@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/dist/ucsc-trackhub/ucscTrackHub.js.map

@@ -0,0 +1 @@
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package/esm/AddConnectionWidget/components/AddConnectionWidget.d.ts

@@ -0,0 +1,9 @@
+declare function _default({ model }: {
+    model: any;
+}): JSX.Element;
+declare namespace _default {
+    namespace propTypes {
+        const model: import("prop-types").Validator<any>;
+    }
+}
+export default _default;

package/esm/AddConnectionWidget/components/AddConnectionWidget.js

@@ -0,0 +1,86 @@
+import React, { useState } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { Button, Step, StepContent, StepLabel, Stepper, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer, PropTypes as MobxPropTypes } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+// locals
+import ConfigureConnection from './ConfigureConnection';
+import ConnectionTypeSelect from './ConnectionTypeSelect';
+const useStyles = makeStyles()(theme => ({
+    root: {
+        marginTop: theme.spacing(1),
+    },
+    stepper: {
+        backgroundColor: theme.palette.background.default,
+    },
+    button: {
+        marginTop: theme.spacing(1),
+        marginRight: theme.spacing(1),
+    },
+    actionsContainer: {
+        marginBottom: theme.spacing(2),
+    },
+}));
+const steps = ['Select a Connection Type', 'Configure Connection'];
+function AddConnectionWidget({ model }) {
+    const [connectionType, setConnectionType] = useState({});
+    const [configModel, setConfigModel] = useState({});
+    const [configModelReady, setConfigModelReady] = useState(true);
+    const [activeStep, setActiveStep] = useState(0);
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { pluginManager } = getEnv(session);
+    function handleSetConnectionType(newConnectionType) {
+        setConnectionType(newConnectionType);
+        setConfigModel(newConnectionType.configSchema.create({
+            connectionId: `${newConnectionType.name}-${Date.now()}`,
+        }, getEnv(model)));
+    }
+    function stepContent() {
+        switch (activeStep) {
+            case 0:
+                return (React.createElement(ConnectionTypeSelect, { connectionTypeChoices: pluginManager.getElementTypesInGroup('connection'), connectionType: connectionType, setConnectionType: handleSetConnectionType }));
+            case 1:
+                return (React.createElement(ConfigureConnection, { connectionType: connectionType, model: configModel, setModelReady: setConfigModelReady }));
+            default:
+                return React.createElement(Typography, null, "Unknown step");
+        }
+    }
+    function handleNext() {
+        if (activeStep === steps.length - 1) {
+            handleFinish();
+        }
+        else {
+            setActiveStep(activeStep + 1);
+        }
+    }
+    function handleBack() {
+        setActiveStep(activeStep - 1);
+    }
+    function handleFinish() {
+        const connectionConf = session.addConnectionConf(configModel);
+        session.makeConnection(connectionConf);
+        session.hideWidget(model);
+    }
+    function checkNextEnabled() {
+        if ((activeStep === 0 && connectionType.name) ||
+            (activeStep === 1 && configModel && configModelReady)) {
+            return true;
+        }
+        return false;
+    }
+    return (React.createElement("div", { className: classes.root },
+        React.createElement(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map(label => (React.createElement(Step, { key: label },
+            React.createElement(StepLabel, null, label),
+            React.createElement(StepContent, null,
+                stepContent(),
+                React.createElement("div", { className: classes.actionsContainer },
+                    React.createElement(Button, { disabled: activeStep === 0, onClick: handleBack, className: classes.button }, "Back"),
+                    React.createElement(Button, { disabled: !checkNextEnabled(), variant: "contained", color: "primary", onClick: handleNext, className: classes.button, "data-testid": "addConnectionNext" }, activeStep === steps.length - 1 ? 'Connect' : 'Next')))))))));
+}
+AddConnectionWidget.propTypes = {
+    model: MobxPropTypes.observableObject.isRequired,
+};
+export default observer(AddConnectionWidget);
+//# sourceMappingURL=AddConnectionWidget.js.map

package/esm/AddConnectionWidget/components/AddConnectionWidget.js.map

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package/esm/AddConnectionWidget/components/ConfigureConnection.d.ts

