Release 1.1.0

## What's Changed ### New Features 🚀 * remove queries to user database, use user from known locations by @wow-such-code in #20 * Allow for property name adjustment in the LIMS by @KochTobi in #21 ### Bugfixes 🪲 * update workflows by @wow-such-code in #19 * Ignore sequencing completed status. by @KochTobi in #22 ## New Contributors * @JohnnyQ5 made their first contribution in #18 * @wow-such-code made their first contribution in #19 **Full Changelog**: 1.0.2...1.1.0
qbicsoftware · Jul 20, 2022 · 8c791fe · 8c791fe
2 parents 48b2044 + ad3fd9c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,9 +2,9 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+For releases after 1.0.0 please refer to [GitHub Releases](https://github.com/qbicsoftware/sample-status-reporter/releases)
+
 ## 1.0.0 (2022-01-28)
 
 * Add first working implementation to report updates based on a point in time.
 * The application fails when any problems arise retrieving samples 
-
-
diff --git a/README.md b/README.md
@@ -1,9 +1,8 @@
 <div align="center">
 
 # LIMS Sample Status Reporter
-<i>A command line tool to report LIMS changes to the sample-tracking service</i>.
-
 
+<i>A command line tool to report LIMS changes to the sample-tracking service</i>.
 
 [![Build Maven Package](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/build_package.yml/badge.svg)](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/build_package.yml)
 [![Run Maven Tests](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/run_tests.yml/badge.svg)](https://github.com/qbicsoftware/sample-status-reporter/actions/workflows/run_tests.yml)
@@ -20,7 +19,7 @@
 
 As updating sample statuses in more then one place can lead to errors and frustration, automation of
 this process is deemed important. The `sample-status-reporter` automates the migration of updated
-sample statuses from an openBis LIMS to the 
+sample statuses from an openBis LIMS to the
 [sample-tracking-service](https://github.com/qbicsoftware/sample-tracking-service).
 
 **Interaction with the sample-tracking-service**
@@ -37,12 +36,13 @@ entry for further detail.
 **Integration with the openBIS LIMS**
 
 The sample information is retrieved automatically from an openBIS instance acting as LIMS. The
-configuration of the openBIS needs to make sure each sample proviedes the following properties:
+configuration of the openBIS needs to make sure each sample provides a QBiC barcode (containing `Q`) and a sample status.
+Furthermore, the names of the properties providing this information needs to be provided (see [Environment Variables](#environment-variables)).
 
-* `QBIC_BARCODE` containing `Q`
-* `SAMPLE_STATUS` containing values
-  from `[SAMPLE_RECEIVED, QC_PASSED, QC_FAILED, LIBRARY_PREP_FINISHED]`.
+* The sample status may contain values
+  from `["Sample received", "QC passed", "QC failed", "Library completed"]`.
 
+Besides that you can configure LIMS statuses this tools will ignore. For this pass a comma-separated list in the `LIMS_IGNORED_STATUSES` environment variable.
 This tool acts in the role of a user configured by you. Please make sure, that the configured user
 only sees projects where you want to propagate the status to the sample-tracking system.
 
@@ -97,22 +97,22 @@ Please note that this project requires `java 17`.
 
 For this application to be run the following environment variables need to be set:
 
