Merge pull request #25 from cancogen-virus-seq/rc/0.3.0

Release 0.3.0
virusseq · Sep 15, 2021 · 784966d · 784966d
2 parents cf8e6b2 + 3cd0224
commit 784966d
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Showing 4 changed files with 47 additions and 11 deletions.
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>org.cancogen-virus-seq</groupId>
     <artifactId>singularity</artifactId>
-    <version>0.2.1</version>
+    <version>0.3.0</version>
     <name>singularity</name>
     <description>Singularity - All contributors, All files</description>
     <properties>

diff --git a/...in/java/org/cancogenvirusseq/singularity/components/hoc/InstantToArchiveBuildRequest.java b/...in/java/org/cancogenvirusseq/singularity/components/hoc/InstantToArchiveBuildRequest.java
@@ -11,8 +11,6 @@
 import org.cancogenvirusseq.singularity.components.model.CountAndLastUpdatedResult;
 import org.cancogenvirusseq.singularity.repository.ArchivesRepo;
 import org.cancogenvirusseq.singularity.repository.model.Archive;
-import org.cancogenvirusseq.singularity.repository.model.ArchiveStatus;
-import org.cancogenvirusseq.singularity.repository.model.ArchiveType;
 import org.elasticsearch.index.query.QueryBuilders;
 import org.springframework.stereotype.Component;
 import reactor.core.publisher.Mono;
@@ -40,12 +38,7 @@ public Mono<ArchiveBuildRequest> apply(Instant instant) {
   private Mono<Archive> createAndSaveArchiveToDatabase(
       CountAndLastUpdatedResult countAndLastUpdatedResult) {
     return archivesRepo.save(
-        Archive.builder()
-            .status(ArchiveStatus.BUILDING)
-            .type(ArchiveType.ALL)
-            .hashInfo(countAndLastUpdatedResult.getLastUpdatedDate().getValueAsString())
-            .numOfSamples(countAndLastUpdatedResult.getNumDocuments().getValue())
-            .build());
+        Archive.newAllArchiveFromCountAndLastUpdatedResult(countAndLastUpdatedResult));
   }
 
   private Function<Archive, ArchiveBuildRequest> transformToArchiveBuildRequest(Instant instant) {

diff --git a/src/main/java/org/cancogenvirusseq/singularity/components/model/AllArchiveHashInfo.java b/src/main/java/org/cancogenvirusseq/singularity/components/model/AllArchiveHashInfo.java
@@ -0,0 +1,28 @@
+package org.cancogenvirusseq.singularity.components.model;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lombok.Getter;
+import lombok.RequiredArgsConstructor;
+import lombok.SneakyThrows;
+
+@Getter
+@RequiredArgsConstructor
+public class AllArchiveHashInfo {
+  private static final ObjectMapper objectMapper = new ObjectMapper();
+
+  private final Long numSamples;
+  private final String lastUpdated;
+
+  public static AllArchiveHashInfo parseFromCountAndLastUpdatedResult(
+      CountAndLastUpdatedResult countAndLastUpdatedResult) {
+    return new AllArchiveHashInfo(
+        countAndLastUpdatedResult.getNumDocuments().getValue(),
+        countAndLastUpdatedResult.getLastUpdatedDate().getValueAsString());
+  }
+
+  @Override
+  @SneakyThrows
+  public String toString() {
+    return AllArchiveHashInfo.objectMapper.writeValueAsString(this);
+  }
+}
diff --git a/src/main/java/org/cancogenvirusseq/singularity/repository/model/Archive.java b/src/main/java/org/cancogenvirusseq/singularity/repository/model/Archive.java
@@ -5,6 +5,8 @@
 import java.time.Instant;
 import java.util.UUID;
 import lombok.*;
+import org.cancogenvirusseq.singularity.components.model.AllArchiveHashInfo;
+import org.cancogenvirusseq.singularity.components.model.CountAndLastUpdatedResult;
 import org.cancogenvirusseq.singularity.components.model.SetQueryArchiveHashInfo;
 import org.springframework.data.annotation.Id;
 import org.springframework.data.relational.core.mapping.Table;
@@ -45,6 +47,18 @@ public String toString() {
     }
   }
 
+  public static Archive newAllArchiveFromCountAndLastUpdatedResult(
+      CountAndLastUpdatedResult countAndLastUpdatedResult) {
+    return Archive.builder()
+        .status(ArchiveStatus.BUILDING)
+        .type(ArchiveType.ALL)
+        .hashInfo(
+            AllArchiveHashInfo.parseFromCountAndLastUpdatedResult(countAndLastUpdatedResult)
+                .toString())
+        .numOfSamples(countAndLastUpdatedResult.getNumDocuments().getValue())
+        .build();
+  }
+
   public static Archive newFromSetQueryArchiveHashInfo(
       SetQueryArchiveHashInfo setQueryArchiveHashInfo) {
     return Archive.builder()
@@ -62,8 +76,9 @@ public static Archive incrementDownloadsForArchive(Archive archive) {
 
   public static String parseFilenameFromArchive(Archive archive) {
     if (archive.getType().equals(ArchiveType.ALL)) {
-      // for a download all entry the hash info is the instant string for the release
-      return format("virusseq-data-release-%s.tar.gz", archive.getHashInfo());
+      // for a download all entry, use the createdAt timestamp for the filename
+      return format(
+          "virusseq-data-release-%s.tar.gz", Instant.ofEpochSecond(archive.getCreatedAt()));
     } else {
       // for all other export types just note that it's an export and the download time
       return format("virusseq-search-export-%s.tar.gz", Instant.now());