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Adding in more metrics to internal endpoint, fixing logging issues,
changing wiring in of external nodes to reading in from JSON file as inspired by Jules Jacobsen strategy of using a YAML file for this. For now using JSON for ease, can swtich to YAML if needed later
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7 files changed

+96
-25
lines changed

7 files changed

+96
-25
lines changed

Diff for: ‎config/nodes.json

+2-2
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
44
"token" : "abcd",
55
"url" : "https://localhost:8443/match",
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"contentTypeHeader" : "application/vnd.ga4gh.matchmaker.v1.0+json",
7-
"contentLanguage" : "application/vnd.ga4gh.matchmaker.v1.0+json",
8-
"acceptHeader" : "en-US",
7+
"contentLanguage" : "en-US",
8+
"acceptHeader" : "application/vnd.ga4gh.matchmaker.v1.0+json",
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"selfSignedCertificate": true
1010
}]
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}

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/authentication/AuthenticationFilter.java

+16-14
Original file line numberDiff line numberDiff line change
@@ -46,8 +46,7 @@ public AuthenticationFilter(){
4646
String configFile = "file:" + System.getProperty("user.dir") + "/config/config.xml";
4747
ApplicationContext context = new ClassPathXmlApplicationContext(configFile);
4848
this.accessAuthorizedNode = context.getBean("accessAuthorizedNode", AccessAuthorizedNode.class);
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System.out.println(this.getAccessAuthorizedNode());
49+
5150
Map<String,String> tokenToMMECenterMapping = new HashMap<String,String>();
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List<String> authorizedTokes=new ArrayList<String>();
5352
for(AuthorizedToken authorizeNode : this.getAccessAuthorizedNode().getAccessAuthorizedNodes()){
@@ -71,25 +70,28 @@ public void doFilter(ServletRequest req, ServletResponse res,
7170
HttpServletResponse response = (HttpServletResponse) res;
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//----extract and validate headers from request----
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//Unauthorized
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//if Unauthorized, kick back immediately
7675
Map<String,String> validationResult=validateXAuthToken(request.getHeader(AuthenticationFilter.getxAuthTokenHeader()));
7776
if (validationResult.get("validated").equals("no")){
78-
this.getLogger().warn("authentication failed for: "+req.getServerName());
77+
this.getLogger().warn("authentication failed for: "+req.getServerName() + ": from node: " + validationResult.get("originMatchmakerNodeName"));
7978
response.sendError(401,"authentication failed");
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}
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//if authorized append the name of the center the match request came in from
8281
if (validationResult.get("validated").equals("yes")){
83-
request.setAttribute("originMatchmakerNodeName",validationResult.get("originMatchmakerNodeName"));
84-
}
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//unsupported API version
88-
if (!validateAcceptHeader(request.getHeader(AuthenticationFilter.getAcceptHeader()))){
89-
this.getLogger().warn("Accept header validation failed for: "+req.getServerName());
90-
response.sendError(406,"unsupported API version, supported versions=[1.0]");
82+
request.setAttribute("originMatchmakerNodeName",validationResult.get("originMatchmakerNodeName"));
83+
//then check if API version is supported
84+
if (!validateAcceptHeader(request.getHeader(AuthenticationFilter.getAcceptHeader()))){
85+
this.getLogger().warn("Accept header validation failed for: "+req.getServerName());
86+
this.getLogger().warn("This accept header provided is wrong: "+ request.getHeader(AuthenticationFilter.getAcceptHeader()));
87+
response.sendError(406,"unsupported API version, supported versions=[1.0]");
88+
}
89+
//OK everything looks good, move forward with this request
90+
else{
91+
this.getLogger().info("request passes access criteria, processing: " + validationResult.get("originMatchmakerNodeName"));
92+
chain.doFilter(request, response);
93+
}
9194
}
92-
chain.doFilter(request, response);
9395
}
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9597

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/entities/MatchmakerNode.java

+4-1
Original file line numberDiff line numberDiff line change
@@ -53,13 +53,16 @@ public String getUrl() {
5353
}
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5555

56+
57+
5658
/* (non-Javadoc)
5759
* @see java.lang.Object#toString()
5860
*/
5961
@Override
6062
public String toString() {
6163
return "MatchmakerNode [name=" + name + ", token=" + token + ", url=" + url + ", acceptHeader=" + acceptHeader
62-
+ ", contentHeader=" + contentTypeHeader + ", contentLanguage=" + contentLanguage + "]";
64+
+ ", contentTypeHeader=" + contentTypeHeader + ", contentLanguage=" + contentLanguage
65+
+ ", selfSignedCertificate=" + selfSignedCertificate + "]";
6366
}
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6568

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/entities/PrivilegedMetric.java

+68-3
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,17 @@
77
*/
88
package org.broadinstitute.macarthurlab.matchbox.entities;
99

10+
11+
import java.util.Map;
12+
1013
/**
1114
* @author harindra
1215
*
1316
*/
1417
public class PrivilegedMetric extends PublicMetric{
18+
19+
private Map<String,Integer> geneCounts;
20+
private Map<String,Integer> phenotypeCounts;
1521

1622
/**
1723
* default constructor
@@ -20,17 +26,76 @@ public PrivilegedMetric() {
2026
super();
2127
}
2228