@@ -0,0 +1,2 @@
+export default ConfigureConnection;
+declare function ConfigureConnection(props: any): JSX.Element;

package/esm/AddConnectionWidget/components/ConfigureConnection.js

@@ -0,0 +1,11 @@
+import React, { Suspense } from 'react';
+import { ConfigurationEditor } from '@jbrowse/plugin-config';
+import { observer } from 'mobx-react';
+const ConfigureConnection = observer(props => {
+    const { connectionType, model, setModelReady } = props;
+    const ConfigEditorComponent = connectionType.configEditorComponent || ConfigurationEditor;
+    return (React.createElement(Suspense, { fallback: React.createElement("div", null, "Loading...") },
+        React.createElement(ConfigEditorComponent, { model: { target: model }, setModelReady: setModelReady })));
+});
+export default ConfigureConnection;
+//# sourceMappingURL=ConfigureConnection.js.map

package/esm/AddConnectionWidget/components/ConfigureConnection.js.map

@@ -0,0 +1 @@
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package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
+declare function ConnectionTypeSelect(props: {
+    connectionTypeChoices: ConnectionType[];
+    connectionType: ConnectionType;
+    setConnectionType: Function;
+}): JSX.Element | null;
+export default ConnectionTypeSelect;

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -0,0 +1,24 @@
+import React, { useEffect } from 'react';
+import { IconButton, MenuItem, TextField } from '@mui/material';
+import OpenInNewIcon from '@mui/icons-material/OpenInNew';
+function ConnectionTypeSelect(props) {
+    const { connectionTypeChoices, connectionType, setConnectionType } = props;
+    useEffect(() => {
+        if (!connectionType.name) {
+            setConnectionType(connectionTypeChoices[0]);
+        }
+    });
+    function handleChange(event) {
+        setConnectionType(connectionTypeChoices.find((connectionTypeChoice) => connectionTypeChoice.name === event.target.value));
+    }
+    if (!connectionType.name) {
+        return null;
+    }
+    return (React.createElement("form", { autoComplete: "off" },
+        React.createElement(TextField, { value: connectionType.name, label: "connectionType", helperText: connectionType.description ? (React.createElement(React.Fragment, null,
+                connectionType.description,
+                connectionType.url ? (React.createElement(IconButton, { href: connectionType.url, rel: "noopener noreferrer", target: "_blank", color: "secondary" },
+                    React.createElement(OpenInNewIcon, null))) : null)) : null, select: true, fullWidth: true, onChange: handleChange, variant: "outlined" }, connectionTypeChoices.map((connectionTypeChoice) => (React.createElement(MenuItem, { key: connectionTypeChoice.name, value: connectionTypeChoice.name }, connectionTypeChoice.displayName || connectionTypeChoice.name))))));
+}
+export default ConnectionTypeSelect;
+//# sourceMappingURL=ConnectionTypeSelect.js.map

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js.map

@@ -0,0 +1 @@
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package/esm/AddConnectionWidget/index.d.ts

@@ -0,0 +1,2 @@
+export { default as stateModel } from "./model";
+export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/AddConnectionWidget/index.js

@@ -0,0 +1,4 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export { default as stateModel } from './model';
+export const configSchema = ConfigurationSchema('AddConnectionWidget', {});
+//# sourceMappingURL=index.js.map

package/esm/AddConnectionWidget/index.js.map

@@ -0,0 +1 @@
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package/esm/AddConnectionWidget/model.d.ts

@@ -0,0 +1,5 @@
+declare const _default: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"AddConnectionWidget">;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default _default;

package/esm/AddConnectionWidget/model.js

@@ -0,0 +1,7 @@
+import { types } from 'mobx-state-tree';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+export default types.model('AddConnectionModel', {
+    id: ElementId,
+    type: types.literal('AddConnectionWidget'),
+});
+//# sourceMappingURL=model.js.map

package/esm/AddConnectionWidget/model.js.map

@@ -0,0 +1 @@
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package/esm/AddTrackWidget/components/AddTrackWidget.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWidget({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWidget;
+export default _default;

