parse domain

hms-dbmi · Oct 8, 2023 · 7c02fd6 · 7c02fd6
1 parent b3e5448
commit 7c02fd6
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Showing 6 changed files with 117 additions and 7 deletions.
diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java
@@ -0,0 +1,53 @@
+package edu.harvard.dbmi.avillach.data.entity;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+@Schema(description = "A site that contains a PIC-SURE installation that we can send data to")
+@Table(uniqueConstraints = {
+    @UniqueConstraint(name = "unique_code", columnNames = { "code" }),
+    @UniqueConstraint(name = "unique_email", columnNames = { "domain" })
+})
+@Entity(name = "site")
+public class Site extends BaseEntity {
+
+    @Schema(description = "The site code. Ex: BCH")
+    @Column(length = 15)
+    private String code;
+
+    @Schema(description = "The site name. Ex: Boston Children's")
+    @Column(length = 255)
+    private String name;
+
+    @Schema(description = "The email domain of users for this site. Ex: childrens.harvard.edu")
+    @Column(length = 255)
+    private String domain;
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getDomain() {
+        return domain;
+    }
+
+    public void setDomain(String domain) {
+        this.domain = domain;
+    }
+}
diff --git a/...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java b/...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java
@@ -0,0 +1,14 @@
+package edu.harvard.dbmi.avillach.data.repository;
+
+import edu.harvard.dbmi.avillach.data.entity.NamedDataset;
+import edu.harvard.dbmi.avillach.data.entity.Site;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.transaction.Transactional;
+import java.util.UUID;
+
+@Transactional
+@ApplicationScoped
+public class SiteRepository extends BaseRepository<Site, UUID>{
+    protected SiteRepository() {super(Site.class);}
+}
diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java
@@ -11,10 +11,7 @@
 import javax.ws.rs.core.SecurityContext;
 
 import edu.harvard.dbmi.avillach.domain.*;
-import edu.harvard.dbmi.avillach.service.FormatService;
-import edu.harvard.dbmi.avillach.service.PicsureInfoService;
-import edu.harvard.dbmi.avillach.service.PicsureQueryService;
-import edu.harvard.dbmi.avillach.service.PicsureSearchService;
+import edu.harvard.dbmi.avillach.service.*;
 import io.swagger.v3.oas.annotations.OpenAPIDefinition;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.info.Info;
@@ -161,8 +158,7 @@ public QueryStatus query(
 		if (isInstitutionQuery == null || !isInstitutionQuery) {
 			return queryService.query(dataQueryRequest, headers);
 		} else {
-			dataQueryRequest.setInstitutionOfOrigin(context.getUserPrincipal().getName());
-			return queryService.institutionalQuery(dataQueryRequest, headers);
+			return queryService.institutionalQuery(dataQueryRequest, headers, context.getUserPrincipal().getName());
 		}
 	}
 

diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java
@@ -47,6 +47,9 @@ public class PicsureQueryService {
 	@Inject
 	ResourceWebClient resourceWebClient;
 
+	@Inject
+	SiteParsingService siteParsingService;
+
 	/**
 	 * Executes a query on a PIC-SURE resource and creates a Query entity in the
 	 * database for the query.
@@ -277,7 +280,9 @@ public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers){
 	 *                         and resource specific query (could be a string or a json object)
 	 * @return {@link QueryStatus}
 	 */
-	public QueryStatus institutionalQuery(QueryRequest dataQueryRequest, HttpHeaders headers) {
+	public QueryStatus institutionalQuery(QueryRequest dataQueryRequest, HttpHeaders headers, String email) {
+		String siteCode = siteParsingService.parseSiteOfOrigin(email).orElseThrow(() -> new RuntimeException("Bad email"));
+		dataQueryRequest.setInstitutionOfOrigin(siteCode);
 		Resource resource = verifyQueryRequest(dataQueryRequest, headers);
 		dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 

diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java
@@ -0,0 +1,41 @@
+package edu.harvard.dbmi.avillach.service;
+
+import edu.harvard.dbmi.avillach.data.entity.Site;
+import edu.harvard.dbmi.avillach.data.repository.SiteRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.inject.Inject;
+import java.util.List;
+import java.util.Optional;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class SiteParsingService {
+
+    private static final Logger LOG = LoggerFactory.getLogger(SiteParsingService.class);
+
+    private static final Pattern emailRegex = Pattern.compile("^([^@]+)(@)(.*)$");
+
+    @Inject
+    SiteRepository repository;
+
+    public Optional<String> parseSiteOfOrigin(String email) {
+        Matcher matcher = emailRegex.matcher(email);
+        if (!matcher.find()) {
+            LOG.warn("Unable to parse domain for email: {}", email);
+            return Optional.empty();
+        }
+
+        List<Site> matchingDomains = repository.getByColumn("domain", matcher.group(3));
+        if (matchingDomains.isEmpty()) {
+            LOG.warn("Unable to match domain for email: {}, looked for domain: {}", email, matcher.group(3));
+            return Optional.empty();
+        }
+        if (matchingDomains.size() > 1) {
+            LOG.warn("Multiple domains match email. This should never happen! Email: {}", email);
+            return Optional.empty();
+        }
+        return Optional.of(matchingDomains.get(0).getCode());
+    }
+}
diff --git a/pic-sure-api-war/src/main/resources/META-INF/persistence.xml b/pic-sure-api-war/src/main/resources/META-INF/persistence.xml
@@ -7,6 +7,7 @@
 		<class>edu.harvard.dbmi.avillach.data.entity.Query</class>
 		<class>edu.harvard.dbmi.avillach.data.entity.Resource</class>
 		<class>edu.harvard.dbmi.avillach.data.entity.NamedDataset</class>
+		<class>edu.harvard.dbmi.avillach.data.entity.Site</class>
 
 		<properties>
 			<property name="hibernate.archive.autodetection" value="class" />