Merge pull request #96 from MyersResearchGroup/clean-download-auto

Clean SBOL upon edit

apps/server/app.py

@@ -302,6 +302,32 @@ def convert_genbank_to_sbol2(genbank_content, uri_prefix):
 
     return result_sbol_content
 
+def run_synbio2easy(sbol_content):
+    namespace = 'https://seqimprove.synbiohub.org'
+
+    try:
+        with tempfile.NamedTemporaryFile() as input_file:
+            input_file.write(bytes(sbol_content, 'utf-8'))
+            input_file.flush()
+            with tempfile.NamedTemporaryFile() as output_file:
+
+                command = [
+                    'java', '-jar', 'SynBio2Easy.jar', 'clean',
+                    f'--input-file={input_file.name}',
+                    f'--output-file={output_file.name}',
+                    f'--namespace={namespace}',
+                    f'--remove-collections=Y'
+                ]
+                print(command)
+                output = subprocess.check_output(command, universal_newlines=True, stderr=subprocess.STDOUT)
+                print(output)
+                cleaned_data = output_file.read().decode('utf-8')
+                return cleaned_data
+
+    except Exception as e:
+        print(e)
+        return sbol_content
+
 #  _______  _______ _________     _______  _______          _________ _______  _______ 
 # (  ___  )(  ____ )\__   __/    (  ____ )(  ___  )|\     /|\__   __/(  ____ \(  ____ \
 # | (   ) || (    )|   ) (       | (    )|| (   ) || )   ( |   ) (   | (    \/| (    \/
@@ -345,14 +371,24 @@ def genbank_to_sbol2():
 
         return {"sbol2_content": "", "err": error_message };
 
-
+@app.post("/api/cleanSBOL")
+def clean_SBOL():
+    request_data = request.get_json()
+    sbol_content = request_data['completeSbolContent']
+
+    return {"sbol": run_synbio2easy(sbol_content)}
+
 
 
 @app.post("/api/annotateSequence")
 def annotate_sequence():
     request_data = request.get_json()
     sbol_content = request_data['completeSbolContent']
     part_library_file_names = request_data['partLibraries'] 
+    clean_document = request_data['cleanDocument']
+
+    if clean_document: 
+        sbol_content = run_synbio2easy(sbol_content)
 
     print("Running SYNBICT...")
     # Run SYNBICT
@@ -372,7 +408,6 @@ def annotate_sequence():
         print(str(e))
         return {"sbol": sbol_content}, status.HTTP_500_INTERNAL_SERVER_ERROR
     else:
-        # return {"annotations": annotations}
         return {"annotations": anno_lib_assoc}
 
 @app.post("/api/findSimilarParts")

apps/web/src/App.jsx

@@ -12,12 +12,35 @@ export default function App() {
     bootAPIserver();
     const loadSBOL = useStore(s => s.loadSBOL)
     const documentLoaded = useStore(s => !!s.document)
+    const isFileEdited = useStore((s) => s.isFileEdited);
+    const cleanSBOLDocument = useStore((s) => s.cleanSBOLDocument);
+    const isUriCleaned = useStore((s => s.isUriCleaned))
+    const nameChanged = useStore((s => s.nameChanged))
+
+    //add variable to keep track of name change
 
-    // load SBOL into store if we have a complete_sbol parameter
     useEffect(() => {
+        // && !nameChanged
+        if (isFileEdited && !isUriCleaned) {
+            cleanSBOLDocument();
+        }
         const paramsUri = getSearchParams().complete_sbol
         paramsUri && loadSBOL(paramsUri)
-    }, [])
+    }, [isFileEdited]);
+
+    //name change effect
+    useEffect(() => {
+        if (nameChanged && !isUriCleaned) {
+            cleanSBOLDocument();
+        }
+    }, [nameChanged])
+
+
+    // load SBOL into store if we have a complete_sbol parameter
+    // useEffect(() => {
+    //     const paramsUri = getSearchParams().complete_sbol
+    //     paramsUri && loadSBOL(paramsUri)
+    // }, [])
 
     return (
         <MantineProvider theme={theme} withNormalizeCSS withGlobalStyles>

apps/web/src/components/CurationForm.jsx

@@ -1,5 +1,5 @@
 import { Container, Title, Tabs, Text, Space, LoadingOverlay, Button, Group, Header, List, ActionIcon, Tooltip, Textarea, Menu, Modal, TextInput, PasswordInput, Loader, Center, Select, SegmentedControl, Checkbox } from '@mantine/core'
-import { useStore, mutateDocument } from '../modules/store'
+import { useStore, mutateDocument, mutateDocumentForDisplayID } from '../modules/store'
 import { useCyclicalColors } from "../hooks/misc"
 import SimilarParts from './SimilarParts'
 import RoleSelection from "./RoleSelection"
@@ -17,6 +17,8 @@ import References from './References'
 import { FaHome, FaPencilAlt, FaTimes, FaCheck } from 'react-icons/fa'
 import { useState } from "react"
 import { showErrorNotification, showNotificationSuccess } from "../modules/util"
+import { Graph, SBOL2GraphView } from "sbolgraph"
+import { createSBOLDocument } from '../modules/sbol'
 
