 46 |
|
44 |
String query = "for $x in collection('/db/DRIVER/GroovyProcessingDSResource/GroovyProcessingDSResourceType')" |
|
45 |
+ "where $x[.//RESOURCE_IDENTIFIER/@value='" + transformationRuleId + "']" |
|
47 |
final String query = "for $x in collection('/db/DRIVER/GroovyProcessingDSResource/GroovyProcessingDSResourceType')"
|
|
48 |
+ "where $x[.//RESOURCE_IDENTIFIER/@value='" + this.transformationRuleId + "']"
|
|
46 | 49 |
+ "return concat($x//GROOVY_CLASSPATH/text(),':::',$x//GROOVY_DNETCLASS/text())"; |
47 | 50 |
try { |
48 |
String result = serviceLocator.getService(ISLookUpService.class).quickSearchProfile(query).get(0);
|
|
51 |
final String result = this.serviceLocator.getService(ISLookUpService.class).quickSearchProfile(query).get(0);
|
|
49 | 52 |
if (result == null) { return null; } |
50 |
String[] data = result.trim().split(":::"); |
|
53 |
final String[] data = result.trim().split(":::");
|
|
51 | 54 |
if (data.length == 2) { |
52 | 55 |
out.put("classpath", data[0]); |
53 | 56 |
out.put("mainClass", data[1]); |
54 | 57 |
} |
55 | 58 |
|
56 | 59 |
return out; |
57 |
} catch (Exception e) { |
|
60 |
} catch (final Exception e) {
|
|
58 | 61 |
log.error(e); |
59 | 62 |
return null; |
60 | 63 |
} |
... | ... | |
62 | 65 |
|
63 | 66 |
@Override |
64 | 67 |
protected String execute(final Env env) throws Exception { |
65 |
final String inputEprString = env.getAttribute(inputEprParam, String.class); |
|
66 |
if (inputEprString == null || inputEprString.isEmpty()) { throw new MSROException("InputEprParam (" + inputEprParam + ") not found in ENV"); } |
|
68 |
final String inputEprString = env.getAttribute(this.inputEprParam, String.class);
|
|
69 |
if (inputEprString == null || inputEprString.isEmpty()) { throw new MSROException("InputEprParam (" + this.inputEprParam + ") not found in ENV"); }
|
|
67 | 70 |
final W3CEndpointReference inputEpr = new EPRUtils().getEpr(inputEprString); |
68 | 71 |
String groovyClasspath, groovyDnetClass; |
69 |
Map<String, String> prop = retrieveGroovyParameter(); |
|
72 |
final Map<String, String> prop = retrieveGroovyParameter();
|
|
70 | 73 |
groovyClasspath = prop.get("classpath"); |
71 | 74 |
groovyDnetClass = prop.get("mainClass"); |
72 |
W3CEndpointReference epr = transformGroovy(inputEpr, groovyClasspath, groovyDnetClass, parseJsonParameters(env));
|
|
73 |
env.setAttribute(outputEprParam, epr.toString()); |
|
75 |
final W3CEndpointReference epr = transformGroovy(inputEpr, groovyClasspath, groovyDnetClass, this.groovyParams);
|
|
76 |
env.setAttribute(this.outputEprParam, epr.toString());
|
|
74 | 77 |
return Arc.DEFAULT_ARC; |
75 | 78 |
} |
76 | 79 |
|
77 | 80 |
private W3CEndpointReference transformGroovy(final W3CEndpointReference source, |
78 | 81 |
final String groovyClasspath, |
79 | 82 |
final String groovyDnetClass, |
80 |
final Map<String, Object> params) throws ClassNotFoundException, IOException {
|
|
83 |
final Map<String, String> params) throws ClassNotFoundException, IOException {
|
|
81 | 84 |
|
82 |
GroovyScriptEngine gse = new GroovyScriptEngine(groovyClasspath); |
|
85 |
final GroovyScriptEngine gse = new GroovyScriptEngine(groovyClasspath);
|
|
83 | 86 |
gse.getGroovyClassLoader().loadClass(groovyDnetClass); |
84 | 87 |
log.info("***********************************************"); |
85 | 88 |
log.info("Loaded Groovy classes:"); |
86 |
for (Class<?> c : gse.getGroovyClassLoader().getLoadedClasses()) { |
|
89 |
for (final Class<?> c : gse.getGroovyClassLoader().getLoadedClasses()) {
|
|
87 | 90 |
log.info(c.getCanonicalName()); |
88 | 91 |
} |
89 | 92 |
log.info("***********************************************"); |
90 |
GroovyShell groovyShell = new GroovyShell(gse.getGroovyClassLoader()); |
|
93 |
final GroovyShell groovyShell = new GroovyShell(gse.getGroovyClassLoader());
|
|
91 | 94 |
|
92 |
Object go = groovyShell.evaluate("new " + groovyDnetClass + "()"); |
|
95 |
final Object go = groovyShell.evaluate("new " + groovyDnetClass + "()");
|
|
93 | 96 |
if (go instanceof GroovyUnaryFunction) { |
94 |
GroovyUnaryFunction groovyUnaryFunction = (GroovyUnaryFunction) go; |
|
97 |
final GroovyUnaryFunction groovyUnaryFunction = (GroovyUnaryFunction) go;
|
|
95 | 98 |
if (params != null) { |
96 | 99 |
groovyUnaryFunction.setParams(params); |
97 | 100 |
} |
98 |
return mappedResultSetFactory.createMappedResultSet(source, groovyUnaryFunction); |
|
101 |
return this.mappedResultSetFactory.createMappedResultSet(source, groovyUnaryFunction);
|
|
99 | 102 |
} else { |
100 | 103 |
throw new RuntimeException("Groovy object " + go + " is not supported"); |
101 | 104 |
} |
102 | 105 |
} |
103 | 106 |
|
104 | 107 |