-| Environment Variable                | Description                                                            | Default Value                          |
-|-------------------------------------|------------------------------------------------------------------------|----------------------------------------|
-| `LAST_UPDATE_FILE`                  | A path to a persistent file. The last successful run is stored here.   | `last-updated.txt `                    |
-| `LIMS_PASSWORD`                     | The password to access the OpenBiS LIMS                                |                                        |
-| `LIMS_SERVER_URL`                   | The URL to the OpenBiS LIMS API                                        |                                        |
-| `LIMS_USER`                         | The user to access the OpenBiS LIMS                                    |                                        |
-| `SAMPLE_TRACKING_AUTH_PASSWORD`     | The password for the sample tracking user                              | `astrongpassphrase! `                  |
-| `SAMPLE_TRACKING_AUTH_USER`         | The username for the sample tracking service                           | `qbic`                                 |
-| `SAMPLE_TRACKING_LOCATION_ENDPOINT` | The endpoint to list all locations. This does not contain the base url | `/locations`                           |
-| `SAMPLE_TRACKING_LOCATION_USER`     | The sample tracking user currently using the application               | `[email protected]`                 |
-| `SAMPLE_TRACKING_URL`               | The base URL for the sample tracking service                           | `http://localhost.de`                  |
-| `USER_DB_DIALECT`                   | The database dialect of the user database                              | `org.hibernate.dialect.MariaDBDialect` |
-| `USER_DB_DRIVER`                    | The database driver for the user database                              | `com.mysql.cj.jdbc.Driver`             |
-| `USER_DB_HOST`                      | The URL to the host of the user database containing the database name  | `localhost`                            |
-| `USER_DB_USER_NAME`                 | The database user name                                                 | `myusername`                           |
-| `USER_DB_USER_PW`                   | The database user password                                             | ` astrongpassphrase!`                  |
-
-
-
+| Environment Variable                | Description                                                                                   | Default Value                          |
+|-------------------------------------|-----------------------------------------------------------------------------------------------|----------------------------------------|
+| `LAST_UPDATE_FILE`                  | A path to a persistent file. The last successful run is stored here.                          | `last-updated.txt `                    |
+| `LIMS_PASSWORD`                     | The password to access the OpenBiS LIMS                                                       |                                        |
+| `LIMS_SERVER_URL`                   | The URL to the OpenBiS LIMS API                                                               |                                        |
+| `LIMS_USER`                         | The user to access the OpenBiS LIMS                                                           |                                        |
+| `LIMS_BARCODE_PROPERTY`             | The name of the property in the OpenBiS LIMS from which to read the QBiC barcode              |                                        |
+| `LIMS_STATUS_PROPERTY`              | The name of the property in the OpenBis LIMS from which to read the sample status information |                                        |
+| `LIMS_IGNORED_STATUSES`             | A comma-separated list of LIMS sample statuses to be ignored by the reporter                  |                                        |
+| `SAMPLE_TRACKING_AUTH_PASSWORD`     | The password for the sample tracking user                                                     | `astrongpassphrase! `                  |
+| `SAMPLE_TRACKING_AUTH_USER`         | The username for the sample tracking service                                                  | `qbic`                                 |
+| `SAMPLE_TRACKING_LOCATION_ENDPOINT` | The endpoint to list all locations. This does not contain the base url                        | `/locations`                           |
+| `SAMPLE_TRACKING_LOCATION_USER`     | The sample tracking user currently using the application                                      | `[email protected]`                 |
+| `SAMPLE_TRACKING_URL`               | The base URL for the sample tracking service                                                  | `http://localhost.de`                  |
+| `USER_DB_DIALECT`                   | The database dialect of the user database                                                     | `org.hibernate.dialect.MariaDBDialect` |
+| `USER_DB_DRIVER`                    | The database driver for the user database                                                     | `com.mysql.cj.jdbc.Driver`             |
+| `USER_DB_HOST`                      | The URL to the host of the user database containing the database name                         | `localhost`                            |
+| `USER_DB_USER_NAME`                 | The database user name                                                                        | `myusername`                           |
+| `USER_DB_USER_PW`                   | The database user password                                                                    | ` astrongpassphrase!`                  |
diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/QbicSampleStatusReporter.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/QbicSampleStatusReporter.groovy
@@ -16,24 +16,21 @@ import java.time.Instant
 @Component
 class QbicSampleStatusReporter implements SampleStatusReporter {
 
-  @Autowired
-  private SampleTrackingService sampleTrackingService
+    @Autowired
+    private SampleTrackingService sampleTrackingService
 
