Multi Issue PR (See comments)

src/activities.js

@@ -4,7 +4,7 @@ import GitHubView from "./components/activities/explorer/GitHubView";
 import LoginStatus from "./components/activities/explorer/LoginStatus";
 import { FileIcon, RemoteControlIcon, BugReport, ProfileGreen, ProfileOrange, ProfileRed, ProfileWhite } from "./icons"
 import { RiGithubFill } from "react-icons/ri";
-import { GiThorHammer} from "react-icons/gi";
+import { TiPipette } from "react-icons/ti";
 import { ObjectTypes } from "./objectTypes";
 import { FaGraduationCap } from "react-icons/fa";
 import { BsGraphUpArrow } from "react-icons/bs";
@@ -22,7 +22,7 @@ export const Activities = {
     },
     ResourceSelection: {
         id: "synbio.activity.resource-selection",
-        title: "Resource Selection",
+        title: "Resources",
         component: ExplorerActivityView,
         icon: HiOutlinePuzzlePiece,
         objectTypesToList: [
@@ -57,13 +57,12 @@ export const Activities = {
         id: "synbio.activity.build",
         title: "Build",
         component: ExplorerActivityView,
-        icon: GiThorHammer,
+        icon: TiPipette,
         objectTypesToList: [
             ObjectTypes.Plasmids.id,
+            ObjectTypes.Strains.id,
             ObjectTypes.Assembly.id, 
             ObjectTypes.Build.id,
-            ObjectTypes.SampleDesigns.id,
-            ObjectTypes.Strains.id
         ]
     },
     Test: {
@@ -72,6 +71,7 @@ export const Activities = {
         component: ExplorerActivityView,
         icon: BiSolidFlask,
         objectTypesToList: [
+            ObjectTypes.SampleDesigns.id,
             ObjectTypes.Experiments.id,
             ObjectTypes.Metadata.id,
             ObjectTypes.Results.id //note: not all of these have templates

src/commands.js

@@ -1,6 +1,7 @@
 import store from "./redux/store"
 import { isPanelOpen, panelsActions, serializePanel } from "./redux/hooks/panelsHooks"
 import { workDirActions, writeToFileHandle } from "./redux/hooks/workingDirectoryHooks"
+import { useOpenPanel } from "./redux/hooks/panelsHooks"
 
 
 export default {
@@ -67,6 +68,60 @@ export default {
             // save
             await writeToFileHandle(file, serializePanel(file.id))
         }
+    },
+
+    FileDownload: {
+        id: createId("file-download"),
+        title: "Download File",
+        shortTitle: "Download",
+        description: "Download a file",
+        arguments: [
+            {
+                name: "fileNameOrId",
+                prompt: "Enter the file name or ID"
+            }
+        ],
+        execute: async fileNameOrId => {
+            const file = findFileByNameOrId(fileNameOrId);
+            if (!file) return "File doesn't exist.";
+
+            const state = store.getState().workingDirectory;
+            let fileData = state.entities[file.id]?.data;
+
+            if (!fileData) {
+                const dirHandle = state.directoryHandle;
+                if (dirHandle && typeof dirHandle.getFileHandle === 'function') {
+                    try {
+                        const parts = file.id.split('/');
+                        let cur = dirHandle;
+                        for (let i = 0; i < parts.length - 1; i++) {
+                            cur = await cur.getDirectoryHandle(parts[i]);
+                        }
+                        const fh = await cur.getFileHandle(parts[parts.length - 1]);
+                        fileData = await fh.getFile();
+                    } catch (err) {
+                        console.warn('Failed to read file from directoryHandle', err);
+                    }
+                } else {
+                    console.warn('No usable directoryHandle in store. directoryHandle:', dirHandle);
+                }
+            }
+
+            if (!fileData) {
+                console.log("File data not found.");
+                return "File data not found.";
+            }
+
+            const blob = typeof fileData === "string" ? new Blob([fileData], { type: "text/plain" }) : fileData;
+            const url = URL.createObjectURL(blob);
+            const a = document.createElement("a");
+            a.href = url;
+            a.download = file.name;
+            document.body.appendChild(a);
+            a.click();
+            document.body.removeChild(a);
+            URL.revokeObjectURL(url);
+        }
     }
 }
 

