Moved text/csv and text/xml

fda-identifier-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java

@@ -59,6 +59,7 @@ public class IdentifierEndpoint {
     }
 
     @GetMapping("/{id}")
+    @Deprecated
     @Transactional(readOnly = true)
     @Timed(value = "identifier.export", description = "Time needed to export an identifier")
     @Operation(summary = "Export some identifier metadata")

fda-identifier-service/rest-service/src/main/java/at/tuwien/endpoints/PersistenceEndpoint.java

 package at.tuwien.endpoints;
 
+import at.tuwien.ExportResource;
 import at.tuwien.config.EndpointConfig;
 import at.tuwien.entities.identifier.Identifier;
 import at.tuwien.exception.IdentifierNotFoundException;
@@ -43,7 +44,7 @@ public class PersistenceEndpoint {
     @Operation(summary = "Find some identifier")
     public ResponseEntity<?> find(@Valid @PathVariable("pid") Long pid,
                                   @RequestHeader(HttpHeaders.ACCEPT) String accept) throws IdentifierNotFoundException,
-            QueryNotFoundException, RemoteUnavailableException, IdentifierRequestException {
+            QueryNotFoundException, RemoteUnavailableException {
         log.debug("find identifier endpoint, pid={}, accept={}", pid, accept);
         final Identifier identifier = identifierService.find(pid);
         log.info("Found persistent identifier with id {}", identifier.getId());
@@ -56,6 +57,13 @@ public class PersistenceEndpoint {
             } else if (accept.equals("text/csv")) {
                 log.trace("accept header matches csv");
                 return ResponseEntity.ok(identifierService.exportResource(pid));
+            } else if (accept.equals("text/xml")) {
+                final HttpHeaders headers = new HttpHeaders();
+                final ExportResource resource = identifierService.exportMetadata(pid);
+                headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
+                return ResponseEntity.ok()
+                        .headers(headers)
+                        .body(resource.getResource());
             }
         }
         log.trace("no accept header present, serving http redirect");

fda-identifier-service/services/src/main/java/at/tuwien/gateway/QueryServiceGateway.java

@@ -25,6 +25,16 @@ public interface QueryServiceGateway {
     QueryDto find(Long containerId, Long databaseId, IdentifierCreateDto identifier, String authorization)
             throws QueryNotFoundException, RemoteUnavailableException;
 
-    ExportDto export(Long containerId, Long databaseId, Long queryId) throws RemoteUnavailableException,
+    /**
+     * Exports a query by given id.
+     *
+     * @param containerId The container id.
+     * @param databaseId  The database id.
+     * @param queryId     The query id.
+     * @return The exported resource as bytes.
+     * @throws RemoteUnavailableException The remote service is not available.
+     * @throws QueryNotFoundException     The query was not found.
+     */
+    byte[] export(Long containerId, Long databaseId, Long queryId) throws RemoteUnavailableException,
             QueryNotFoundException;
 }

fda-identifier-service/services/src/main/java/at/tuwien/gateway/impl/QueryServiceGatewayImpl.java

@@ -57,13 +57,15 @@ public class QueryServiceGatewayImpl implements QueryServiceGateway {
     }
 
     @Override
-    public ExportDto export(Long containerId, Long databaseId, Long queryId)
+    public byte[] export(Long containerId, Long databaseId, Long queryId)
             throws RemoteUnavailableException, QueryNotFoundException {
         final String url = "/api/container/" + containerId + "/database/" + databaseId + "/query/" + queryId + "/export";
-        final ResponseEntity<ExportDto> response;
+        final HttpHeaders headers = new HttpHeaders();
+        headers.add("Accept", "text/csv");
+        final ResponseEntity<byte[]> response;
         try {
             log.trace("call gateway path {}", url);
-            response = restTemplate.exchange(url, HttpMethod.GET, null, ExportDto.class);
+            response = restTemplate.exchange(url, HttpMethod.GET, new HttpEntity<>(null, headers), byte[].class);
         } catch (HttpServerErrorException.ServiceUnavailable e) {
             log.error("Query service not available: {}", e.getMessage());
             throw new RemoteUnavailableException("Query service not available", e);

fda-identifier-service/services/src/main/java/at/tuwien/service/IdentifierService.java

