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- Requirement: in order to know where to send data, we need to associate each query with the requester's site - Create table of site code, site name, site email domain - When an institutional query request is made: - Parse the site code from the email of the requesting user - Add that site code to the query request - When persisting a query object after starting a query request - Check for a site code in the query request - Add it to the query meta if it exists - Add some extra niceness for later data transfer work - S3 status code - Interface, implementations for general use, GIC - Repos I verified this change with: - pic-sure-auth-microapp: master and fence branches - pic-sure-gic-common-frontend: Search resource, UUID gen resource
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5 changes: 5 additions & 0 deletions
5
pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/DataSharingStatus.java
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| package edu.harvard.dbmi.avillach.data.entity; | ||
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| public enum DataSharingStatus { | ||
| Unknown, Pending, Error, Complete, NotShared | ||
| } |
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pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java
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| package edu.harvard.dbmi.avillach.data.entity; | ||
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| import io.swagger.v3.oas.annotations.media.Schema; | ||
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| import javax.persistence.Column; | ||
| import javax.persistence.Entity; | ||
| import javax.persistence.Table; | ||
| import javax.persistence.UniqueConstraint; | ||
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| @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 { | ||
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| @Schema(description = "The site code. Ex: BCH") | ||
| @Column(length = 15) | ||
| private String code; | ||
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| @Schema(description = "The site name. Ex: Boston Children's") | ||
| @Column(length = 255) | ||
| private String name; | ||
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| @Schema(description = "The email domain of users for this site. Ex: childrens.harvard.edu") | ||
| @Column(length = 255) | ||
| private String domain; | ||
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| public String getCode() { | ||
| return code; | ||
| } | ||
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| public void setCode(String code) { | ||
| this.code = code; | ||
| } | ||
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| public String getName() { | ||
| return name; | ||
| } | ||
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| public void setName(String name) { | ||
| this.name = name; | ||
| } | ||
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| public String getDomain() { | ||
| return domain; | ||
| } | ||
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| public void setDomain(String domain) { | ||
| this.domain = domain; | ||
| } | ||
| } |
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...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java
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| package edu.harvard.dbmi.avillach.data.repository; | ||
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| import edu.harvard.dbmi.avillach.data.entity.NamedDataset; | ||
| import edu.harvard.dbmi.avillach.data.entity.Site; | ||
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| import javax.enterprise.context.ApplicationScoped; | ||
| import javax.transaction.Transactional; | ||
| import java.util.UUID; | ||
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| @Transactional | ||
| @ApplicationScoped | ||
| public class SiteRepository extends BaseRepository<Site, UUID>{ | ||
| protected SiteRepository() {super(Site.class);} | ||
| } |
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pic-sure-api-data/src/main/resources/db/sql/V6__ADD_SITE_TABLE.sql
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| USE `picsure`; | ||
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| CREATE TABLE `site` ( | ||
| `uuid` binary(16) NOT NULL, | ||
| `code` varchar(15) COLLATE utf8_bin DEFAULT NULL, | ||
| `name` varchar(255) COLLATE utf8_bin DEFAULT NULL, | ||
| `domain` varchar(255) COLLATE utf8_bin DEFAULT NULL, | ||
| PRIMARY KEY (`uuid`), | ||
| CONSTRAINT `unique_code` UNIQUE (`code`), | ||
| CONSTRAINT `unique_domain` UNIQUE (`domain`) | ||
| ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin; |
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41 changes: 41 additions & 0 deletions
41
pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java
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| package edu.harvard.dbmi.avillach.service; | ||
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| import edu.harvard.dbmi.avillach.data.entity.Site; | ||
| import edu.harvard.dbmi.avillach.data.repository.SiteRepository; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import javax.inject.Inject; | ||
| import java.util.List; | ||
| import java.util.Optional; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
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| public class SiteParsingService { | ||
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| private static final Logger LOG = LoggerFactory.getLogger(SiteParsingService.class); | ||
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| private static final Pattern emailRegex = Pattern.compile("^([^@]+)(@)(.*)$"); | ||
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| @Inject | ||
| SiteRepository repository; | ||
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| 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(); | ||
| } | ||
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| 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()); | ||
| } | ||
| } |
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