23-
/**
24-
* Primary constructor
29+
30+
/**
31+
* @param numberOfSubmitters
32+
* @param numberOfUniqueGenes
33+
* @param numberOfUniqueFeatures
34+
* @param numberOfCasesWithDiagnosis
35+
* @param numberOfCases
36+
* @param percentageOfGenesThatMatch
37+
* @param meanNumberOfGenesPerCase
38+
* @param meanNumberOfVariantsPerCase
39+
* @param meanNumberOfPhenotypesPerCase
40+
* @param numberOfRequestsReceived
41+
* @param numberOfPotentialMatchesSent
42+
* @param geneCounts
2543
*/
2644
public PrivilegedMetric(int numberOfSubmitters, int numberOfUniqueGenes, int numberOfUniqueFeatures,
2745
int numberOfCasesWithDiagnosis, int numberOfCases, double percentageOfGenesThatMatch,
2846
double meanNumberOfGenesPerCase, double meanNumberOfVariantsPerCase, double meanNumberOfPhenotypesPerCase,
29-
int numberOfRequestsReceived, int numberOfPotentialMatchesSent) {
47+
int numberOfRequestsReceived, int numberOfPotentialMatchesSent,
48+
Map<String,Integer> geneCounts,
49+
Map<String,Integer> phenotypeCounts) {
50+
3051
super(numberOfSubmitters, numberOfUniqueGenes, numberOfUniqueFeatures, numberOfCasesWithDiagnosis, numberOfCases,
3152
percentageOfGenesThatMatch, meanNumberOfGenesPerCase, meanNumberOfVariantsPerCase,
3253
meanNumberOfPhenotypesPerCase, numberOfRequestsReceived, numberOfPotentialMatchesSent);
54+
55+
this.geneCounts = geneCounts;
56+
this.phenotypeCounts = phenotypeCounts;
57+
}
58+
59+
60+
61+
62+
63+
64+
/**
65+
* @return the geneCounts
66+
*/
67+
public Map<String, Integer> getGeneCounts() {
68+
return geneCounts;
69+
}
70+
71+
/**
72+
* @param geneCounts the geneCounts to set
73+
*/
74+
public void setGeneCounts(Map<String, Integer> geneCounts) {
75+
this.geneCounts = geneCounts;
3376
}
77+
78+
79+
/**
80+
* @return the phenotypeCounts
81+
*/
82+
public Map<String, Integer> getPhenotypeCounts() {
83+
return phenotypeCounts;
84+
}
85+
86+
87+
/**
88+
* @param phenotypeCounts the phenotypeCounts to set
89+
*/
90+
public void setPhenotypeCounts(Map<String, Integer> phenotypeCounts) {
91+
this.phenotypeCounts = phenotypeCounts;
92+
}
93+
94+
95+
96+
97+
98+
3499

35100

36101
}

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/metrics/PrivilegedMetricServiceImpl.java

+3-1
Original file line numberDiff line numberDiff line change
@@ -63,7 +63,9 @@ public Metric getMetrics() {
6363
this.getMeanNumberOfVariantsPerCase(allPatients),
6464
this.getMeanNumberOfPhenotypesPerCase(allPatients),
6565
this.getNumOfIncomingMatchRequests(),
66-
this.getNumOfMatches());
66+
this.getNumOfMatches(),
67+
this.countGenesInSystem(allPatients),
68+
this.countPhenotypesInSystem(allPatients));
6769
}
6870

6971

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/network/Communication.java

+2-3
Original file line numberDiff line numberDiff line change
@@ -71,8 +71,8 @@ public List<MatchmakerResult> callNode(Node matchmakerNode, Patient queryPatient
7171
connection.setRequestProperty("X-Auth-Token",matchmakerNode.getToken());
7272
connection.setRequestProperty("Content-Type",matchmakerNode.getContentTypeHeader());
7373
connection.setRequestProperty("Accept",matchmakerNode.getAcceptHeader());
74-
connection.setRequestProperty("Content-Language",matchmakerNode.getContentLanguage());
75-
74+
connection.setRequestProperty("Content-Language",matchmakerNode.getContentLanguage());
75+
7676
connection.setUseCaches(false);
7777
connection.setDoOutput(true);
7878

@@ -114,7 +114,6 @@ public List<MatchmakerResult> callNode(Node matchmakerNode, Patient queryPatient
114114

115115
}
116116
} catch (Exception e) {
117-
e.printStackTrace();
118117
this.getLogger().error("error connecting to: " + matchmakerNode.getName() + ", moving on.. : "+e.getMessage());
119118
} finally {
120119
if(connection != null) {

Diff for: ‎src/main/java/org/broadinstitute/macarthurlab/matchbox/search/MatchmakerSearchImpl.java

+1-1
Original file line numberDiff line numberDiff line change
@@ -179,7 +179,7 @@ public List<String> searchInLocalDatabaseOnly(Patient queryPatient, String hostN
179179
*/
180180
private List<MatchmakerResult> searchNode(Node matchmakerNode, Patient queryPatient) {
181181
this.getLogger().info("searching in external node: "+matchmakerNode.getName());
182-
return this.getHttpCommunication().callNode(matchmakerNode, queryPatient);
182+
return this.getHttpCommunication().callNode(matchmakerNode, queryPatient);
183183
}
184184

185185

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