Updated frontend to include publication, fixed the table import

Former-commit-id: 97beba2e

fda-authentication-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-citation-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-container-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-database-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-discovery-service/Dockerfile

@@ -9,8 +9,6 @@ RUN mvn -fn -B dependency:go-offline > /dev/null
 COPY ./discovery ./discovery
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-gateway-service/Dockerfile

@@ -9,8 +9,6 @@ RUN mvn -fn -B dependency:go-offline > /dev/null
 COPY ./gateway ./gateway
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-metadata-db/Dockerfile

@@ -9,8 +9,6 @@ RUN mvn -fn -B dependency:go-offline > /dev/null
 COPY ./api ./api
 COPY ./entities ./entities
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-metadata-db/api/src/main/java/at/tuwien/api/database/query/QueryDto.java

@@ -3,6 +3,7 @@ package at.tuwien.api.database.query;
 import at.tuwien.api.database.deposit.files.FileDto;
 import at.tuwien.api.database.table.TableDto;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.annotations.ApiModelProperty;
 import lombok.*;
 
 import javax.persistence.Column;
@@ -29,11 +30,18 @@ public class QueryDto {
     private Instant executionTimestamp;
 
     @NotBlank
+    @ApiModelProperty(name = "query raw", example = "select * from table")
     private String query;
 
     @NotBlank
+    @ApiModelProperty(name = "query title", example = "Select all weather events for 2012")
     private String title;
 
+    @NotBlank
+    @ApiModelProperty(name = "query description", example = "Returns a list of measurements for the year 2012")
+    private String description;
+
+    @ApiModelProperty(name = "doi", example = "Digital Object Identifier")
     private String doi;
 
     @JsonProperty("deposit_id")
@@ -44,6 +52,7 @@ public class QueryDto {
     private TableDto table;
 
     @JsonProperty("query_normalized")
+    @ApiModelProperty(name = "query normalized", example = "select id, name from table")
     private String queryNormalized;
 
     @JsonProperty("query_hash")

fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/query/Query.java

@@ -46,6 +46,9 @@ public class Query {
     @Column
     private String query;
 
+    @Column
+    private String description;
+
     @Column
     private String queryNormalized;
 

fda-metadata-db/initi.sh

@@ -203,6 +203,7 @@ psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-E
     title character varying(255) NULL,
     doi character varying(255),
     query TEXT NULL,
+    description TEXT NULL,
     query_normalized TEXT NULL,
     query_hash character varying(255) NULL,
     result_hash character varying(255) NULL,

fda-query-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

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

@@ -11,6 +11,7 @@ import org.mapstruct.Mapping;
 import org.mapstruct.Mappings;
 import org.mapstruct.Named;
 
+import java.sql.Timestamp;
 import java.time.Instant;
 import java.time.ZoneId;
 import java.time.format.DateTimeFormatter;

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

@@ -2,6 +2,7 @@ package at.tuwien.service;
 
 
 import at.tuwien.entities.database.Database;
+import at.tuwien.entities.database.table.Table;
 import at.tuwien.exception.ImageNotSupportedException;
 import at.tuwien.mapper.ImageMapper;
 import lombok.extern.log4j.Log4j2;
@@ -11,8 +12,12 @@ import org.jooq.*;
 import org.jooq.impl.DSL;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.math.BigInteger;
 import java.sql.*;
 
+import static org.jooq.impl.DSL.name;
+import static org.jooq.impl.DSL.sequence;
+
 @Log4j2
 public abstract class JdbcConnector {
 
@@ -25,9 +30,23 @@ public abstract class JdbcConnector {
 
     protected DSLContext open(Database database) throws SQLException, ImageNotSupportedException {
         final String url = "jdbc:" + database.getContainer().getImage().getJdbcMethod() + "://" + database.getContainer().getInternalName() + "/" + database.getInternalName();
-        log.trace("Attempt to connect to '{}'", url);
         final Connection connection = DriverManager.getConnection(url, imageMapper.containerImageToProperties(database.getContainer().getImage()));
         return DSL.using(connection, SQLDialect.valueOf(database.getContainer().getImage().getDialect()));
     }
 
+    /**
+     * Retrieve the next id from the sequence of a database
+     *
+     * @param database The database.
+     * @return The next id.
+     * @throws SQLException
+     * @throws ImageNotSupportedException
+     */
+    protected BigInteger nextSequence(Database database) throws SQLException, ImageNotSupportedException {
+        final DSLContext context = open(database);
+        final Field<BigInteger> id = sequence(name(QueryStoreService.QUERYSTORE_SEQ_NAME))
+                .nextval();
+        return context.select(id).fetchOne(id);
+    }
+
 }

