@jbrowse/plugin-legacy-jbrowse 4.3.0 → 5.0.0-beta.10

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -1,6 +1,66 @@
+import { matchFormat, trackTypeForAdapter } from '@jbrowse/add-track-core';
 import { objectHash } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
-import { UNKNOWN, UNSUPPORTED, generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
+import { generateUnknownTrackConf, generateUnsupportedTrackConf, } from '@jbrowse/core/util/tracks';
+/**
+ * The JBrowse 2 adapter each JBrowse 1 storeClass becomes, keyed by the part
+ * after `JBrowse/Store/`. This is the only JBrowse-1-specific knowledge here:
+ * which location field an adapter stores its file under, and what it names the
+ * index or sidecar beside it, comes from `@jbrowse/add-track-core`'s format
+ * table — the one the add-track form and the CLI already read. A hand-written
+ * branch per store is what let one of three sequence stores drift into calling
+ * its track a `SequenceTrack`, a type JBrowse does not register.
+ */
+const STORE_ADAPTERS = {
+    'SeqFeature/BAM': 'BamAdapter',
+    'SeqFeature/CRAM': 'CramAdapter',
+    'SeqFeature/NCList': 'NCListAdapter',
+    'SeqFeature/BigWig': 'BigWigAdapter',
+    BigWig: 'BigWigAdapter',
+    'SeqFeature/BigBed': 'BigBedAdapter',
+    'SeqFeature/VCFTabix': 'VcfTabixAdapter',
+    'SeqFeature/GFF3': 'Gff3Adapter',
+    'SeqFeature/GFF3Tabix': 'Gff3TabixAdapter',
+    'SeqFeature/GTF': 'GtfAdapter',
+    'SeqFeature/BED': 'BedAdapter',
+    'SeqFeature/BEDTabix': 'BedTabixAdapter',
+    'SeqFeature/TwoBit': 'TwoBitAdapter',
+    'SeqFeature/IndexedFasta': 'IndexedFastaAdapter',
+    'SeqFeature/BgzipIndexedFasta': 'BgzipFastaAdapter',
+    // nothing guesses a plain `.fa` as unindexed, so this is the one store whose
+    // spec the format table cannot supply
+    'SeqFeature/UnindexedFasta': {
+        kind: 'single',
+        adapterType: 'UnindexedFastaAdapter',
+        locField: 'fastaLocation',
+    },
+};
+// JBrowse 1 stores JBrowse 2 has no adapter for. The value names the format in
+// the placeholder track the reader gets instead.
+const NO_ADAPTER = {
+    'SeqFeature/VCFTribble': 'VCFTribble',
+    'SeqFeature/StaticChunked': 'StaticChunked',
+    'Sequence/StaticChunked': 'StaticChunked',
+};
+/**
+ * `mark` is a slot on LinearWiggleDisplay, not on the track — a track-level
+ * one is a key JBrowse does not declare, and is ignored.
+ */
+function wiggleDisplays(jb1TrackConfig, jb2TrackConfig) {
+    const mark = jb1TrackConfig.type?.endsWith('Density')
+        ? 'heatmap'
+        : jb1TrackConfig.type?.endsWith('XYPlot')
+            ? 'bar'
+            : undefined;
+    return mark
+        ? [
+            {
+                type: 'LinearWiggleDisplay',
+                displayId: `${jb2TrackConfig.trackId}-LinearWiggleDisplay`,
+                mark,
+            },
+        ]
+        : undefined;
+}
 export function convertTrackConfig(jb1TrackConfig, dataRoot) {
     const jb2TrackConfig = {
         trackId: objectHash(jb1TrackConfig),
@@ -13,390 +73,86 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot) {
     }
     const category = jb1TrackConfig.category || jb1TrackConfig.metadata?.category;
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
+    const unsupported = (detail) => generateUnsupportedTrackConf(jb2TrackConfig.name, detail, jb2TrackConfig.category);
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
         if (!storeClass?.endsWith('FromConfig')) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
-            return generateUnsupportedTrackConf(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
+            return unsupported(trackIdentifier);
         }
         return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
     }
-    const resolveUrlTemplate = (urlTemplate) => {
-        return new URL(urlTemplate, `${dataRoot}/`).href
-            .replaceAll(/%7B/gi, '{')
-            .replaceAll(/%7D/gi, '}');
+    // a JBrowse 1 urlTemplate is relative to the data directory, and NCList's
+    // `{refseq}` has to survive the round trip through URL escaping
+    const resolve = (urlTemplate) => new URL(urlTemplate, `${dataRoot}/`).href
+        .replaceAll(/%7B/gi, '{')
+        .replaceAll(/%7D/gi, '}');
+    const urlTemplate = resolve(jb1TrackConfig.urlTemplate);
+    const fileName = urlTemplate.split(/[?#]/)[0];
+    const loc = (uri) => ({
+        uri,
+        locationType: 'UriLocation',
+    });
+    const key = storeClass?.replace(/^JBrowse\/Store\//, '');
+    const noAdapter = key === undefined ? undefined : NO_ADAPTER[key];
+    if (noAdapter) {
+        return unsupported(`${noAdapter} (${urlTemplate})`);
+    }
+    // JBrowse 1 named an override for a sidecar after its own suffix, so `.bai`
+    // is `baiUrlTemplate` and `.gzi` is `gziUrlTemplate`
+    const named = (suffix) => jb1TrackConfig[`${suffix.slice(1)}UrlTemplate`];
+    const beside = (suffix) => {
+        const override = named(suffix);
+        return loc(override ? resolve(override) : `${urlTemplate}${suffix}`);
     };
-    const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
-    if (storeClass) {
-        if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
-            const adapter = {
-                type: 'BamAdapter',
-                bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.baiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'AlignmentsTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
-            const adapter = {
-                type: 'CramAdapter',
-                cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                craiLocation: jb1TrackConfig.craiUrlTemplate
-                    ? {
-                        uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-                        locationType: 'UriLocation',
-                    }
-                    : {
