Merge 4a6ea7e into 8213766

.coveralls.yml

@@ -1 +1 @@
-repo_token: sKBVzfBUvZi7I4DDFAn4SLzdyLCBQb3rd
+repo_token: 5OBT9Dq2n5pQfhOV9gJNu8THW8O1qUxdg

askomics/api/auth.py

@@ -115,7 +115,14 @@ def login_api_key(key):
         except Exception:
             pass
 
-        return render_template('index.html', project="AskOmics", proxy_path=proxy_path, redirect="/")
+        title = "AskOmics"
+        try:
+            subtitle = current_app.iniconfig.get('askomics', 'subtitle')
+            title = "AskOmics | {}".format(subtitle)
+        except Exception:
+            pass
+
+        return render_template('index.html', title=title, proxy_path=proxy_path, redirect="/")
 
     else:
 

askomics/libaskomics/CsvFile.py

@@ -491,7 +491,7 @@ def generate_rdf_content(self):
                         relation = self.askomics_prefix[self.format_uri(current_header, remove_space=True)]
                         attribute = rdflib.Literal(self.convert_type(cell))
 
-                    if entity and relation and attribute:
+                    if entity and relation is not None and attribute is not None:
                         self.graph_chunk.add((entity, relation, attribute))
                         if symetric_relation:
                             self.graph_chunk.add((attribute, relation, entity))

askomics/react/src/classes/utils.jsx

@@ -22,4 +22,10 @@ export default class Utils {
     let event = new Date(date * 1000)
     return event.toUTCString()
   }
+
+  objectHaveKeys(obj, level, ...rest) {
+    if (obj === undefined) return false
+    if (rest.length == 0 && obj.hasOwnProperty(level)) return true
+    return this.objectHaveKeys(obj[level], ...rest)
+  }
 }

askomics/react/src/routes.jsx

@@ -4,7 +4,6 @@ import axios from 'axios'
 
 import Ask from './routes/ask/ask'
 import About from './routes/about/about'
-import Jobs from './routes/jobs/jobs'
 import Upload from './routes/upload/upload'
 import Integration from './routes/integration/integration'
 import Datasets from './routes/datasets/datasets'
@@ -72,6 +71,12 @@ export default class Routes extends Component {
 
   render () {
 
+    let redirectRoot
+
+    if (document.getElementById('redirect').getAttribute('redirect') == "/") {
+      redirectRoot = <Redirect to="/" />
+    }
+
     let admin = false
     if (this.state.config.user) {
       admin = this.state.config.user.admin
@@ -92,6 +97,7 @@ export default class Routes extends Component {
     return (
       <Router basename={this.state.config.proxyPath}>
         <div>
+          {redirectRoot}
           <AskoNavbar waitForStart={this.state.waiting} config={this.state.config} />
           <Switch>
             <Route path="/" exact component={() => (<Ask waitForStart={this.state.waiting} config={this.state.config} />)} />

askomics/react/src/routes/ask/ask.jsx

@@ -268,6 +268,7 @@ export default class Ask extends Component {
               {exempleQueries}
             </Col>
           </Row>
+          <br />
         <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )

askomics/react/src/routes/datasets/datasets.jsx

@@ -3,6 +3,7 @@ import axios from 'axios'
 import DatasetsTable from './datasetstable'
 import { Button } from 'reactstrap'
 import PropTypes from 'prop-types'
+import ErrorDiv from '../error/error'
 
 export default class Datasets extends Component {
   constructor (props) {
@@ -87,6 +88,7 @@ export default class Datasets extends Component {
           <br />
           <Button disabled={this.isDisabled()} onClick={this.deleteSelectedDatasets} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
         </div>
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )
   }

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

@@ -2,10 +2,12 @@ import React, { Component } from 'react'
 import { Alert } from 'reactstrap'
 import { Redirect } from 'react-router'
 import PropTypes from 'prop-types'
+import Utils from '../../classes/utils'
 
 export default class ErrorDiv extends Component {
   constructor (props) {
     super(props)
+    this.utils = new Utils()
   }
 
   render () {
@@ -17,19 +19,31 @@ export default class ErrorDiv extends Component {
       return null
     }
 