@@ -79,13 +79,12 @@ public interface IdentifierService {
      *
      * @param identifierId The identifier id.
      * @return The XML resource, if successful.
-     * @throws IdentifierNotFoundException
-     * @throws QueryNotFoundException
+     * @throws IdentifierNotFoundException The identifier was not found in the metadata database or was deleted.
+     * @throws QueryNotFoundException      The query was not found in the metadata database or was deleted.
      * @throws RemoteUnavailableException
-     * @throws IdentifierRequestException
      */
     InputStreamResource exportResource(Long identifierId)
-            throws IdentifierNotFoundException, QueryNotFoundException, RemoteUnavailableException, IdentifierRequestException;
+            throws IdentifierNotFoundException, QueryNotFoundException, RemoteUnavailableException;
 
     /**
      * Updated the metadata (only) on the identifier for a given id in the metadata database.

fda-identifier-service/services/src/main/java/at/tuwien/service/impl/IdentifierServiceImpl.java

@@ -25,6 +25,7 @@ import org.springframework.core.io.InputStreamResource;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
 import java.security.Principal;
@@ -184,8 +185,7 @@ public class IdentifierServiceImpl implements IdentifierService {
     @Override
     @Transactional(readOnly = true)
     public InputStreamResource exportResource(Long identifierId)
-            throws IdentifierNotFoundException, QueryNotFoundException, RemoteUnavailableException,
-            IdentifierRequestException {
+            throws IdentifierNotFoundException, QueryNotFoundException, RemoteUnavailableException {
         /* check */
         final Identifier identifier = find(identifierId);
         if (identifier.getType().equals(IdentifierType.DATABASE)) {
@@ -194,15 +194,9 @@ public class IdentifierServiceImpl implements IdentifierService {
             throw new IdentifierNotFoundException("Failed to find identifier");
         }
         /* export */
-        final ExportDto export = queryServiceGateway.export(identifier.getContainerId(),
+        final byte[] file = queryServiceGateway.export(identifier.getContainerId(),
                 identifier.getDatabaseId(), identifier.getQueryId());
-        final InputStreamResource resource;
-        try {
-            resource = new InputStreamResource(FileUtils.openInputStream(new File("/tmp/" + export.getLocation())));
-        } catch (IOException e) {
-            log.error("Failed to open export file: {}", e.getMessage());
-            throw new IdentifierRequestException("Failed to open export file", e);
-        }
+        final InputStreamResource resource = new InputStreamResource(new ByteArrayInputStream(file));
         log.trace("found resource {}", resource);
         return resource;
     }

fda-query-service/rest-service/src/main/java/at/tuwien/endpoint/QueryEndpoint.java

@@ -112,13 +112,13 @@ public class QueryEndpoint extends AbstractEndpoint {
     public ResponseEntity<?> export(@NotNull @PathVariable("id") Long containerId,
                                     @NotNull @PathVariable("databaseId") Long databaseId,
                                     @NotNull @PathVariable("queryId") Long queryId,
-                                    @RequestParam(value = "download", required = false) String download,
+                                    @RequestHeader(HttpHeaders.ACCEPT) String accept,
                                     Principal principal)
             throws QueryStoreException, QueryNotFoundException, DatabaseNotFoundException, ImageNotSupportedException,
             ContainerNotFoundException, TableMalformedException, FileStorageException, NotAllowedException,
             QueryMalformedException, DatabaseConnectionException {
-        log.debug("endpoint export query, containerId={}, databaseId={}, queryId={}, download={}, principal={}",
-                containerId, databaseId, queryId, download, principal);
+        log.debug("endpoint export query, containerId={}, databaseId={}, queryId={}, accept={}, principal={}",
+                containerId, databaseId, queryId, accept, principal);
         if (!hasQueryPermission(containerId, databaseId, queryId, "QUERY_EXPORT", principal)) {
             log.error("Missing export query permission");
             throw new NotAllowedException("Missing export query permission");
@@ -127,7 +127,7 @@ public class QueryEndpoint extends AbstractEndpoint {
         final Query query = storeService.findOne(containerId, databaseId, queryId);
         log.trace("querystore returned query {}", query);
         final ExportResource resource = queryService.findOne(containerId, databaseId, queryId);
-        if (download != null) {
+        if (accept.equals("text/csv")) {
             final HttpHeaders headers = new HttpHeaders();
             headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
             log.trace("export query resulted in resource {}", resource);
@@ -135,12 +135,9 @@ public class QueryEndpoint extends AbstractEndpoint {
                     .headers(headers)
                     .body(resource.getResource());
         }
-        final ExportDto dto = ExportDto.builder()
-                .location(resource.getFilename())
+        log.error("Failed to export, non-csv exports are not supported");
+        return ResponseEntity.status(HttpStatus.NOT_IMPLEMENTED)
                 .build();
-        log.trace("export query resulted in export file {}", dto);
-        return ResponseEntity.ok()
-                .body(dto);
     }
 