src/components/activities/explorer/ExplorerList.jsx

@@ -118,11 +118,15 @@ export default function ExplorerList({workDir, objectTypesToList}) {
                                             </CreateNewButton>
                                         }
                                         {createListItems(filesOfType, objectType.icon)}
-                                    {objectType.isRepository && 
+                                    {objectType.isRepository ? objectType.id == "synbio.object-type.flapjack" ? 
                                         <Registries 
-                                        defaultRegistry={objectType.defaultRegistry} 
+                                        typeOfRegistry={objectType.listTitle}
+                                        title={objectType.title}/>:
+                                        <Registries 
+                                        defaultRegistry={objectType?.defaultRegistry} 
                                         typeOfRegistry={objectType.listTitle}
                                         title={objectType.title}/>
+                                        : <></>
                                     }
                                     </Accordion.Panel>
                                 </Accordion.Item>

src/components/activities/explorer/ExplorerListItem.jsx

@@ -27,6 +27,7 @@ export default function ExplorerListItem({ fileId, icon }) {
 
     // command list
     const contextMenuCommands = [
+        commands.FileDownload,
         commands.FileDelete
     ]
 

src/components/activities/explorer/ListRegistries.jsx

@@ -29,10 +29,8 @@ export default function ListRegistries({registry, defaultRegistry, onConfirmDele
     // right click handler, opens up delete option
     const handleRightClick = (event) => {
         event.preventDefault()
-        if (registry !== defaultRegistry){
-            setRegistryToDelete(registry)
-            setContextMenuOpen(true)
-        }
+        setRegistryToDelete(registry)
+        setContextMenuOpen(true)
     }
 
     // command list

src/components/activities/explorer/Registries.jsx

@@ -12,12 +12,12 @@ import { showNotification } from '@mantine/notifications';
 /**
  * Component to handle the creation, deletion, and containment of SynBioHub registries.
  */
-export default function Registries({defaultRegistry, typeOfRegistry, title}){
+export default function Registries({typeOfRegistry, title, defaultRegistry = null}){
     const dispatch = useDispatch()
 
     // Get default registry and additional ones from localStorage 
     const storedRegistries = JSON.parse(localStorage.getItem(typeOfRegistry)) || [];
-    const [registries, setRegistries] = useState([defaultRegistry, ...storedRegistries])
+    const [registries, setRegistries] = useState(defaultRegistry ? [defaultRegistry, ...storedRegistries] : [...storedRegistries])
 
 
     const onCreate = (inputValue) => {

src/modules/modular_login/FJInstanceSelector.jsx

@@ -39,7 +39,7 @@ const FJInstanceSelector = ({onClose, setRepoSelection }) => {
         if (!showNotificationFlag) {
             showNotification({
                 title: 'Logout Successful',
-                message: 'You have successfully logged out of the registry',
+                message: 'You have successfully logged out of the repository',
                 color: 'green',
             });
         }
@@ -125,13 +125,13 @@ const FJInstanceSelector = ({onClose, setRepoSelection }) => {
             ) : (
                 <>
                     <Select
-                        label={`Select a Flapjack registry`}
+                        label={`Select a Flapjack repository`}
                         placeholder="Pick one"
                         data={instanceData}
                         onChange={(value) => {setNullSelected(false); setSelected(value)}}
                         value={selected}
                     />
-                    {nullSelected && <div style={{ color: 'red', marginTop: '1px', fontSize: '12px' }}>No selected registry. Please select an registry</div>}
+                    {nullSelected && <div style={{ color: 'red', marginTop: '1px', fontSize: '12px' }}>No selected repository. Please select an repository</div>}
                     <div style={{ marginTop: '20px', display: 'flex' }}>
                         <Button mr="md" onClick={() => {setAddingInstance(null)}}>Add</Button>
                         {selected && (