+    let messages = {
+      "404": this.utils.objectHaveKeys(this.props, "customMessages", "404") ? this.props.customMessages["404"] : "404 Not Found",
+      "503": this.utils.objectHaveKeys(this.props, "customMessages", "503") ? this.props.customMessages["503"] : "503 Service Unavailable ",
+      "504": this.utils.objectHaveKeys(this.props, "customMessages", "504") ? this.props.customMessages["504"] : "504 Gateway Time-out",
+      "500": this.utils.objectHaveKeys(this.props, "customMessages", "500") ? this.props.customMessages["500"] : this.props.errorMessage ? this.props.errorMessage : "500 Internal Server Error",
+    }
+
+    let errorMessage = this.props.errorMessage
+    if (this.utils.objectHaveKeys(this.props, "status")) {
+      errorMessage = messages[this.props.status.toString()]
+    }
+
     let error
-    if (Array.isArray(this.props.errorMessage)) {
+    if (Array.isArray(errorMessage)) {
       error = (
         <Alert color="danger">
-          {this.props.errorMessage.map((item, index) => (
+          {errorMessage.map((item, index) => (
             <div key={index}><i className="fas fa-exclamation-circle"></i> {item}</div>
           ))}
         </Alert>
       )
     } else {
       error = (
         <Alert color="danger">
-          <div><i className="fas fa-exclamation-circle"></i> {this.props.errorMessage}</div>
+          <div><i className="fas fa-exclamation-circle"></i> {errorMessage}</div>
         </Alert>
       )
     }
@@ -45,5 +59,6 @@ export default class ErrorDiv extends Component {
 ErrorDiv.propTypes = {
   status: PropTypes.number,
   error: PropTypes.bool,
-  errorMessage: PropTypes.string
+  errorMessage: PropTypes.string,
+  customMessages: PropTypes.object
 }

askomics/react/src/routes/integration/bedpreview.jsx

@@ -3,6 +3,7 @@ import axios from 'axios'
 import { CustomInput, Input, FormGroup, Label, ButtonGroup, Button, Col } from 'reactstrap'
 import update from 'react-addons-update'
 import PropTypes from 'prop-types'
+import ErrorDiv from '../error/error'
 
 export default class BedPreview extends Component {
   constructor (props) {
@@ -14,7 +15,10 @@ export default class BedPreview extends Component {
       id: props.file.id,
       integrated: false,
       publicTick: false,
-      privateTick: false
+      privateTick: false,
+      error: false,
+      errorMessage: null,
+      status: null
     }
     this.cancelRequest
     this.integrate = this.integrate.bind(this)
@@ -87,6 +91,8 @@ export default class BedPreview extends Component {
           <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
           {publicButton}
         </ButtonGroup>
+        <br />
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )
   }

askomics/react/src/routes/integration/csvtable.jsx

@@ -4,6 +4,7 @@ import BootstrapTable from 'react-bootstrap-table-next'
 import { CustomInput, Input, FormGroup, ButtonGroup, Button } from 'reactstrap'
 import update from 'react-addons-update'
 import PropTypes from 'prop-types'
+import ErrorDiv from '../error/error'
 
 export default class CsvTable extends Component {
   constructor (props) {
@@ -15,7 +16,10 @@ export default class CsvTable extends Component {
       columns_type: props.file.data.columns_type,
       integrated: false,
       publicTick: false,
-      privateTick: false
+      privateTick: false,
+      error: false,
+      errorMessage: null,
+      status: null
     }
     this.cancelRequest
     this.headerFormatter = this.headerFormatter.bind(this)
@@ -148,6 +152,8 @@ export default class CsvTable extends Component {
             {publicButton}
           </ButtonGroup>
         </div>
+        <br />
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )
   }

askomics/react/src/routes/integration/gffpreview.jsx

@@ -3,6 +3,7 @@ import axios from 'axios'
 import { CustomInput, Input, FormGroup, ButtonGroup, Button } from 'reactstrap'
 import update from 'react-addons-update'
 import PropTypes from 'prop-types'
+import ErrorDiv from '../error/error'
 
 export default class GffPreview extends Component {
   constructor (props) {
@@ -99,6 +100,8 @@ export default class GffPreview extends Component {
             <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
             {publicButton}
           </ButtonGroup>
+          <br />
+          <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )
   }

askomics/react/src/routes/integration/integration.jsx

@@ -89,6 +89,7 @@ export default class Integration extends Component {
         }
 
         <WaitingDiv waiting={this.state.waiting} center="center" />
+        <br />
         <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )

askomics/react/src/routes/integration/ttlpreview.jsx

@@ -3,11 +3,11 @@ import axios from 'axios'
 import { CustomInput, Input, FormGroup, ButtonGroup, Button } from 'reactstrap'
 import update from 'react-addons-update'
 import PropTypes from 'prop-types'
-import brace from 'brace'
 import AceEditor from 'react-ace'
+import ErrorDiv from '../error/error'
 
