Fixed the mapping for data

.jupyter/api_authentication/models/user_dto.py

@@ -41,6 +41,7 @@ class UserDto(object):
         'email': 'str',
         'titles_before': 'str',
         'titles_after': 'str',
+        'theme_dark': 'bool',
         'email_verified': 'bool'
     }
 
@@ -58,10 +59,11 @@ class UserDto(object):
         'email': 'email',
         'titles_before': 'titles_before',
         'titles_after': 'titles_after',
+        'theme_dark': 'theme_dark',
         'email_verified': 'email_verified'
     }
 
-    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, email_verified=None):  # noqa: E501
+    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, theme_dark=None, email_verified=None):  # noqa: E501
         """UserDto - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._authorities = None
@@ -76,6 +78,7 @@ class UserDto(object):
         self._email = None
         self._titles_before = None
         self._titles_after = None
+        self._theme_dark = None
         self._email_verified = None
         self.discriminator = None
         self.id = id
@@ -101,6 +104,7 @@ class UserDto(object):
             self.titles_before = titles_before
         if titles_after is not None:
             self.titles_after = titles_after
+        self.theme_dark = theme_dark
         if email_verified is not None:
             self.email_verified = email_verified
 
@@ -383,6 +387,29 @@ class UserDto(object):
 
         self._titles_after = titles_after
 
+    @property
+    def theme_dark(self):
+        """Gets the theme_dark of this UserDto.  # noqa: E501
+
+
+        :return: The theme_dark of this UserDto.  # noqa: E501
+        :rtype: bool
+        """
+        return self._theme_dark
+
+    @theme_dark.setter
+    def theme_dark(self, theme_dark):
+        """Sets the theme_dark of this UserDto.
+
+
+        :param theme_dark: The theme_dark of this UserDto.  # noqa: E501
+        :type: bool
+        """
+        if theme_dark is None:
+            raise ValueError("Invalid value for `theme_dark`, must not be `None`")  # noqa: E501
+
+        self._theme_dark = theme_dark
+
     @property
     def email_verified(self):
         """Gets the email_verified of this UserDto.  # noqa: E501

.jupyter/api_container/models/user_dto.py

@@ -41,6 +41,7 @@ class UserDto(object):
         'email': 'str',
         'titles_before': 'str',
         'titles_after': 'str',
+        'theme_dark': 'bool',
         'email_verified': 'bool'
     }
 
@@ -58,10 +59,11 @@ class UserDto(object):
         'email': 'email',
         'titles_before': 'titles_before',
         'titles_after': 'titles_after',
+        'theme_dark': 'theme_dark',
         'email_verified': 'email_verified'
     }
 
-    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, email_verified=None):  # noqa: E501
+    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, theme_dark=None, email_verified=None):  # noqa: E501
         """UserDto - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._authorities = None
@@ -76,6 +78,7 @@ class UserDto(object):
         self._email = None
         self._titles_before = None
         self._titles_after = None
+        self._theme_dark = None
         self._email_verified = None
         self.discriminator = None
         self.id = id
@@ -101,6 +104,7 @@ class UserDto(object):
             self.titles_before = titles_before
         if titles_after is not None:
             self.titles_after = titles_after
+        self.theme_dark = theme_dark
         if email_verified is not None:
             self.email_verified = email_verified
 
@@ -383,6 +387,29 @@ class UserDto(object):
 
         self._titles_after = titles_after
 
+    @property
+    def theme_dark(self):
+        """Gets the theme_dark of this UserDto.  # noqa: E501
+
+
+        :return: The theme_dark of this UserDto.  # noqa: E501
+        :rtype: bool
+        """
+        return self._theme_dark
+
+    @theme_dark.setter
+    def theme_dark(self, theme_dark):
+        """Sets the theme_dark of this UserDto.
+
+
+        :param theme_dark: The theme_dark of this UserDto.  # noqa: E501
+        :type: bool
+        """
+        if theme_dark is None:
+            raise ValueError("Invalid value for `theme_dark`, must not be `None`")  # noqa: E501
+
+        self._theme_dark = theme_dark
+
     @property
     def email_verified(self):
         """Gets the email_verified of this UserDto.  # noqa: E501

.jupyter/api_database/models/user_dto.py

@@ -41,6 +41,7 @@ class UserDto(object):
         'email': 'str',
         'titles_before': 'str',
         'titles_after': 'str',
+        'theme_dark': 'bool',
         'email_verified': 'bool'
     }
 