src/modules/modular_login/FJModal.jsx

@@ -25,7 +25,7 @@ function FJModal({ opened, onClose, repoName }) {
     }, [opened]);
 
     return (
-        <Modal opened={opened} onClose={onClose} title={`Choose Registry`} size="lg">
+        <Modal opened={opened} onClose={onClose} title={`Choose Repository`} size="lg">
             {repoSelection === "" ? (
                 <>
                     <Grid justify="center">
@@ -38,7 +38,7 @@ function FJModal({ opened, onClose, repoName }) {
                             />
                             <div>
                                 <Text fz="xs" mt={10} fw={700} c="dimmed">
-                                    Registry: {selectedFJ ? findInstance(selectedFJ, "FJ").instance : "Not Logged In"}
+                                    Repository: {selectedFJ ? findInstance(selectedFJ, "FJ").instance : "Not Logged In"}
                                 </Text>
 
                                 <Text fz="lg" fw={500}>
@@ -49,13 +49,13 @@ function FJModal({ opened, onClose, repoName }) {
                                 </Text>
                                 {selectedFJ ? <>
                                     <Button mt="md" mr="sm" onClick={() => {handleRemoveInstance("Flapjack"); setRepoSelection("Flapjack")}}>
-                                        Change Flapjack Registry
+                                        Change Flapjack Repository
                                     </Button>
                                     <Button mt="md" ml="sm" onClick={() => {onClose(); setRepoSelection("")}}>
-                                        Confirm Registry Selection
+                                        Confirm Repository Selection
                                     </Button>
                                 </> : <Button mt="md" onClick={() => {setRepoSelection("Flapjack")}}>
-                                    Select Flapjack Registry
+                                    Select Flapjack Repository
                                 </Button>}
                             </div>
                         </Grid.Col>

src/modules/modular_login/SBHInstanceSelector.jsx

@@ -41,7 +41,7 @@ const SBHInstanceSelector = ({onClose, setRepoSelection }) => {
         if (!showNotificationFlag) {
             showNotification({
                 title: 'Logout Successful',
-                message: 'You have successfully logged out of the registry',
+                message: 'You have successfully logged out of the repository',
                 color: 'green',
             });
         }
@@ -137,13 +137,13 @@ const SBHInstanceSelector = ({onClose, setRepoSelection }) => {
                     <SBHInstanceLogin onClose={onClose} goBack={setShowLogin} setRepoSelection={setRepoSelection}/>
             : ( <>
                     <Select
-                        label={`Select a SynbioHub registry`}
+                        label={`Select a SynbioHub repository`}
                         placeholder="Pick one"
                         data={instanceData}
                         onChange={(value) => {setNullSelected(false); setSelected(value)}}
                         value={selected}
                     />
-                    {nullSelected && <div style={{ color: 'red', marginTop: '1px', fontSize: '12px' }}>No selected registry. Please select an registry</div>}
+                    {nullSelected && <div style={{ color: 'red', marginTop: '1px', fontSize: '12px' }}>No selected repository. Please select an repository</div>}
                     <div style={{ marginTop: '20px', display: 'flex' }}>
                         <Button mr="md" onClick={() => {setAddingInstance(null)}}>Add</Button>
                         {selected && (

src/modules/modular_login/SBHModal.jsx

@@ -26,7 +26,7 @@ function SBHModal({ opened, onClose, repoName }) {
     }, [opened]);
 
     return (
-        <Modal opened={opened} onClose={onClose} title={`Choose Registry`} size="lg">
+        <Modal opened={opened} onClose={onClose} title={`Choose Repository`} size="lg">
             {repoSelection === "" ? (
                 <>
                     <Grid justify="center">
@@ -39,7 +39,7 @@ function SBHModal({ opened, onClose, repoName }) {
                             />
                             <div>
                                 <Text fz="xs" mt={10} fw={700} c="dimmed">
-                                    Registry: {selectedSBH ? findInstance(selectedSBH, "SBH").instance : "Not Logged In"}
+                                    Repository: {selectedSBH ? findInstance(selectedSBH, "SBH").instance : "Not Logged In"}
                                 </Text>
 