 }

fda-query-service/rest-service/src/main/java/at/tuwien/endpoint/TableDataEndpoint.java

@@ -61,6 +61,7 @@ public class TableDataEndpoint extends AbstractEndpoint {
     }
 
     @PutMapping
+    @Deprecated
     @Transactional
     @Timed(value = "data.update", description = "Time needed to update data in a table")
     @Operation(summary = "Update data", security = @SecurityRequirement(name = "bearerAuth"))

fda-query-service/services/src/main/java/at/tuwien/mapper/QueryMapper.java

@@ -323,6 +323,16 @@ public interface QueryMapper {
                             .append("`");
                     idx[0]++;
                 });
+        statement.append(" UNION ALL SELECT ");
+        int[] jdx = new int[]{0};
+        table.getColumns()
+                .forEach(column -> {
+                    statement.append(jdx[0] != 0 ? "," : "")
+                            .append("`")
+                            .append(column.getInternalName())
+                            .append("`");
+                    jdx[0]++;
+                });
         statement.append("FROM `")
                 .append(table.getInternalName())
                 .append("`");

fda-ui/components/TableList.vue

@@ -96,6 +96,7 @@
               disable-sort
               :loading="loadingDetails"
               hide-default-footer
+              items-per-page="-1"
               :headers="headers"
               :items="tableDetails.columns">
               <template v-slot:item.is_null_allowed="{ item }">

fda-ui/components/query/Builder.vue

@@ -97,6 +97,15 @@
               </v-row>
             </v-tab-item>
             <v-tab-item>
+              <v-row>
+                <v-col>
+                  <v-alert
+                    border="left"
+                    color="info">
+                    Currently, comments in the query (e.g. <code>-- Comment</code>) are not supported!
+                  </v-alert>
+                </v-col>
+              </v-row>
               <v-row>
                 <v-col>
                   <QueryRaw
@@ -165,9 +174,6 @@ export default {
     columnNames () {
       return this.selectItems && this.selectItems.map(s => s.internal_name)
     },
-    defaultRawSqlText () {
-      return '-- MariaDB 10.5 Query'
-    },
     tableId () {
       return this.table.id
     },
@@ -198,10 +204,7 @@ export default {
       return null
     },
     canExecute () {
-      if (!this.sql || this.sql.length === 0) {
-        return false
-      }
-      return this.sql.trim() !== this.defaultRawSqlText
+      return !(!this.sql || this.sql.length === 0)
     },
     backTo () {
       return `/container/${this.$route.params.container_id}/database/${this.$route.params.database_id}/` + (this.isView ? 'view' : 'query')
@@ -293,13 +296,8 @@ export default {
         this.resultId = res.data.id
         console.debug('view', res.data)
       } catch (err) {
-        if (err.response.status === 423) {
-          console.error('View name exist', err)
-          this.$toast.error('View name already exists')
-          return
-        }
         console.error('Failed to create view', err)
-        this.$toast.error('Failed to create view ' + err.response.text)
+        this.$toast.error(err.response.data.message)
       }
       this.loadingQuery = false
       await this.$refs.queryResults.reExecute(this.resultId)

fda-ui/components/query/Raw.vue

@@ -29,7 +29,7 @@ export default {
   },
   data () {
     return {
-      content: this.value || '-- MariaDB 10.5 Query\n'
+      content: this.value
     }
   },
   computed: {

fda-ui/pages/container/_container_id/database/_database_id/query/_query_id/index.vue