@@ -58,10 +59,11 @@ class UserDto(object):
         'email': 'email',
         'titles_before': 'titles_before',
         'titles_after': 'titles_after',
+        'theme_dark': 'theme_dark',
         'email_verified': 'email_verified'
     }
 
-    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, email_verified=None):  # noqa: E501
+    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, theme_dark=None, email_verified=None):  # noqa: E501
         """UserDto - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._authorities = None
@@ -76,6 +78,7 @@ class UserDto(object):
         self._email = None
         self._titles_before = None
         self._titles_after = None
+        self._theme_dark = None
         self._email_verified = None
         self.discriminator = None
         self.id = id
@@ -101,6 +104,7 @@ class UserDto(object):
             self.titles_before = titles_before
         if titles_after is not None:
             self.titles_after = titles_after
+        self.theme_dark = theme_dark
         if email_verified is not None:
             self.email_verified = email_verified
 
@@ -383,6 +387,29 @@ class UserDto(object):
 
         self._titles_after = titles_after
 
+    @property
+    def theme_dark(self):
+        """Gets the theme_dark of this UserDto.  # noqa: E501
+
+
+        :return: The theme_dark of this UserDto.  # noqa: E501
+        :rtype: bool
+        """
+        return self._theme_dark
+
+    @theme_dark.setter
+    def theme_dark(self, theme_dark):
+        """Sets the theme_dark of this UserDto.
+
+
+        :param theme_dark: The theme_dark of this UserDto.  # noqa: E501
+        :type: bool
+        """
+        if theme_dark is None:
+            raise ValueError("Invalid value for `theme_dark`, must not be `None`")  # noqa: E501
+
+        self._theme_dark = theme_dark
+
     @property
     def email_verified(self):
         """Gets the email_verified of this UserDto.  # noqa: E501

.jupyter/api_query/models/user_dto.py

@@ -41,6 +41,7 @@ class UserDto(object):
         'email': 'str',
         'titles_before': 'str',
         'titles_after': 'str',
+        'theme_dark': 'bool',
         'email_verified': 'bool'
     }
 
@@ -58,10 +59,11 @@ class UserDto(object):
         'email': 'email',
         'titles_before': 'titles_before',
         'titles_after': 'titles_after',
+        'theme_dark': 'theme_dark',
         'email_verified': 'email_verified'
     }
 
-    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, email_verified=None):  # noqa: E501
+    def __init__(self, id=None, authorities=None, username=None, firstname=None, lastname=None, affiliation=None, orcid=None, containers=None, databases=None, identifiers=None, email=None, titles_before=None, titles_after=None, theme_dark=None, email_verified=None):  # noqa: E501
         """UserDto - a model defined in Swagger"""  # noqa: E501
         self._id = None
         self._authorities = None
@@ -76,6 +78,7 @@ class UserDto(object):
         self._email = None
         self._titles_before = None
         self._titles_after = None
+        self._theme_dark = None
         self._email_verified = None
         self.discriminator = None
         self.id = id
@@ -101,6 +104,7 @@ class UserDto(object):
             self.titles_before = titles_before
         if titles_after is not None:
             self.titles_after = titles_after
+        self.theme_dark = theme_dark
         if email_verified is not None:
             self.email_verified = email_verified
 
@@ -383,6 +387,29 @@ class UserDto(object):
 
         self._titles_after = titles_after
 
+    @property
+    def theme_dark(self):
+        """Gets the theme_dark of this UserDto.  # noqa: E501
+
+
+        :return: The theme_dark of this UserDto.  # noqa: E501
+        :rtype: bool
+        """
+        return self._theme_dark
+
+    @theme_dark.setter
+    def theme_dark(self, theme_dark):
+        """Sets the theme_dark of this UserDto.
+
+
+        :param theme_dark: The theme_dark of this UserDto.  # noqa: E501
+        :type: bool
+        """
+        if theme_dark is None:
+            raise ValueError("Invalid value for `theme_dark`, must not be `None`")  # noqa: E501
+
+        self._theme_dark = theme_dark
+
     @property
     def email_verified(self):
         """Gets the email_verified of this UserDto.  # noqa: E501