-                        uri: `${urlTemplate}.crai`,
-                        locationType: 'UriLocation',
-                    },
-            };
-            return {
-                ...jb2TrackConfig,
-                type: 'AlignmentsTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'NCListAdapter',
-                    rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
-            storeClass === 'JBrowse/Store/BigWig') {
-            if (jb1TrackConfig.type?.endsWith('XYPlot')) {
-                jb2TrackConfig.defaultRendering = 'xyplot';
-            }
-            else if (jb1TrackConfig.type?.endsWith('Density')) {
-                jb2TrackConfig.defaultRendering = 'density';
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'QuantitativeTrack',
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
-            const adapter = {
-                type: 'VcfTabixAdapter',
-                vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'VariantTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
-            return generateUnsupportedTrackConf(jb2TrackConfig.name, `VCFTribble (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'Gff3Adapter',
-                    gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
-            const adapter = {
-                type: 'Gff3TabixAdapter',
-                gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
-            return generateUnsupportedTrackConf(jb2TrackConfig.name, `BED (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
-            const adapter = {
-                type: 'BedTabixAdapter',
-                bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'GtfAdapter',
-                    gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
-            storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
-            return generateUnsupportedTrackConf(jb2TrackConfig.name, `StaticChunked (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
-            return generateUnsupportedTrackConf(jb2TrackConfig.name, `UnindexedFasta (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
-            const adapter = {
-                type: 'IndexedFastaAdapter',
-                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                faiLocation: jb1TrackConfig.faiUrlTemplate
-                    ? {
-                        uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                        locationType: 'UriLocation',
-                    }
-                    : {
-                        uri: `${urlTemplate}.fai`,
-                        locationType: 'UriLocation',
-                    },
-            };
-            return {
-                ...jb2TrackConfig,
-                type: 'SequenceTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
-            const adapter = {
-                type: 'BgzipFastaAdapter',
-                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                faiLocation: jb1TrackConfig.faiUrlTemplate
-                    ? {
-                        uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                        locationType: 'UriLocation',
-                    }
-                    : {
-                        uri: `${urlTemplate}.fai`,
-                        locationType: 'UriLocation',
-                    },
-                gziLocation: jb1TrackConfig.gziUrlTemplate
-                    ? {
-                        uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-                        locationType: 'UriLocation',
-                    }
-                    : {
-                        uri: `${urlTemplate}.gzi`,
-                        locationType: 'UriLocation',
-                    },
-            };
-            return {
-                ...jb2TrackConfig,
-                type: 'ReferenceSequenceTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
-            return {
-                ...jb2TrackConfig,
-                type: 'ReferenceSequenceTrack',
-                adapter: {
-                    type: 'TwoBitAdapter',
-                    twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
+    const entry = key === undefined
+        ? undefined
+        : typeof STORE_ADAPTERS[key] === 'string'
+            ? matchFormat(fileName, STORE_ADAPTERS[key])?.spec
+            : STORE_ADAPTERS[key];
+    // an unrecognized storeClass, or none, falls back to what the filename says
+    const spec = entry ?? matchFormat(fileName)?.spec;
+    if (!spec || spec.kind === 'unsupported') {
+        return spec
+            ? unsupported(urlTemplate)
+            : generateUnknownTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
     }
-    jb2TrackConfig.adapter = guessAdapter({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
-    if (jb2TrackConfig.adapter.type === UNSUPPORTED) {
-        return generateUnsupportedTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+    const adapter = {
+        type: spec.adapterType,
+        [spec.locField]: loc(urlTemplate),
+    };
+    if (spec.kind === 'indexed') {
+        const csi = jb1TrackConfig.csiUrlTemplate;
+        adapter.index =
+            !named(spec.suffix) && csi
+                ? { location: loc(resolve(csi)), indexType: 'CSI' }
+                : { location: beside(spec.suffix) };
     }
-    if (jb2TrackConfig.adapter.type === UNKNOWN) {
-        return generateUnknownTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+    else if (spec.kind === 'sidecar') {
+        for (const { field, suffix } of spec.sidecars) {
+            adapter[field] = beside(suffix);
+        }
     }
-    jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type);
+    jb2TrackConfig.adapter = adapter;
+    jb2TrackConfig.type =
+        trackTypeForAdapter(spec.adapterType, fileName) ?? 'FeatureTrack';
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if (jb1TrackConfig.type?.endsWith('XYPlot')) {