@@ -18,7 +18,7 @@
         <v-btn v-if="token && query.is_persisted && !identifier.id && !loadingIdentifier && is_owner" class="mb-1 mr-2" color="primary" :disabled="error || erroneous || !executionUTC" @click.stop="openDialog()">
           <v-icon left>mdi-content-save-outline</v-icon> Get PID
         </v-btn>
-        <v-btn v-if="result_visibility" class="mb-1" :loading="downloadLoading" @click.stop="download">
+        <v-btn v-if="result_visibility" class="mb-1" :loading="downloadLoading" @click.stop="download('text/csv')">
           <v-icon left>mdi-download</v-icon> Data .csv
         </v-btn>
         <v-btn
@@ -26,7 +26,7 @@
           color="secondary"
           class="ml-2"
           :loading="metadataLoading"
-          @click.stop="metadata">
+          @click.stop="download('text/xml')">
           <v-icon left>mdi-code-tags</v-icon> Metadata .xml
         </v-btn>
       </v-toolbar-title>
@@ -39,7 +39,7 @@
         <v-list dense>
           <v-list-item>
             <v-list-item-icon>
-              <v-icon :color="database_visibility ? 'success' : 'error'">mdi-database-outline</v-icon>
+              <v-icon v-if="database_visibility" :color="database_visibility ? 'success' : 'error'">mdi-database-outline</v-icon>
             </v-list-item-icon>
             <v-list-item-content>
               <v-list-item-title>
@@ -187,7 +187,7 @@
           </v-list-item>
           <v-list-item>
             <v-list-item-icon>
-              <v-icon :color="result_visibility_icon ? 'success' : 'error'">{{ result_icon }}</v-icon>
+              <v-icon v-if="result_visibility_icon" :color="result_visibility_icon ? 'success' : 'error'">{{ result_icon }}</v-icon>
             </v-list-item-icon>
             <v-list-item-content v-if="!erroneous">
               <v-list-item-title>
@@ -365,7 +365,7 @@ export default {
       return this.$store.state.user && this.$store.state.user.username
     },
     database_visibility () {
-      return this.database.is_public
+      return this.database.is_public !== null ? this.database.is_public : false
     },
     is_owner () {
       return this.token && this.query.creator.username === this.user.username
@@ -377,6 +377,9 @@ export default {
       if (this.erroneous) {
         return false
       }
+      if (this.database.is_public === null) {
+        return false
+      }
       if (this.database.is_public) {
         return true
       }
@@ -389,6 +392,9 @@ export default {
       if (this.erroneous) {
         return false
       }
+      if (this.database.is_public === null) {
+        return false
+      }
       if (this.database.is_public) {
         return true
       }
@@ -439,41 +445,29 @@ export default {
       .then(() => this.loadMetadata())
   },
   methods: {
-    async metadata () {
-      this.metadataLoading = true
-      try {
-        const res = await this.$axios.get(`/api/identifier/${this.identifier.id}`, this.config)
-        console.debug('identifier result', res)
-        const url = window.URL.createObjectURL(new Blob([res.data]))
-        const link = document.createElement('a')
-        link.href = url
-        link.setAttribute('download', 'metadata.xml')
-        document.body.appendChild(link)
-        link.click()
-      } catch (err) {
-        console.error('Could not export metadata', err)
-        this.$toast.error('Could not export metadata')
-        this.error = true
-      }
-      this.metadataLoading = false
-    },
     loadResult () {
       this.$refs.queryResults.reExecute(this.query.id)
     },
-    async download () {
+    async download (mime) {
       this.downloadLoading = true
       try {
-        const res = await this.$axios.get(`/api/container/${this.$route.params.container_id}/database/${this.$route.params.database_id}/query/${this.$route.params.query_id}/export`, this.config)
-        console.debug('export query result', res)
+        const config = this.config
+        config.headers.Accept = mime
+        const res = await this.$axios.get(`/api/pid/${this.identifier.id}`, config)
+        console.debug('export identifier', res)
         const url = window.URL.createObjectURL(new Blob([res.data]))
         const link = document.createElement('a')
         link.href = url
-        link.setAttribute('download', 'query.csv')
+        if (mime === 'text/csv') {
+          link.setAttribute('download', 'subset.csv')
+        } else if (mime === 'text/xml') {
+          link.setAttribute('download', 'identifier.xml')
+        }
         document.body.appendChild(link)
         link.click()
       } catch (err) {
-        console.error('Could not export query result', err)
-        this.$toast.error('Could not export query result')
+        console.error('Could not export identifier', err)
+        this.$toast.error('Could not export identifier')
         this.error = true
       }
       this.downloadLoading = false