Fix ui and some bugs

CHANGELOG.md

@@ -14,9 +14,11 @@ This changelog was started for release 4.2.0.
 - "askomics:instancesLabel" predicate can be defined at the entity-level, to set a specific attribute URI as the 'label' (ie, visible by default)
   - Play the same role as 'askomics:instancesHaveNoLabels', except a specific attribute is visible instead of the URI attribute.
 - Added the *TIMEOUT* env variable, which will set the web workers tiemout value. Default 300s
+- Added the 'skip_rdf_preview' config option. This will skip loading RDF files in memory to get the location and remote graph. Warning: This means you must enter the values at the integration step yourself.
 
 ### Changed
 
+- Now pre-process files to store integration parameters (column, entities, etc...) in DB, to avoid re-processing every time.
 - Rewrote the ontology part. Instead of specifying 'children of' and other values, users can tick the 'recursive' button to customize the query. While this is less intuitive, this change is more flexible for the various types of ontological relations
 
 ## [4.5.0] - 2023-10-20

askomics/api/file.py

@@ -261,15 +261,17 @@ def get_preview():
 
     errorMessage = ''
     error = False
+    errorCode = 200
     if not results:
         errorMessage = "None of the selected files are in an integrable state"
         error = True
+        errorCode = 400
 
     return jsonify({
         'previewFiles': results,
         'error': error,
         'errorMessage': errorMessage
-    })
+    }), errorCode
 
 
 @file_bp.route('/api/files/delete', methods=['POST'])

askomics/libaskomics/GffFile.py

@@ -81,7 +81,7 @@ def save_preview(self):
         if self.error:
             error = self.error_message
         else:
-            data = {'entities': self.entity_name}
+            data = {'entities': self.entities}
         self.save_preview_in_db(data, error)
 
     def get_preview(self):

askomics/libaskomics/RdfFile.py

@@ -59,6 +59,10 @@ def get_location_and_remote_graph(self):
         str
             Location
         """
+
+        if self.settings.get('skip_rdf_preview', False):
+            return "", ""
+
         graph = RdfGraph(self.app, self.session)
         graph.parse(self.path, format=self.type_dict[self.type])
         triple_loc = (None, self.prov.atLocation, None)

askomics/react/src/routes/error/error.jsx

@@ -39,7 +39,7 @@ export default class ErrorDiv extends Component {
     }
 
     let error
-
+ 
     if (Array.isArray(this.props.errorMessage)) {
       error = (
         <Alert color="danger">
@@ -48,12 +48,18 @@ export default class ErrorDiv extends Component {
           ))}
         </Alert>
       )
-    } else {
+    } else if (! this.props.errorMessage){
       error = (
         <Alert color="danger">
           <div><i className="fas fa-exclamation-circle"></i> {messages[this.props.status.toString()]}</div>
         </Alert>
       )
+    } else {
+      error = (
+        <Alert color="danger">
+          <div><i className="fas fa-exclamation-circle"></i> {this.props.errorMessage}</div>
+        </Alert>
+      )
     }
 
     return (

askomics/react/src/routes/upload/filestable.jsx

@@ -3,17 +3,26 @@ import axios from 'axios'
 import BootstrapTable from 'react-bootstrap-table-next'
 import paginationFactory from 'react-bootstrap-table2-paginator'
 import cellEditFactory from 'react-bootstrap-table2-editor'
-import {Badge} from 'reactstrap'
+import {Badge, Modal, ModalHeader, ModalBody, ModalFooter, Button} from 'reactstrap'
 import WaitingDiv from '../../components/waiting'
 import Utils from '../../classes/utils'
+import SyntaxHighlighter from 'react-syntax-highlighter'
+import { monokai } from 'react-syntax-highlighter/dist/esm/styles/hljs'
 import PropTypes from 'prop-types'
 
 export default class FilesTable extends Component {
   constructor (props) {
     super(props)
+    this.state = {
+      modalTracebackTitle: "",
+      modalTracebackContent: "",
+      modalTraceback: false
+    }
     this.utils = new Utils()
     this.handleSelection = this.handleSelection.bind(this)
     this.handleSelectionAll = this.handleSelectionAll.bind(this)
+    this.handleClickError = this.handleClickError.bind(this)
+    this.toggleModalTraceback = this.toggleModalTraceback.bind(this)
   }
 
   handleSelection (row, isSelect) {
@@ -41,6 +50,24 @@ export default class FilesTable extends Component {
     }
   }
 