 function validDisplayID(displayID) {
     return displayID.match(/^[a-z_]\w+$/i);
@@ -231,6 +233,7 @@ function SynBioHubClientUpload({ setIsInteractingWithSynBioHub }) {
                          }}                         
                          error={inputError != false}
                      />
+                     <Checkbox checked={overwrite} label="Overwrite?" description="Overwrite if submission exists" onChange={(event) => setOverwrite(event.currentTarget.checked)} />
                      <Button onClick={async () => {
                                  if (inputErrorID || inputErrorVersion) {
                                      showErrorNotification("Invalid Input", "Please address the issue and then submit.");
@@ -374,7 +377,7 @@ export default function CurationForm({ }) {
         setIsEditingDisplayID(true);
         setWorkingDisplayID(displayId);
     };
-
+    
     const handleEndDisplayIDEdit = (cancelled = false) => {
         if (cancelled) {
             setIsEditingDisplayID(false);
@@ -388,7 +391,7 @@ export default function CurationForm({ }) {
 
         setIsEditingDisplayID(false);       
 
-        mutateDocument(useStore.setState, state => {
+        mutateDocumentForDisplayID(useStore.setState, async state => {
             // updateChildURIDisplayIDs(workingDisplayID, state.document.root.displayId, state.document);
 
             // Replace displayId in URIs in xml            
@@ -426,7 +429,7 @@ export default function CurationForm({ }) {
 
             const newSBOLcontent = xmlChunks.concat(remainingXML).join('');
 
-            state.loadSBOL(newSBOLcontent);            
+            await state.replaceDocumentForIDChange(newSBOLcontent);      
         });
     };
 

apps/web/src/components/SequenceSection.jsx

@@ -1,5 +1,6 @@
 import { useState, useEffect, forwardRef, createElement } from "react"
 import { useForceUpdate } from "@mantine/hooks"
+import { Checkbox } from '@mantine/core';
 import { Button, Center, Group, Loader, NavLink, Space, CopyButton, ActionIcon, Tooltip, Textarea, MultiSelect, Text, Highlight} from "@mantine/core"
 import { FiDownloadCloud } from "react-icons/fi"
 import { FaCheck, FaPencilAlt, FaPlus, FaTimes, FaArrowRight } from "react-icons/fa"
@@ -321,7 +322,7 @@ function Annotations({ colors }) {
                     setSequencePartLibrariesSelected(...librariesSelected);
                 })}               
             />
-
+            
             {loading ?
                 <Center>
                     <Loader my={30} size="sm" variant="dots" /> :
@@ -334,7 +335,8 @@ function Annotations({ colors }) {
                     color="blue"
                     onClick={handleAnalyzeSequenceClick}
                     sx={{ borderRadius: 6 }}
-               />}
+               />
+            }
         </FormSection>
     )
 }

apps/web/src/modules/api.js

@@ -71,7 +71,41 @@ export async function fetchSBOL(url) {
     }
 }
 
-export async function fetchAnnotateSequence({ sbolContent, selectedLibraryFileNames }) {
+export async function cleanSBOL(sbolContent) {
+    try {
+        var response = await fetchWithTimeout(`${import.meta.env.VITE_API_LOCATION}/api/cleanSBOL`, {
+            method: "POST",
+            headers: {
+                "Content-Type": "application/json"
+            },
+            body: JSON.stringify({
+                completeSbolContent: sbolContent,
+            }),
+            timeout: 120000,
+        });
+    }
+    catch (err) {
+        console.error("Failed to fetch.");
+        showServerErrorNotification();
+        return;
+    }
+
+    try {
+        var result = await response.json();
+    }
+    catch (err) {
+        console.error("Couldn't parse JSON.");
+        showServerErrorNotification();
+        return;
+    }
+
+    if (response.status == 200) {
+        console.log("Clean SBOL fetched.");
+        return result.sbol
+    }
+}
+
+export async function fetchAnnotateSequence({ sbolContent, selectedLibraryFileNames, isUriCleaned }) {
     console.log("Annotating sequence...")
 
     // Fetch
@@ -84,6 +118,7 @@ export async function fetchAnnotateSequence({ sbolContent, selectedLibraryFileNa
             body: JSON.stringify({
                 completeSbolContent: sbolContent,
                 partLibraries: selectedLibraryFileNames,
+                cleanDocument: !isUriCleaned,
             }),
             timeout: 120000,
         });

apps/web/src/modules/sbol.js

@@ -3,6 +3,7 @@ import { Graph, S2ComponentDefinition, S2ComponentInstance, SBOL2GraphView } fro
 import { TextBuffer } from "text-ranger"
 import { mutateDocument, useAsyncLoader, useStore } from "./store"
 
+//change to seqimprove.synbiohub.org?
 const Prefix = "https://seqimprove.org/"
 
 const Predicates = {
@@ -134,6 +135,13 @@ export async function createSBOLDocument(sbolContent) {
     return document
 }
 
+export function isfromSynBioHub(componentDefinition) {
+    //expand to include every sbh instance
+    if (componentDefinition.uriChain.includes('https://synbiohub.org')) return true
+
+    return false
+}
+
 /**
  * Return the active status of any annotation in the sequenceAnnotations array
  *
@@ -239,6 +247,12 @@ export function removeAnnotationWithDefinition(componentDefinition, id) {
     definition.destroy()
 }
 
+export function incrementVersion(componentDefinition) {
+    const version = Number(componentDefinition.version)
+
+    componentDefinition.version = version + 1
+}
+
 /**
  * Finds existing SequenceAnnotations on a ComponentDefinition and returns
  * them in a form suitable for the store.