fda-gateway-service/gateway/src/main/java/at/tuwien/config/GatewayConfig.java

@@ -35,8 +35,9 @@ public class GatewayConfig {
                         .uri("lb://fda-identifier-service"))
                 .route("fda-query-service", r -> r.path("/api/container/**/database/**/query/**",
                                 "/api/container/**/database/**/table/**/history/**",
-                                "/api/container/**/database/**/table/**/data/**", // TODO
-                                "/api/container/**/database/**/table/**/query/**", // TODO
+                                "/api/container/**/database/**/table/**/data/**",
+                                "/api/container/**/database/**/table/**/query/**",
+                                "/api/container/**/database/**/table/**/export/**",
                                 "/api/container/**/database/**/version/**")
                         .and()
                         .method("POST", "GET", "PUT", "DELETE")

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

@@ -104,7 +104,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -121,7 +121,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -177,7 +177,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -323,7 +323,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -337,7 +337,7 @@ public interface QueryMapper {
         final StringBuilder versionPart = new StringBuilder(" FOR SYSTEM_TIME AS OF TIMESTAMP'")
                 .append(mariaDbFormatter.format(query.getExecution()))
                 .append("' ");
-        final Pattern pattern = Pattern.compile("from `?[a-zA-Z0-9_]+`?", Pattern.CASE_INSENSITIVE) /* https://mariadb.com/kb/en/columnstore-naming-conventions/ */;
+        final Pattern pattern = Pattern.compile("from `?[a-zA-Z0-9_-]+`?", Pattern.CASE_INSENSITIVE) /* https://mariadb.com/kb/en/columnstore-naming-conventions/ */;
         final Matcher matcher = pattern.matcher(query.getQuery());
         if (!matcher.find()) {
             log.error("Failed to find 'from' clause in query");
@@ -355,7 +355,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -407,7 +407,7 @@ public interface QueryMapper {
             return ps;
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -440,7 +440,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -509,7 +509,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -560,7 +560,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement);
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -626,7 +626,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement);
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -681,7 +681,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -690,7 +690,7 @@ public interface QueryMapper {
         final List<Map<String, Object>> queryResult = new LinkedList<>();
         while (result.next()) {
             /* map the result set to the columns through the stored metadata in the metadata database */
-            int[] idx = new int[]{0};
+            int[] idx = new int[]{1};
             final Map<String, Object> map = new HashMap<>();
             for (int i = 0; i < table.getColumns().size(); i++) {
                 map.put(table.getColumns().get(i).getInternalName(), dataColumnToObject(result.getObject(idx[0]++), table.getColumns().get(i)));
@@ -717,7 +717,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }
@@ -857,7 +857,7 @@ public interface QueryMapper {
             return connection.prepareStatement(statement.toString());
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryMalformedException("Failed to prepare statement", e);
         }
     }

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

@@ -58,7 +58,7 @@ public interface StoreMapper {
             return ps;
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryStoreException("Failed to prepare statement", e);
         }
     }
@@ -69,7 +69,7 @@ public interface StoreMapper {
             return connection.prepareStatement(statement);
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryStoreException("Failed to prepare statement", e);
         }
     }
@@ -84,7 +84,7 @@ public interface StoreMapper {
             return ps;
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryStoreException("Failed to prepare statement", e);
         }
     }
@@ -107,7 +107,7 @@ public interface StoreMapper {
             return ps;
         } catch (SQLException e) {
             log.error("Failed to prepare statement");
-            log.debug("failed to prepare statement {} reason {}", statement, e.getMessage());
+            log.debug("failed to prepare statement {} reason: {}", statement, e.getMessage());
             throw new QueryStoreException("Failed to prepare statement", e);
         }
     }

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

@@ -134,6 +134,7 @@ public class QueryServiceImpl extends HibernateConnector implements QueryService
             throw new TableMalformedException("Could not parse date from format", e);
         } catch (SQLException e) {
             log.error("Failed to map object");
+            log.debug("failed to map object, reason: {}", e.getMessage());
             throw new TableMalformedException("Failed to map object", e);
         } finally {
             dataSource.close();