-  @Autowired
-  private LocationService locationService
+    @Autowired
+    private LocationService locationService
 
+    @Override
+    void reportSampleStatusUpdate(SampleUpdate sampleUpdate) {
+        Location currentLocation = locationService.getUpdatingPersonLocation().orElseThrow({
+            new RuntimeException("No current location could be determined for the provided user.")
+        })
+        String sampleCode = sampleUpdate.getSample().getSampleCode()
+        String status = sampleUpdate.getUpdatedStatus()
+        Instant updateTimepoint = sampleUpdate.getModificationDate()
+        sampleTrackingService.updateSampleLocation(sampleCode, currentLocation, status, updateTimepoint)
+    }
 
-  @Override
-  void reportSampleStatusUpdate(SampleUpdate sampleUpdate) {
-    Location currentLocation = locationService.getCurrentLocation().orElseThrow({
-      new RuntimeException("No current location could be determined.")
-    })
-    String sampleCode = sampleUpdate.getSample().getSampleCode()
-    String status = sampleUpdate.getUpdatedStatus()
-    Instant updateTimepoint = sampleUpdate.getModificationDate()
-    Person responsiblePerson = locationService.getResponsiblePerson().orElseThrow({
-      new RuntimeException("No responsible person for the update was determined.")
-    })
-    sampleTrackingService.updateSampleLocation(sampleCode, currentLocation, status, updateTimepoint, responsiblePerson)
-  }
 }
diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/api/LocationService.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/api/LocationService.groovy
@@ -8,16 +8,16 @@ package life.qbic.samplestatus.reporter.api
  * @since 1.0.0
  */
 interface LocationService {
-  /**
-   * <p>Returns an {@link Optional} of the current location the LIMS is configured for. <b>Must</b> return an
-   * object of type {@link Optional#empty} if no matching location was found.</p>
-   *
-   * @return an {@link Optional} wrapping a matching current {@link Location} or empty, if none was found.
-   * @throws ServiceException in case the service cannot retrieve the location due to for example connection issues.
-   * Must not be thrown, if the internal query was successful but no matching location was found. Instead, return an {@link Optional#empty}.
-   * @since 1.0.0
-   */
-  Optional<Location> getCurrentLocation() throws ServiceException
 
-  Optional<Person> getResponsiblePerson() throws ServiceException
+    /**
+     * <p>Returns an {@link Optional} of the location the LIMS is configured for, determined by the user. <b>Must</b> return an
+     * object of type {@link Optional#empty} if no matching location was found.</p>
+     *
+     * @return an {@link Optional} wrapping a matching current {@link Location} or empty, if none was found.
+     * @throws ServiceException in case the service cannot retrieve the location due to for example connection issues.
+     * Must not be thrown, if the internal query was successful but no matching location was found. Instead, return an {@link Optional#empty}.
+     * @since 0.1.0
+     */
+    Optional<Location> getUpdatingPersonLocation()
+
 }
diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/api/SampleTrackingService.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/api/SampleTrackingService.groovy
@@ -14,24 +14,24 @@ import java.time.Instant
  */
 interface SampleTrackingService {
 
-  /**
-   * Retrieves the location associated with the userId provided.
-   * @param userId an identifier for a user in the sample tracking system
-   * @return the location that this user is associated with
-   * @since 1.0.0
-   */
-  Optional<Location> getLocationForUser(String userId)
+    /**
+     * Retrieves the location associated with the userId provided.
+     * @param userId an identifier for a user in the sample tracking system
+     * @return the location that this user is associated with
+     * @since 1.0.0
+     */
+    Optional<Location> getLocationForUser(String userId)
+
+    /**
+     * Updates a sample to a given location with a status set in the location.
+     * This information is stored on the persistence layer.
+     * @param sampleCode the code of the sample changing status or location
+     * @param location the new location with a sample status already set
+     * @param status sample status to be set
+     * @param timestamp time of the update
+     * @throws SampleUpdateException in case the sample update was unsuccessful
+     * @since 1.0.0
+     */
+    void updateSampleLocation(String sampleCode, Location location, String status, Instant timestamp) throws SampleUpdateException
 