-import 'brace/mode/turtle'
-import 'brace/theme/tomorrow'
+import "ace-builds/src-noconflict/mode-turtle";
+import "ace-builds/src-noconflict/theme-tomorrow";
 
 export default class TtlPreview extends Component {
   constructor (props) {
@@ -18,7 +18,10 @@ export default class TtlPreview extends Component {
       id: props.file.id,
       integrated: false,
       publicTick: false,
-      privateTick: false
+      privateTick: false,
+      error: false,
+      errorMessage: null,
+      status: null
     }
     this.cancelRequest
     this.integrate = this.integrate.bind(this)
@@ -101,6 +104,8 @@ export default class TtlPreview extends Component {
             {publicButton}
           </ButtonGroup>
         </div>
+        <br />
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
     )
   }

askomics/react/src/routes/query/query.jsx

@@ -1,6 +1,6 @@
 import React, { Component } from 'react'
 import axios from 'axios'
-import { Alert, Button, Row, Col, ButtonGroup, Input } from 'reactstrap'
+import { Alert, Button, Row, Col, ButtonGroup, Input, Spinner } from 'reactstrap'
 import { Redirect } from 'react-router-dom'
 import ErrorDiv from '../error/error'
 import WaitingDiv from '../../components/waiting'
@@ -1196,7 +1196,11 @@ export default class Query extends Component {
       )
 
       // buttons
-      previewButton = <Button onClick={this.handlePreview} color="secondary" disabled={this.state.disablePreview}><i className={"fas fa-" + this.state.previewIcon}></i> Run & preview</Button>
+      let previewIcon = <i className={"fas fa-" + this.state.previewIcon}></i>
+      if (this.state.previewIcon == "spinner") {
+        previewIcon = <Spinner size="sm" color="light" />
+      }
+      previewButton = <Button onClick={this.handlePreview} color="secondary" disabled={this.state.disablePreview}>{previewIcon} Run & preview</Button>
       if (this.state.config.logged) {
         launchQueryButton = <Button onClick={this.handleQuery} color="secondary" disabled={this.state.disableSave || this.state.exceededQuota}><i className={"fas fa-" + this.state.saveIcon}></i> Run & save</Button>
       }
@@ -1267,7 +1271,7 @@ export default class Query extends Component {
         <div>
           {resultsTable}
         </div>
-        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} customMessages={{"504": "Query time is too long, use Run & Save to get your results"}} />
       </div>
     )
   }

askomics/react/src/routes/results/resultsfilestable.jsx

@@ -9,6 +9,7 @@ import Utils from '../../classes/utils'
 import { Badge, Button, ButtonGroup, FormGroup, CustomInput, Input, Modal, ModalHeader, ModalBody, ModalFooter } from 'reactstrap'
 import FileDownload from 'js-file-download'
 import PropTypes from 'prop-types'
+import ErrorDiv from '../error/error'
 
 export default class ResultsFilesTable extends Component {
   constructor (props) {
@@ -18,7 +19,10 @@ export default class ResultsFilesTable extends Component {
       graphState: [],
       modal: false,
       idToPublish: null,
-      description: ''
+      description: '',
+      error: false,
+      errorMessage: null,
+      status: null
     }
     this.utils = new Utils()
     this.handleSelection = this.handleSelection.bind(this)
@@ -334,7 +338,7 @@ export default class ResultsFilesTable extends Component {
             <Button disabled={row.sparqlQuery != null ? true : false} id={row.id} size="sm" outline color="secondary" onClick={this.handleRedo}>Redo</Button>
             <Button disabled={row.status == "success" ? false : true} id={row.id} size="sm" outline color="secondary" onClick={this.handleEditQuery}>Sparql</Button>
             {this.props.config.user.galaxy ? <Button disabled={row.status == "success" ? false : true} name="result" id={row.id} size="sm" outline color="secondary" onClick={this.handleSendToGalaxy}>Send result to Galaxy</Button> : null}
-            {this.props.config.user.galaxy ? <Button disabled={row.sparqlQuery != "null" ? true : false} name="query" id={row.id} size="sm" outline color="secondary" onClick={this.handleSendToGalaxy}>Send query to Galaxy</Button> : null}
+            {this.props.config.user.galaxy ? <Button disabled={row.sparqlQuery != null ? true : false} name="query" id={row.id} size="sm" outline color="secondary" onClick={this.handleSendToGalaxy}>Send query to Galaxy</Button> : null}
           </ButtonGroup>
         )
       },
@@ -384,6 +388,8 @@ export default class ResultsFilesTable extends Component {
             })}
           />
         </div>
+        <br />
+        <ErrorDiv status={this.state.status} error={this.state.error} errorMessage={this.state.errorMessage} />
       </div>
 
     )