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

@@ -19,13 +19,16 @@ import net.sf.jsqlparser.parser.CCJSqlParserManager;
 import net.sf.jsqlparser.statement.Statement;
 import net.sf.jsqlparser.statement.select.*;
 import net.sf.jsqlparser.statement.select.Select;
+import org.apache.commons.codec.digest.DigestUtils;
 import org.jooq.*;
+import org.jooq.exception.DataAccessException;
 import org.junit.jupiter.params.shadow.com.univocity.parsers.common.DataProcessingException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.io.StringReader;
+import java.math.BigInteger;
 import java.sql.SQLException;
 import java.sql.Timestamp;
 import java.time.Instant;
@@ -43,7 +46,8 @@ import static org.jooq.impl.SQLDataType.*;
 @Service
 public class QueryStoreService extends JdbcConnector {
 
-    private final static String QUERYSTORENAME = "mdb_querystore";
+    public final static String QUERYSTORE_NAME = "userdb_querystore";
+    public final static String QUERYSTORE_SEQ_NAME = "seq_querystore_id";
 
     private final DatabaseRepository databaseRepository;
     private final QueryRepository queryRepository;
@@ -75,7 +79,7 @@ public class QueryStoreService extends JdbcConnector {
                 .fetch()
                 .toString());
         return queryMapper.recordListToQueryList(context
-                .selectFrom(QUERYSTORENAME)
+                .selectFrom(QUERYSTORE_NAME)
                 .orderBy(field("execution_timestamp"))
                 .fetch());
     }
@@ -93,9 +97,16 @@ public class QueryStoreService extends JdbcConnector {
         log.trace("select query {}", context.selectQuery()
                 .fetch()
                 .toString());
-        final List<org.jooq.Record> records = context
-                .selectFrom(QUERYSTORENAME).where(condition("id = " + queryId))
+        List<org.jooq.Record> records;
+        try {
+            records = context
+                    .selectFrom(QUERYSTORE_NAME)
+                    .where(condition("id = " + queryId))
                     .fetch();
+        } catch (DataAccessException e) {
+            log.error("Failed to select records: {}", e.getMessage());
+            throw new QueryStoreException("Failed to select records", e);
+        }
         if (records.size() != 1) {
             throw new QueryStoreException("Failed to get query from querystore");
         }
@@ -123,9 +134,9 @@ public class QueryStoreService extends JdbcConnector {
         /* create database in container */
         try {
             final DSLContext context = open(database);
-            context.createSequence("seq_id")
+            context.createSequence(QUERYSTORE_SEQ_NAME)
                     .execute();
-            context.createTable(QUERYSTORENAME)
+            context.createTable(QUERYSTORE_NAME)
                     .column("id", BIGINT)
                     .column("doi", VARCHAR(255).nullable(false))
                     .column("title", VARCHAR(255).nullable(false))
@@ -156,7 +167,8 @@ public class QueryStoreService extends JdbcConnector {
         query.setResultNumber(0L);
         try {
             final DSLContext context = open(database);
-            int success = context.insertInto(table(QUERYSTORENAME))
+            final BigInteger idVal = nextSequence(database);
+            int success = context.insertInto(table(QUERYSTORE_NAME))
                     .columns(field("id"),
                             field("doi"),
                             field("title"),
@@ -165,9 +177,9 @@ public class QueryStoreService extends JdbcConnector {
                             field("execution_timestamp"),
                             field("result_hash"),
                             field("result_number"))
-                    .values(sequence("seq_id").nextval(), "doi/" + query.getId(), query.getTitle(), query.getQuery(),
+                    .values(idVal, "doi/" + idVal, query.getTitle(), query.getQuery(),
                             query.getQueryHash(), LocalDateTime.ofInstant(query.getExecutionTimestamp(),
-                                    ZoneId.of("Europe/Vienna")), "" + queryResult.hashCode(),
+                                    ZoneId.of("Europe/Vienna")), getResultHash(queryResult),
                             queryResult.getResult().size())
                     .execute();
             log.info("Saved query into query store id {}", query.getId());
@@ -188,6 +200,16 @@ public class QueryStoreService extends JdbcConnector {
         return query;
     }
 
+    /**
+     * Retrieve the result hash
+     *
+     * @param result The result.
+     * @return The hash.
+     */
+    private String getResultHash(QueryResultDto result) {
+        return "sha256:" + DigestUtils.sha256Hex(result.getResult().toString());
+    }
+
     @Deprecated
     private boolean checkValidity(String query) {
         String queryparts[] = query.toLowerCase().split("from");
@@ -449,7 +471,7 @@ public class QueryStoreService extends JdbcConnector {
         }
         return context.select(count())
                 .from("information_schema.tables")
-                .where("table_name like '" + QUERYSTORENAME + "'")
+                .where("table_name like '" + QUERYSTORE_NAME + "'")
                 .fetchOne(0, int.class) == 1;
     }
 

fda-table-service/Dockerfile

@@ -15,8 +15,6 @@ COPY ./rest-service ./rest-service
 COPY ./services ./services
 COPY ./report ./report
 
