@opencloning/ui 1.0.0

package/src/components/assembler/sbol_visual_glyphs/origin-of-replication.svg

@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="origin-of-replication.svg"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="640"
+     inkscape:window-height="480"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="2.36"
+     inkscape:cx="25"
+     inkscape:cy="50"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><circle
+     cx="22.499998"
+     cy="22.499998"
+     r="12"
+     id="circle8"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/primer-binding-site.svg

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="primer-binding-site.svg"
+   inkscape:export-filename="/Users/jakebeal/projects/SBOL/SBOLv-realizations/Glyphs/primer-binding-site/primer-binding-site-specification.png"
+   inkscape:export-xdpi="300"
+   inkscape:export-ydpi="300"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="916"
+     inkscape:window-height="792"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="18.88"
+     inkscape:cx="25"
+     inkscape:cy="14.045418"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 9.510842,22.532046 26,0 -10,-7"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/promoter.svg

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="promoter.svg"><metadata
+     id="metadata14"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="945"
+     inkscape:window-height="775"
+     id="namedview12"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="13.350176"
+     inkscape:cx="25"
+     inkscape:cy="26.030279"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 29.000111,5.2464081 8.5,7.4999999 -8.5,7.3333"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /><path
+     d="m 7.5001114,39.746408 0,-27 28.9999996,0"
+     id="path10"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/ribosome-entry-site.svg

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="ribosome-entry-site.svg"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="640"
+     inkscape:window-height="480"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="2.36"
+     inkscape:cx="25"
+     inkscape:cy="50"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 9.4999973,32.499997 25.9999997,0 0,-5 c 0,-10 -6,-15 -13,-15 -7,0 -12.9999997,5 -12.9999997,15 z"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/specific-recombination-site.svg

@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="specific-recombination-site.svg"
+   inkscape:export-filename="/Users/jakebeal/projects/SBOL/SBOLv-realizations/Glyphs/inverter/inverter-specification.png"
+   inkscape:export-xdpi="300"
+   inkscape:export-ydpi="300"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="922"
+     inkscape:window-height="720"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="13.350176"
+     inkscape:cx="25"
+     inkscape:cy="26.030279"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 12.50009,32.499997 20,-10 -20,-10 0,20 z"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/terminator.svg

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="terminator.svg"><metadata
+     id="metadata14"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="1008"
+     inkscape:window-height="746"
+     id="namedview12"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="13.350176"
+     inkscape:cx="25"
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+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 22.499997,34.989391 0,-24.000001"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /><path
+     d="m 7.4999973,9.9893904 29.9999997,0"
+     id="path10"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs/three-prime-sticky-restriction-site.svg

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   viewBox="0 0 44.999998 44.999998"
+   version="1.1"
+   xml:space="preserve"
+   x="0px"
+   y="0px"
+   width="0.5in"
+   height="0.5in"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="three-prime-sticky-restriction-site.svg"><metadata
+     id="metadata12"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="640"
+     inkscape:window-height="480"
+     id="namedview10"
+     showgrid="false"
+     units="in"
+     inkscape:zoom="2.36"
+     inkscape:cx="25"
+     inkscape:cy="50"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0"
+     inkscape:current-layer="svg2" /><defs
+     id="defs4"><style
+       type="text/css"
+       id="style6"><![CDATA[
+      path,circle {
+        stroke:#000000;
+        stroke-width: 3;
+        stroke-linecap: round;
+        stroke-linejoin: round;
+        fill: none
+      }]]></style></defs><path
+     d="m 37.499997,9.4999972 0,12.9999998 -29.9999997,0 0,13"
+     id="path8"
+     inkscape:connector-curvature="0"
+     style="fill:none;stroke:#000000;stroke-width:3;stroke-linecap:round;stroke-linejoin:round" /></svg>