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -0,0 +1,139 @@
+import React, { useState } from 'react';
+import { Alert, Button, Step, StepContent, StepLabel, Stepper, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getSession, isElectron, supportedIndexingAdapters, } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+// locals
+import ConfirmTrack from './ConfirmTrack';
+import TrackSourceSelect from './TrackSourceSelect';
+const useStyles = makeStyles()(theme => ({
+    root: {
+        marginTop: theme.spacing(1),
+    },
+    stepper: {
+        backgroundColor: theme.palette.background.default,
+    },
+    button: {
+        marginTop: theme.spacing(1),
+        marginRight: theme.spacing(1),
+    },
+    actionsContainer: {
+        marginBottom: theme.spacing(2),
+    },
+    stepContent: {
+        margin: theme.spacing(1),
+    },
+    alertContainer: {
+        padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
+    },
+}));
+const steps = ['Enter track data', 'Confirm track type'];
+function AddTrackWidget({ model }) {
+    const [activeStep, setActiveStep] = useState(0);
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { pluginManager } = getEnv(session);
+    const { rootModel } = pluginManager;
+    const { jobsManager } = rootModel;
+    const { assembly, trackAdapter, trackData, trackName, trackType, textIndexTrack, textIndexingConf, } = model;
+    const [trackErrorMessage, setTrackErrorMessage] = useState();
+    function getStepContent(step) {
+        switch (step) {
+            case 0:
+                return React.createElement(TrackSourceSelect, { model: model });
+            case 1:
+                return React.createElement(ConfirmTrack, { model: model });
+            default:
+                return React.createElement(Typography, null, "Unknown step");
+        }
+    }
+    async function handleNext() {
+        if (activeStep !== steps.length - 1) {
+            setActiveStep(activeStep + 1);
+            return;
+        }
+        const trackId = `${trackName
+            .toLowerCase()
+            .replace(/ /g, '_')}-${Date.now()}${session.adminMode ? '' : '-sessionTrack'}`;
+        const assemblyInstance = session.assemblyManager.get(assembly);
+        if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
+            // @ts-ignore
+            session.addTrackConf({
+                trackId,
+                type: trackType,
+                name: trackName,
+                assemblyNames: [assembly],
+                adapter: {
+                    ...trackAdapter,
+                    sequenceAdapter: getConf(assemblyInstance, ['sequence', 'adapter']),
+                },
+            });
+            const textSearchingDefault = {
+                attributes: ['Name', 'ID'],
+                exclude: ['CDS', 'exon'],
+            };
+            if (model.view) {
+                model.view.showTrack(trackId);
+                if (isElectron) {
+                    if (textIndexTrack && supportedIndexingAdapters(trackAdapter.type)) {
+                        const attr = textIndexingConf || textSearchingDefault;
+                        const indexName = trackName + '-index';
+                        const indexingParams = {
+                            ...attr,
+                            assemblies: [assembly],
+                            tracks: [trackId],
+                            indexType: 'perTrack',
+                            name: indexName,
+                            timestamp: new Date().toISOString(),
+                        };
+                        const newEntry = {
+                            indexingParams: indexingParams,
+                            name: indexName,
+                            cancelCallback: () => {
+                                jobsManager.abortJob();
+                            },
+                        };
+                        jobsManager.queueJob(newEntry);
+                    }
+                }
+            }
+            else {
+                session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
+            }
+            model.clearData();
+            // @ts-ignore
+            session.hideWidget(model);
+        }
+        else {
+            setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
+        }
+    }
+    function handleBack() {
+        setTrackErrorMessage(undefined);
+        setActiveStep(activeStep - 1);
+    }
+    function isNextDisabled() {
+        switch (activeStep) {
+            case 0:
+                return !trackData;
+            case 1:
+                return !(trackName && trackType && (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) && assembly);
+            default:
+                return true;
+        }
+    }
+    return (React.createElement("div", { className: classes.root },
+        React.createElement(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map((label, idx) => (React.createElement(Step, { key: label },
+            React.createElement(StepLabel, null, label),
+            React.createElement(StepContent, null,
+                getStepContent(idx),
+                React.createElement("div", { className: classes.actionsContainer },
+                    React.createElement(Button, { disabled: activeStep === 0, onClick: handleBack, className: classes.button }, "Back"),
+                    React.createElement(Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: handleNext, className: classes.button, "data-testid": "addTrackNextButton" }, activeStep === steps.length - 1 ? 'Add' : 'Next')),
+                trackErrorMessage ? (React.createElement("div", { className: classes.alertContainer },
+                    React.createElement(Alert, { severity: "error" }, trackErrorMessage))) : null)))))));
+}
+export default observer(AddTrackWidget);
+//# sourceMappingURL=AddTrackWidget.js.map

package/esm/AddTrackWidget/components/AddTrackWidget.js.map

@@ -0,0 +1 @@
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package/esm/AddTrackWidget/components/ConfirmTrack.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function ConfirmTrack({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof ConfirmTrack;
+export default _default;