-  /**
-   * Updates a sample to a given location with a status set in the location.
-   * This information is stored on the persistence layer.
-   * @param sampleCode the code of the sample changing status or location
-   * @param location the new location with a sample status already set
-   * @param status sample status to be set.
-   * @param timestamp the point in time that will be recorded as time of this update
-   * @param responsiblePerson the person responsible for this update
-   * @throws SampleUpdateException in case the sample update was unsuccessful
-   * @since 1.0.0
-   */
-  void updateSampleLocation(String sampleCode, Location location, String status, Instant timestamp, Person responsiblePerson) throws SampleUpdateException
 }
diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/commands/ReportSinceInstant.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/commands/ReportSinceInstant.groovy
@@ -82,6 +82,7 @@ class ReportSinceInstant implements Runnable {
       updatedSamples.stream()
               .filter(Result::isOk)
               .map(Result::getValue)
+              .sorted((SampleUpdate su1, SampleUpdate su2) -> su1.getModificationDate().compareTo(su2.getModificationDate()))
               .peek(it -> log.info("\tUpdating $it"))
               .forEach(statusReporter::reportSampleStatusUpdate)
       log.info("Finished processing.")

diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/services/LastUpdateSearch.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/services/LastUpdateSearch.groovy
@@ -28,15 +28,17 @@ class LastUpdateSearch implements UpdateSearchService {
   }
 
   /**
-   * @inheritDocs
+   * {@inheritDoc}
+   * @return {@inheritDoc}
    */
   @Override
   Optional<Instant> getLastUpdateSearchTimePoint() {
     return Optional.ofNullable(this.lastSearch)
   }
 
   /**
-   * @inheritDocs
+   * {@inheritDoc}
+   * @param lastSearchTimePoint {@inheritDoc}
    */
   @Override
   void saveLastSearchTimePoint(Instant lastSearchTimePoint) {

diff --git a/src/main/groovy/life/qbic/samplestatus/reporter/services/NcctLocationService.groovy b/src/main/groovy/life/qbic/samplestatus/reporter/services/NcctLocationService.groovy
@@ -4,7 +4,7 @@ import life.qbic.samplestatus.reporter.api.Location
 import life.qbic.samplestatus.reporter.api.LocationService
 import life.qbic.samplestatus.reporter.api.Person
 import life.qbic.samplestatus.reporter.api.SampleTrackingService
-import life.qbic.samplestatus.reporter.services.users.UserService
+import life.qbic.samplestatus.reporter.api.ServiceException
 import org.springframework.beans.factory.annotation.Autowired
 import org.springframework.beans.factory.annotation.Value
 import org.springframework.boot.context.properties.ConfigurationProperties
@@ -21,23 +21,15 @@ import org.springframework.stereotype.Component
 @ConfigurationProperties
 class NcctLocationService implements LocationService {
 
-  @Value('${service.sampletracking.location.user}')
-  private String userId
+    @Value('${service.sampletracking.location.user}')
+    private String userId
 
-  @Autowired
-  private SampleTrackingService sampleTrackingService
+    @Autowired
+    private SampleTrackingService sampleTrackingService
 
-  @Autowired
-  private UserService userService
+    @Override
+    Optional<Location> getUpdatingPersonLocation() throws ServiceException {
+        return sampleTrackingService.getLocationForUser(userId)
+    }
 
-  @Override
-  Optional<Location> getCurrentLocation() {
-    return sampleTrackingService.getLocationForUser(userId)
-  }
-
-  @Override
-  Optional<Person> getResponsiblePerson() {
-    Optional<Person> responsiblePerson = userService.getPerson(userId)
-    return responsiblePerson
-  }
 }