package/src/components/assembler/sbol_visual_glyphs.js

@@ -0,0 +1,36 @@
+import assemblyScar from './sbol_visual_glyphs/assembly-scar.svg'
+import cds from './sbol_visual_glyphs/cds.svg'
+import chromosomalLocus from './sbol_visual_glyphs/chromosomal-locus.svg'
+import engineeredRegion from './sbol_visual_glyphs/engineered-region.svg'
+import fivePrimeStickyRestrictionSite from './sbol_visual_glyphs/five-prime-sticky-restriction-site.svg'
+import originOfReplication from './sbol_visual_glyphs/origin-of-replication.svg'
+import primerBindingSite from './sbol_visual_glyphs/primer-binding-site.svg'
+import promoter from './sbol_visual_glyphs/promoter.svg'
+import ribosomeEntrySite from './sbol_visual_glyphs/ribosome-entry-site.svg'
+import specificRecombinationSite from './sbol_visual_glyphs/specific-recombination-site.svg'
+import terminator from './sbol_visual_glyphs/terminator.svg'
+import threePrimeStickyRestrictionSite from './sbol_visual_glyphs/three-prime-sticky-restriction-site.svg'
+import cdsStop from './sbol_visual_glyphs/cds-stop.svg'
+
+// Map glyph names (without extension) to their SVG imports
+export const sbolVisualGlyphs = {
+  'assembly-scar': assemblyScar,
+  'cds': cds,
+  'cds-stop': cdsStop,
+  'chromosomal-locus': chromosomalLocus,
+  'engineered-region': engineeredRegion,
+  'five-prime-sticky-restriction-site': fivePrimeStickyRestrictionSite,
+  'origin-of-replication': originOfReplication,
+  'primer-binding-site': primerBindingSite,
+  'promoter': promoter,
+  'ribosome-entry-site': ribosomeEntrySite,
+  'specific-recombination-site': specificRecombinationSite,
+  'terminator': terminator,
+  'three-prime-sticky-restriction-site': threePrimeStickyRestrictionSite,
+}
+
+// Helper function to get SVG by glyph name (without extension)
+export const getSvgByGlyph = (glyphName) => {
+  return sbolVisualGlyphs[glyphName] || sbolVisualGlyphs['engineered-region'] // fallback to engineered-region if not found
+}
+

package/src/components/assembler/useAssembler.js

@@ -0,0 +1,71 @@
+import { useCallback } from 'react'
+import { classNameToEndPointMap } from '@opencloning/utils/sourceFunctions'
+import useBackendRoute from '../../hooks/useBackendRoute'
+import useHttpClient from '../../hooks/useHttpClient'
+import { arrayCombinations } from '../eLabFTW/utils'
+
+
+export const useAssembler = () => {
+  const httpClient = useHttpClient();
+  const backendRoute = useBackendRoute();
+
+  const requestSources = useCallback(async (assemblerOutput) => {
+    const processedOutput = []
+    for (let pos = 0; pos < assemblerOutput.length; pos++) {
+        processedOutput.push([])
+        for (let source of assemblerOutput[pos]) {
+            const url = backendRoute(classNameToEndPointMap[source.type])
+            const {data} = await httpClient.post(url, source)
+            if (data.sources.length !== 1) {
+                console.error('Expected 1 source, got ' + data.sources.length)
+            }
+            const thisData = {
+                source: {...data.sources[0], id: pos + 1},
+                sequence: {...data.sequences[0], id: pos + 1},
+            }
+            processedOutput[pos].push(thisData)
+        }
+    }
+    return processedOutput
+  }, [])
+
+
+  const requestAssemblies = useCallback(async (requestedSources) => {
+
+    const assemblies = arrayCombinations(requestedSources);
+    const output = []
+    for (let assembly of assemblies) {
+      const url = backendRoute('restriction_and_ligation')
+      const config = {
+        params: {
+          circular_only: true,
+        }
+      }
+      const requestData = {
+        source: {
+            type: 'RestrictionAndLigationSource',
+            restriction_enzymes: ['BsaI'],
+            id: assembly.length + 1,
+        },
+        sequences: assembly.map((p) => p.sequence),
+      }
+      const {data} = await httpClient.post(url, requestData, config)
+      const thisSource = data.sources[0]
+      const thisSequence = data.sequences[0]
+      thisSource.id = assembly.length + 1
+      thisSequence.id = assembly.length + 1
+
+
+      const cloningStrategy = {
+        sources: [thisSource, ...assembly.map((p) => p.source)],
+        sequences: [thisSequence, ...assembly.map((p) => p.sequence)],
+        primers: [],
+      }
+      output.push(cloningStrategy)
+    }
+    return output;
+  }, [])
+
+  return { requestSources, requestAssemblies }
+}
+