                                 <Text fz="lg" fw={500}>
@@ -50,13 +50,13 @@ function SBHModal({ opened, onClose, repoName }) {
                                 </Text>
                                 {selectedSBH ? <>
                                     <Button mt="md" onClick={() => {handleRemoveInstance("SynbioHub"); setRepoSelection("SynbioHub")}}>
-                                        Change SynbioHub Registry
+                                        Change SynbioHub Repository
                                     </Button>
                                     <Button mt="md" ml="sm" onClick={() => {onClose(); setRepoSelection("")}}>
-                                        Confirm Registry Selection
+                                        Confirm Repository Selection
                                     </Button>
                                 </> : <Button mt="md" onClick={() => {setRepoSelection("SynbioHub")}}>
-                                    Select SynbioHub Registry
+                                    Select SynbioHub Repository
                                 </Button>}
                             </div>
                         </Grid.Col>

src/modules/modular_login/loginModal.jsx

@@ -35,7 +35,7 @@ function LoginModal({ opened, onClose, repoName }) {
     }, [opened]);
 
     return (
-        <Modal opened={opened} onClose={onClose} title={`Choose Registry`} size="lg">
+        <Modal opened={opened} onClose={onClose} title={`Choose Repository`} size="lg">
             {repoSelection === "" ? (
                 <>
                     <Grid>
@@ -48,7 +48,7 @@ function LoginModal({ opened, onClose, repoName }) {
                             />
                             <div>
                                 <Text fz="xs" mt={10} fw={700} c="dimmed">
-                                    Registry: {selectedSBH ? findInstance(selectedSBH, "SBH").instance : "Not Logged In"}
+                                    Repository: {selectedSBH ? findInstance(selectedSBH, "SBH").instance : "Not Logged In"}
                                 </Text>
 
                                 <Text fz="lg" fw={500}>
@@ -61,9 +61,9 @@ function LoginModal({ opened, onClose, repoName }) {
                                     </Text>
                                 </Group>
                                 {selectedSBH ? <Button mt="md" onClick={() => {handleRemoveInstance("SynbioHub"); setRepoSelection("SynbioHub")}}>
-                                    Change SynbioHub Registry
+                                    Change SynbioHub Repository
                                 </Button> : <Button mt="md" onClick={() => {setRepoSelection("SynbioHub")}}>
-                                    Select SynbioHub Registry
+                                    Select SynbioHub Repository
                                 </Button>}
                             </div>
                         </Grid.Col>
@@ -77,7 +77,7 @@ function LoginModal({ opened, onClose, repoName }) {
                             />
                             <div>
                                 <Text fz="xs" mt={10} fw={700} c="dimmed">
-                                    Registry: {selectedFJ ? findInstance(selectedFJ, "FJ").instance : "Not Logged In"}
+                                    Repository: {selectedFJ ? findInstance(selectedFJ, "FJ").instance : "Not Logged In"}
                                 </Text>
 
                                 <Text fz="lg" fw={500}>
@@ -90,9 +90,9 @@ function LoginModal({ opened, onClose, repoName }) {
                                     </Text>
                                 </Group>
                                 {selectedFJ ? <Button mt="md" onClick={() => {handleRemoveInstance("Flapjack"); setRepoSelection("Flapjack")}}>
-                                    Change Flapjack Registry
+                                    Change Flapjack Repository
                                 </Button> : <Button mt="md" onClick={() => {setRepoSelection("Flapjack")}}>
-                                    Select Flapjack Registry
+                                    Select Flapjack Repository
                                 </Button>}
                             </div>
                         </Grid.Col>