public MappedResultSetFactory getMappedResultSetFactory() { |
105 |
return mappedResultSetFactory; |
|
108 |
return this.mappedResultSetFactory;
|
|
106 | 109 |
} |
107 | 110 |
|
108 | 111 |
@Required |
... | ... | |
111 | 114 |
} |
112 | 115 |
|
113 | 116 |
public String getInputEprParam() { |
114 |
return inputEprParam; |
|
117 |
return this.inputEprParam;
|
|
115 | 118 |
} |
116 | 119 |
|
117 | 120 |
public void setInputEprParam(final String inputEprParam) { |
... | ... | |
119 | 122 |
} |
120 | 123 |
|
121 | 124 |
public String getOutputEprParam() { |
122 |
return outputEprParam; |
|
125 |
return this.outputEprParam;
|
|
123 | 126 |
} |
124 | 127 |
|
125 | 128 |
public void setOutputEprParam(final String outputEprParam) { |
... | ... | |
127 | 130 |
} |
128 | 131 |
|
129 | 132 |
public String getTransformationRuleId() { |
130 |
return transformationRuleId; |
|
133 |
return this.transformationRuleId;
|
|
131 | 134 |
} |
132 | 135 |
|
133 | 136 |
public void setTransformationRuleId(final String transformationRuleId) { |
134 | 137 |
this.transformationRuleId = transformationRuleId; |
135 | 138 |
} |
136 | 139 |
|
140 |
public Map<String, String> getGroovyParams() { |
|
141 |
return this.groovyParams; |
|
142 |
} |
|
143 |
|
|
144 |
public void setGroovyParams(final Map<String, String> groovyParams) { |
|
145 |
this.groovyParams = groovyParams; |
|
146 |
} |
|
147 |
|
|
137 | 148 |
} |
modules/dnet-msro-service/branches/workflow_templates/src/main/java/eu/dnetlib/msro/workflows/nodes/transform/GroovyUnaryFunction.java | ||
---|---|---|
6 | 6 |
|
7 | 7 |
public abstract class GroovyUnaryFunction implements UnaryFunction<String, String> { |
8 | 8 |
|
9 |
private Map<String, Object> params;
|
|
9 |
private Map<String, String> params;
|
|
10 | 10 |
|
11 | 11 |
@Override |
12 | 12 |
abstract public String evaluate(String input); |
13 | 13 |
|
14 |
public Map<String, Object> getParams() {
|
|
15 |
return params; |
|
14 |
public Map<String, String> getParams() {
|
|
15 |
return this.params;
|
|
16 | 16 |
} |
17 | 17 |
|
18 |
public void setParams(final Map<String, Object> params) {
|
|
18 |
public void setParams(final Map<String, String> params) {
|
|
19 | 19 |
this.params = params; |
20 | 20 |
} |
21 | 21 |
|
modules/dnet-msro-service/branches/workflow_templates/src/main/resources/eu/dnetlib/test/schemas/WorkflowTemplateDSResourceType.xsd | ||
---|---|---|
92 | 92 |
<xs:attribute name="key" type="xs:NCName" use="required" /> |
93 | 93 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
94 | 94 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
95 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
95 | 96 |
</xs:complexType> |
96 | 97 |
</xs:element> |
97 | 98 |
</xs:sequence> |
... | ... | |
104 | 105 |
<xs:complexType> |
105 | 106 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
106 | 107 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
108 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
107 | 109 |
</xs:complexType> |
108 | 110 |
</xs:element> |
109 | 111 |
</xs:sequence> |
... | ... | |
113 | 115 |
<xs:attribute name="name" use="required" type="xs:NCName" /> |
114 | 116 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
115 | 117 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
118 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
116 | 119 |
</xs:complexType> |
117 | 120 |
</xs:element> |
118 | 121 |
</xs:sequence> |
modules/dnet-msro-service/branches/workflow_templates/src/main/resources/eu/dnetlib/test/schemas/WorkflowDSResourceType.xsd | ||
---|---|---|
146 | 146 |
<xs:attribute name="key" type="xs:NCName" use="required" /> |
147 | 147 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
148 | 148 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
149 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
149 | 150 |
</xs:complexType> |
150 | 151 |
</xs:element> |
151 | 152 |
</xs:sequence> |
... | ... | |
158 | 159 |
<xs:complexType> |
159 | 160 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
160 | 161 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
162 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
161 | 163 |
</xs:complexType> |
162 | 164 |
</xs:element> |
163 | 165 |
</xs:sequence> |
... | ... | |
167 | 169 |
<xs:attribute name="name" use="required" type="xs:NCName" /> |
168 | 170 |
<xs:attribute name="ref" use="optional" type="xs:string" /> |
169 | 171 |
<xs:attribute name="value" use="optional" type="xs:string" /> |
172 |
<xs:attribute name="property" use="optional" type="xs:string" /> |
|
170 | 173 |
</xs:complexType> |
171 | 174 |
</xs:element> |
172 | 175 |
</xs:sequence> |
Also available in: Unified diff
PROPERTY param