package/src/components/dummy/DummyInterface.js

@@ -0,0 +1,41 @@
+import SaveIcon from '@mui/icons-material/Save';
+import LinkIcon from '@mui/icons-material/Link';
+import GetSequenceFileAndDatabaseIdComponent from './GetSequenceFileAndDatabaseIdComponent';
+
+export default {
+  // Name of the database interface
+  name: 'Dummy',
+  // Returns a link to the sequence in the database
+  getSequenceLink: (databaseId) => `your/url/${databaseId}`,
+  // Returns a link to the primer in the database
+  getPrimerLink: (databaseId) => `your/url/${databaseId}`,
+  // Component for selecting and loading sequence files from the database
+  GetSequenceFileAndDatabaseIdComponent,
+  // Component for selecting and loading primers from the database
+  GetPrimerComponent: null,
+  // Component for submitting resources to the database
+  SubmitToDatabaseComponent: null,
+  // Component for handling primers not yet in database
+  PrimersNotInDatabaseComponent: null,
+  // Function to submit a primer to the database
+  submitPrimerToDatabase: null,
+  // Function to submit a sequence and its history to the database
+  submitSequenceToDatabase: null,
+  // Function to validate submission data
+  isSubmissionDataValid: null,
+  // Icon displayed on the node corner to submit
+  SubmitIcon: SaveIcon,
+  // Icon displayed on the node corner for entities in the database
+  DatabaseIcon: LinkIcon,
+  // OPTIONAL =======================================================================
+  // Component for loading history from the database (can be hook-like does not have to render anything)
+  LoadHistoryComponent: null,
+  // Function to load sequences from url parameters
+  loadSequenceFromUrlParams: null,
+  // Function to get the primer ({name, database_id, sequence}) from the database
+  getPrimer: null,
+  // Function to get the name of a sequence from the database
+  getSequenceName: null,
+  // Function to get the sequencing files from the database, see docs for what the return value should be
+  getSequencingFiles: null,
+};

package/src/components/dummy/GetSequenceFileAndDatabaseIdComponent.jsx

@@ -0,0 +1,59 @@
+import { MenuItem, TextField } from '@mui/material';
+import React from 'react';
+
+function GetSequenceFileAndDatabaseIdComponent({ setFile, setDatabaseId }) {
+  // This component is rendered inside of SourceDatabase.jsx, and must contain
+  // a form that lets the user select an entry from the database. Once setFile
+  // and setDatabaseId are set within this form, the submit button will be shown in
+  // SourceDatabase.jsx. The file can be a sequence file or a json file with the history.
+  const [selectedEntry, setSelectedEntry] = React.useState(null);
+  // Somehow get the entries from the database, could also be gb files, etc.
+  const entries = [
+    {
+      id: 1,
+      name: 'seq1.fasta', // File extension is important, will determine how it's parsed
+      fileContent: '>seq1\nATCG\n',
+    },
+    {
+      id: 2,
+      name: 'seq2.fasta',
+      fileContent: '>seq2\nATCG\n',
+    },
+    {
+      id: 3,
+      name: 'seq3.fasta',
+      fileContent: '>seq3\nATCG\n',
+    },
+  ];
+
+  const handleFileSelect = (e) => {
+    const selectedId = e.target.value;
+    const entry = entries.find((e) => e.id === selectedId);
+    setSelectedEntry(entry);
+    // When you set databaseId and file, the submit button will be shown (see SourceDatabase.jsx)
+    setFile(new File([entry.fileContent], entry.name, { type: 'text/plain' }));
+    setDatabaseId(entry.id);
+  };
+
+  return (
+    <div>
+      {/* You probably need more than one form field */}
+      <TextField
+        select
+        label="Select Sequence"
+        value={selectedEntry?.id || ''}
+        onChange={(e) => handleFileSelect(e)}
+        fullWidth
+        variant="outlined"
+      >
+        {entries.map((entry) => (
+          <MenuItem key={entry.id} value={entry.id}>
+            {entry.name}
+          </MenuItem>
+        ))}
+      </TextField>
+    </div>
+  );
+}
+
+export default GetSequenceFileAndDatabaseIdComponent;