-            jb2TrackConfig.defaultRendering = 'xyplot';
-        }
-        else if (jb1TrackConfig.type?.endsWith('Density')) {
-            jb2TrackConfig.defaultRendering = 'density';
-        }
+        jb2TrackConfig.displays = wiggleDisplays(jb1TrackConfig, jb2TrackConfig);
     }
     return jb2TrackConfig;
 }
 function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
-    const jb1Features = jb1TrackConfig.features || [];
-    const jb2Features = jb1Features.map((feature) => {
-        const jb2Feature = JSON.parse(JSON.stringify(feature));
-        jb2Feature.refName = feature.seq_id;
-        jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${feature.name || ''}`;
-        return jb2Feature;
-    });
-    jb2TrackConfig.adapter = {
-        type: 'FromConfigAdapter',
-        features: jb2Features,
-    };
-    jb2TrackConfig.type = 'FeatureTrack';
-    return jb2TrackConfig;
-}
-export async function createRefSeqsAdapter(refSeqs) {
-    if (typeof refSeqs === 'string') {
-        refSeqs = {
-            url: refSeqs,
-        };
-    }
-    if (refSeqs.url) {
-        if (/.fai$/.exec(refSeqs.url)) {
-            return {
-                type: 'IndexedFastaAdapter',
-                fastaLocation: {
-                    uri: refSeqs.url.slice(0, -4),
-                    locationType: 'UriLocation',
-                },
-                faiLocation: {
-                    uri: refSeqs.url,
-                    locationType: 'UriLocation',
-                },
-            };
-        }
-        if (/.2bit$/.exec(refSeqs.url)) {
-            return {
-                type: 'TwoBitAdapter',
-                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
-            };
-        }
-        if (/.fa$/.exec(refSeqs.url)) {
-            throw new Error('Unindexed FASTA adapter not available');
-        }
-        if (/.sizes/.exec(refSeqs.url)) {
-            throw new Error('chromosome SIZES adapter not available');
-        }
-        const refSeqsJson = await openLocation({
-            uri: refSeqs.url,
-            locationType: 'UriLocation',
-        }).readFile('utf8');
-        const refSeqsData = JSON.parse(refSeqsJson);
-        return refSeqAdapterFromConfig(refSeqsData);
-    }
-    if ('data' in refSeqs) {
-        return refSeqAdapterFromConfig(refSeqs.data || []);
-    }
-    throw new Error(`Could not determine adapter for JBrowse1 refSeqs: ${refSeqs.url || JSON.stringify(refSeqs)}`);
-}
-function refSeqAdapterFromConfig(refSeqsData) {
-    const features = refSeqsData.map((refSeq) => ({
-        refName: refSeq.name,
-        uniqueId: refSeq.name,
-        start: refSeq.start,
-        end: refSeq.end,
+    const jb1Features = jb1TrackConfig.features ?? [];
+    const features = jb1Features.map((f) => ({
+        refName: f.seq_id,
+        uniqueId: `${f.seq_id}:${f.start}-${f.end}:${f.name ?? ''}`,
+        start: f.start,
+        end: f.end,
     }));
     return {
-        type: 'FromConfigAdapter',
-        features,
+        ...jb2TrackConfig,
+        type: 'FeatureTrack',
+        adapter: { type: 'FromConfigAdapter', features },
     };
 }

package/esm/JBrowse1Connection/model.d.ts

@@ -1,67 +1,97 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
-    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
+/**
+ * #stateModel JBrowse1Connection
+ * Connection that imports tracks from a legacy JBrowse 1 data directory,
+ * composed on the base connection model.
+ */
+export default function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<{
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly name: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly assemblyNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        connectionId: {
+            type: "string";
+        } & {
             defaultValue: string;
-            description: string;
         };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
+    silent: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}, "configuration" | "type"> & {
+    configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        connectionId: {
+            type: "string";
+        } & {
+            defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-} & {
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         dataDirLocation: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-            description: string;
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
         };
-        assemblyNames: {
-            description: string;
-            type: string;
-            defaultValue: never[];
+        name: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
+        readonly name: {
+            type: "string";
+        } & {
             defaultValue: string;
-            description: string;
         };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
+        readonly assemblyNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"JBrowse1Connection">;
+        connectionId: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"JBrowse1Connection">;
 }, {
-    connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    loading: boolean;
+} & {
+    readonly connectionId: string;
+    readonly name: string;
+} & {
+    connect(): Promise<void>;
+    setLoading(loading: boolean): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: Record<string, unknown> | ({
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
-    addTrackConfs(trackConfs: (Record<string, unknown> | ({
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
-    clear(): void;
+    addTrackConf(trackConf: Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>) | undefined;
+    addTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
+    setTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
 } & {
     connect(): Promise<void>;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;