+  handleClickError(event) {
+    this.props.files.forEach(file => {
+      if (file.id == event.target.id) {
+        this.setState({
+          modalTracebackTitle: "File processing error",
+          modalTracebackContent: file.preview_error ? file.preview_error : "Internal server error",
+          modalTraceback: true
+        })
+      }
+    })
+  }
+
+  toggleModalTraceback () {
+    this.setState({
+      modalTraceback: !this.state.modalTraceback
+    })
+  }
+
   editFileName (oldValue, newValue, row) {
 
     if (newValue === oldValue) {return}
@@ -102,7 +129,7 @@ export default class FilesTable extends Component {
         if (cell == 'processing') {
           return <Badge color="secondary">Processing</Badge>
         }
-        return <Badge color="danger">Error</Badge>
+        return <Badge style={{cursor: "pointer"}} id={row.id} color="danger" onClick={this.handleClickError}>Error</Badge>
       },
       sort: true,
       editable: false
@@ -147,6 +174,19 @@ export default class FilesTable extends Component {
               })}
             />
           </div>
+          <Modal size="lg" isOpen={this.state.modalTraceback} toggle={this.toggleModalTraceback}>
+          <ModalHeader toggle={this.toggleModalTraceback}>{this.state.modalTracebackTitle.substring(0, 100)}</ModalHeader>
+          <ModalBody>
+            <div>
+              <SyntaxHighlighter language="python" style={monokai}>
+                {this.state.modalTracebackContent}
+              </SyntaxHighlighter>
+            </div>
+          </ModalBody>
+          <ModalFooter>
+            <Button color="secondary" onClick={this.toggleModalTraceback  }>Close</Button>
+          </ModalFooter>
+        </Modal>
       </div>
     )
   }

askomics/react/src/routes/upload/upload.jsx

@@ -28,26 +28,10 @@ export default class Upload extends Component {
 
   componentDidMount () {
     if (!this.props.waitForStart) {
-      let requestUrl = '/api/files'
-      axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
-        .then(response => {
-          console.log(requestUrl, response.data)
-          this.setState({
-            diskSpace: response.data.diskSpace,
-            exceededQuota: this.props.config.user.quota > 0 && response.data.diskSpace >= this.props.config.user.quota,
-            files: response.data.files,
-            waiting: false
-          })
-        })
-        .catch(error => {
-          console.log(error, error.response.data.errorMessage)
-          this.setState({
-            error: true,
-            errorMessage: error.response.data.errorMessage,
-            status: error.response.status,
-            waiting: false
-          })
-        })
+      this.getFiles()
+      this.interval = setInterval(() => {
+        this.getFiles()
+      }, 5000)
     }
   }
 
@@ -57,6 +41,31 @@ export default class Upload extends Component {
     }
   }
 
+
+  getFiles() {
+    let requestUrl = '/api/files'
+    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        this.setState({
+          diskSpace: response.data.diskSpace,
+          exceededQuota: this.props.config.user.quota > 0 && response.data.diskSpace >= this.props.config.user.quota,
+          files: response.data.files,
+          waiting: false
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          error: true,
+          errorMessage: error.response.data.errorMessage,
+          status: error.response.status,
+          waiting: false
+        })
+      })
+  }
+
+
   deleteSelectedFiles () {
     let requestUrl = '/api/files/delete'
     let data = {
@@ -94,6 +103,10 @@ export default class Upload extends Component {
     return this.state.selected.length == 0
   }
 
+  isDisabledIntegrate () {
+    return this.state.selected.length == 0 || this.state.files.some(file => this.state.selected.includes(file.id) && file.status == "error")
+  }
+
   render () {
     let redirectLogin
     if (this.state.status == 401) {
@@ -138,7 +151,7 @@ export default class Upload extends Component {
         <br />
         <ButtonGroup>
           <Button disabled={this.isDisabled()} onClick={this.deleteSelectedFiles} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
-          <Button disabled={this.isDisabled()} onClick={this.integrateSelectedFiles} color="secondary"><i className="fas fa-database"></i> Integrate</Button>
+          <Button disabled={this.isDisabledIntegrate()} onClick={this.integrateSelectedFiles} color="secondary"><i className="fas fa-database"></i> Integrate</Button>
         </ButtonGroup>
         <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>

askomics/tasks.py

@@ -26,7 +26,7 @@
 celery = create_celery(app)
 
 
-@celery.task(bind=True, name="set_preview")
+@celery.task(bind=True, name="save_preview")
 def save_preview(self, session, fileId):
     """Compute the file preview in backend and store it in DB
 

config/askomics.ini.template

@@ -91,6 +91,9 @@ autocomplete_max_results = 10
 anonymous_query = false
 anonymous_query_cleanup = 60
 
+skip_rdf_preview = false
+
+
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
 triplestore = virtuoso