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

@@ -63,7 +63,7 @@ public class StoreServiceImpl extends HibernateConnector implements StoreService
             return storeMapper.resultSetToQueryList(resultSet);
         } catch (SQLException e) {
             log.error("Failed to find queries");
-            log.debug("failed to find queries in container with id {} and database with id {}, reason {}", containerId, databaseId, e.getMessage());
+            log.debug("failed to find queries in container with id {} and database with id {}, reason: {}", containerId, databaseId, e.getMessage());
             throw new QueryStoreException("Query not found");
         } finally {
             dataSource.close();

fda-ui/components/query/Results.vue

@@ -53,21 +53,14 @@ export default {
         console.debug('send data', data)
         const page = 0
         const urlParams = `page=${page}&size=${this.options.itemsPerPage}`
-        const res = await this.$axios.put(`/api/container/
-${this.$route.params.container_id}/database/${this.$route.params.database_id}/query
-${this.parent.queryId ? `/${this.parent.queryId}` : ''}
-?${urlParams}`, data, {
+        const res = await this.$axios.put(`/api/container/${this.$route.params.container_id}/database/${this.$route.params.database_id}/query${this.parent.queryId ? `/${this.parent.queryId}` : ''}?${urlParams}`, data, {
           headers: this.headers
         })
         console.debug('query result', res)
         this.$toast.success('Successfully executed query')
+        this.mapResults(res.data)
         this.loading = false
         this.parent.queryId = res.data.id
-        this.result.headers = this.parent.select.map((s) => {
-          return { text: s.name, value: s.name, sortable: false }
-        })
-        this.result.rows = res.data.result
-        this.total = res.data.resultNumber
       } catch (err) {
         console.error('query execute', err)
         this.$toast.error('Could not execute query')
@@ -95,13 +88,8 @@ ${this.$route.params.container_id}/database/${this.$route.params.database_id}/qu
 ?${urlParams}`, {}, {
           headers: this.headers
         })
+        this.mapResults(res.data)
         this.loading = false
-        if (res.data.result.length) {
-          this.result.headers = this.buildHeaders(res.data.result[0])
-        }
-        console.debug('query result', res.data)
-        this.result.rows = res.data.result
-        this.total = res.data.resultNumber
       } catch (err) {
         if (err.response.status !== 401 && err.response.status !== 405) {
           console.error('query execute', err)
@@ -109,6 +97,14 @@ ${this.$route.params.container_id}/database/${this.$route.params.database_id}/qu
         }
         this.loading = false
       }
+    },
+    mapResults (data) {
+      if (data.result.length) {
+        this.result.headers = this.buildHeaders(data.result[0])
+      }
+      console.debug('query result', data)
+      this.result.rows = data.result
+      this.total = data.resultNumber
     }
   }
 }

fda-ui/pages/container/_container_id/database/_database_id/table/_table_id/index.vue

@@ -27,6 +27,9 @@
         <v-btn :disabled="!token" class="mb-1" :to="`/container/${$route.params.container_id}/database/${$route.params.database_id}/table/${$route.params.table_id}/import`">
           <v-icon left>mdi-cloud-upload</v-icon> Import csv
         </v-btn>
+        <v-btn :disabled="error" class="ml-2 mb-1" :loading="downloadLoading" @click.stop="download">
+          <v-icon left>mdi-download</v-icon> Data .csv
+        </v-btn>
         <v-btn
           v-if="false"
           color="primary"
@@ -96,6 +99,7 @@ export default {
       footerProps: {
         'items-per-page-options': [10, 20, 30, 40, 50]
       },
+      downloadLoading: false,
       dateMenu: false,
       timeMenu: false,
       selection: [],
@@ -172,6 +176,27 @@ export default {
     this.loadData()
   },
   methods: {
+    async download () {
+      this.downloadLoading = true
+      try {
+        const res = await this.$axios.get(`/api/container/${this.$route.params.container_id}/database/${this.$route.params.database_id}/table/${this.$route.params.table_id}/export`, {
+          headers: { Authorization: `Bearer ${this.token}` },
+          responseType: 'text'
+        })
+        console.debug('export table', res)
+        const url = window.URL.createObjectURL(new Blob([res.data]))
+        const link = document.createElement('a')
+        link.href = url
+        link.setAttribute('download', 'table.csv')
+        document.body.appendChild(link)
+        link.click()
+      } catch (err) {
+        console.error('Could not export table', err)
+        this.$toast.error('Could not export table')
+        this.error = true
+      }
+      this.downloadLoading = false
+    },
     addTuple () {
       this.edit = false
       const data = {}