-ARG CI_JOB_STAGE
-
 # Make sure it compiles
 RUN mvn -q clean package -DskipTests > /dev/null
 

fda-ui/components/query/Builder.vue

@@ -29,6 +29,17 @@
                 required />
             </v-col>
           </v-row>
+          <v-row class="mt-2">
+            <v-col cols="6">
+              <v-textarea
+                v-model="description"
+                :rules="[rules.required]"
+                rows="3"
+                class="pa-0"
+                label="Query Description"
+                required />
+            </v-col>
+          </v-row>
           <v-row class="mt-2">
             <v-col cols="6">
               <v-select
@@ -95,6 +106,7 @@ export default {
       table: null,
       tables: [],
       title: null,
+      description: null,
       tableDetails: null,
       queryId: null,
       query: {
@@ -162,7 +174,7 @@ export default {
         this.loading = false
         this.queryId = res.data.id
         this.result.headers = this.select.map((s) => {
-          return { text: s.name, value: 'mdb_' + s.name, sortable: false }
+          return { text: s.name, value: s.name, sortable: false }
         })
         this.result.rows = res.data.result
       } catch (err) {
@@ -196,7 +208,7 @@ export default {
       const url = '/server-middleware/query/build'
       const data = {
         table: this.table.internalName,
-        select: this.select.map(s => 'mdb_' + s.name),
+        select: this.select.map(s => s.name),
         clauses: this.clauses
       }
       try {

fda-ui/layouts/default.vue

@@ -21,9 +21,9 @@
       <v-toolbar-title v-text="title" />
       <v-spacer />
       <v-btn
+        class="mr-2 white--text"
         color="blue-grey"
-        @click="authenticate"
-        class="mr-2 white--text">
+        @click="authenticate">
         <v-icon left>mdi-login</v-icon> Login
       </v-btn>
       <v-menu bottom offset-y left>
@@ -50,7 +50,7 @@
         <nuxt />
       </v-container>
     </v-main>
-    <v-footer padless v-if="sandbox">
+    <v-footer v-if="sandbox" padless>
       <v-card
         flat
         tile

fda-ui/pages/databases/_database_id/admin.vue

@@ -11,6 +11,7 @@
         </v-card-text>
       </v-card>
     </v-tabs-items>
+    <v-breadcrumbs :items="items" class="pa-0 mt-2" />
     <v-dialog v-model="dialogDelete" max-width="500">
       <v-card>
         <v-card-title class="headline">
@@ -45,7 +46,11 @@ export default {
   data () {
     return {
       dialogDelete: false,
-      confirm: null
+      confirm: null,
+      items: [
+        { text: 'Databases', href: '/databases' },
+        { text: `${this.$route.params.database_id}`, href: `/databases/${this.$route.params.database_id}/info` }
+      ]
     }
   },
   computed: {

fda-ui/pages/databases/_database_id/info.vue

 <template>
   <div v-if="db">
     <DBToolbar />
-    <v-tabs-items v-model="tab">
+    <v-tabs-items v-if="!loading" v-model="tab">
       <v-tab-item>
         <v-card flat>
           <v-card-title>
@@ -16,17 +16,19 @@
               <p>{{ description }}</p>
             </blockquote>
             <span>
-              Created {{ db.created }}
+              Created {{ formatDate(db.created) }}
             </span>
           </v-card-text>
         </v-card>
       </v-tab-item>
     </v-tabs-items>
+    <v-breadcrumbs :items="items" class="pa-0 mt-2" />
   </div>
 </template>
 
 <script>
 import DBToolbar from '@/components/DBToolbar'
+import { format } from 'date-fns'
 
 export default {
   components: {
@@ -34,7 +36,11 @@ export default {
   },
   data () {
     return {
-      loading: false
+      loading: false,
+      items: [
+        { text: 'Databases', href: '/databases' },
+        { text: `${this.$route.params.database_id}`, href: `/databases/${this.$route.params.database_id}/info` }
+      ]
     }
   },
   computed: {
@@ -56,11 +62,12 @@ export default {
   },
   methods: {
     async init () {
-      if (this.db != null) {
+      this.loading = true
+      if (this.db != null && this.db.id === this.$route.params.database_id) {
+        this.loading = false
         return
       }
       try {
-        this.loading = true
         const res = await this.$axios.get(`/api/database/${this.$route.params.database_id}`)
         console.debug('database', res.data)
         this.$store.commit('SET_DATABASE', res.data)
@@ -69,6 +76,9 @@ export default {
         this.$toast.error('Could not load database.')
         this.loading = false
       }
+    },
+    formatDate (d) {
+      return format(new Date(d), 'dd.MM.yyyy HH:mm:ss.SSS')
     }
   }
 }

fda-ui/pages/databases/_database_id/queries/create.vue

@@ -11,7 +11,7 @@ export default {
     return {
       items: [
         { text: 'Databases', href: '/databases' },
-        { text: `${this.$route.params.database_id}`, href: `/databases/${this.$route.params.database_id}` },
+        { text: `${this.$route.params.database_id}`, href: `/databases/${this.$route.params.database_id}/info` },
         { text: 'Tables', href: `/databases/${this.$route.params.database_id}/tables` }
       ]
     }