@synsci/sdk 1.3.5 → 1.3.6-test.19.1

package/dist/v2/gen/types.gen.d.ts

@@ -1688,6 +1688,12 @@ export type BadRequestError = {
     }>;
     success: false;
 };
+export type NotFoundError = {
+    name: "NotFoundError";
+    data: {
+        message: string;
+    };
+};
 export type OAuth = {
     type: "oauth";
     refresh: string;
@@ -1706,12 +1712,6 @@ export type WellKnownAuth = {
     token: string;
 };
 export type Auth = OAuth | ApiAuth | WellKnownAuth;
-export type NotFoundError = {
-    name: "NotFoundError";
-    data: {
-        message: string;
-    };
-};
 export type Model = {
     id: string;
     providerID: string;
@@ -1940,6 +1940,8 @@ export type FileContent = {
     };
     encoding?: "base64";
     mimeType?: string;
+    size?: number;
+    truncated?: boolean;
 };
 export type File = {
     path: string;
@@ -2512,6 +2514,8 @@ export type SettingsComputeGetResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2551,6 +2555,8 @@ export type SettingsComputeProviderDisconnectResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2599,6 +2605,8 @@ export type SettingsComputeProviderConnectResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2615,6 +2623,8 @@ export type SettingsComputeSshAddData = {
         host: string;
         user?: string;
         port?: number;
+        scheduler?: "none" | "slurm" | "pbs";
+        workdir?: string;
     };
     path?: never;
     query?: never;
@@ -2648,6 +2658,8 @@ export type SettingsComputeSshAddResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2658,6 +2670,38 @@ export type SettingsComputeSshAddResponses = {
     };
 };
 export type SettingsComputeSshAddResponse = SettingsComputeSshAddResponses[keyof SettingsComputeSshAddResponses];
+export type SettingsComputeSshTestData = {
+    body?: never;
+    path: {
+        id: string;
+    };
+    query?: never;
+    url: "/settings/compute/ssh/{id}/test";
+};
+export type SettingsComputeSshTestErrors = {
+    /**
+     * Not found
+     */
+    404: NotFoundError;
+};
+export type SettingsComputeSshTestError = SettingsComputeSshTestErrors[keyof SettingsComputeSshTestErrors];
+export type SettingsComputeSshTestResponses = {
+    /**
+     * Connection result
+     */
+    200: {
+        ok: boolean;
+        host: string;
+        latency_ms: number;
+        hostname?: string;
+        python: boolean;
+        gpu: boolean;
+        slurm: boolean;
+        pbs: boolean;
+        error?: string;
+    };
+};
+export type SettingsComputeSshTestResponse = SettingsComputeSshTestResponses[keyof SettingsComputeSshTestResponses];
 export type SettingsComputeSshRemoveData = {
     body?: never;
     path: {
@@ -2687,6 +2731,8 @@ export type SettingsComputeSshRemoveResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2735,6 +2781,8 @@ export type SettingsComputeEndpointAddResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2774,6 +2822,8 @@ export type SettingsComputeEndpointRemoveResponses = {
             host: string;
             user?: string;
             port?: number;
+            scheduler?: "none" | "slurm" | "pbs";
+            workdir?: string;
         }>;
         endpoints?: Array<{
             id: string;
@@ -2784,6 +2834,337 @@ export type SettingsComputeEndpointRemoveResponses = {
     };
 };
 export type SettingsComputeEndpointRemoveResponse = SettingsComputeEndpointRemoveResponses[keyof SettingsComputeEndpointRemoveResponses];
+export type SettingsComputeJobsListData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: "/settings/compute/jobs";
+};
+export type SettingsComputeJobsListResponses = {
+    /**
+     * Compute jobs
+     */
+    200: Array<{
+        id: string;
+        name: string;
+        command: string;
+        cwd?: string;
+        target: {
+            kind: "local";
+        } | {
+            kind: "ssh";
+            host_id: string;
+        };
+        target_label: string;
+        scheduler: "none" | "slurm" | "pbs";
+        status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted";
+        created_at: string;
+        started_at?: string;
+        completed_at?: string;
+        exit_code?: number | null;
+        pid?: number;
+        error?: string;
+        resources?: {
+            cpus?: number;
+            gpus?: number;
+            memory_gb?: number;
+            time_minutes?: number;
+            partition?: string;
+        };
+        modules?: Array<string>;
+        container?: string;
+        artifact_patterns?: Array<string>;
+        artifacts?: Array<{
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        }>;
+        checkpoint_path?: string;
+        checkpoint?: {
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        };
+        reproducibility?: {
+            captured_at: string;
+            command: string;
+            cwd: string;
+            platform: string;
+            arch: string;
+            bun: string;
+            node: string;
+            python?: string;
+            git?: {
+                branch?: string;
+                commit?: string;
+                dirty: boolean;
+            };
+            lockfiles: Array<{
+                path: string;
+                size: number;
+                sha256: string;
+                modified_at: string;
+            }>;
+            resources?: {
+                cpus?: number;
+                gpus?: number;
+                memory_gb?: number;
+                time_minutes?: number;
+                partition?: string;
+            };
+        };
+        capture_error?: string;
+    }>;
+};
+export type SettingsComputeJobsListResponse = SettingsComputeJobsListResponses[keyof SettingsComputeJobsListResponses];
+export type SettingsComputeJobsStartData = {
+    body?: {
+        name: string;
+        command: string;
+        cwd?: string;
+        target: {
+            kind: "local";
+        } | {
+            kind: "ssh";
+            host_id: string;
+        };
+        resources?: {
+            cpus?: number;
+            gpus?: number;
+            memory_gb?: number;
+            time_minutes?: number;
+            partition?: string;
+        };
+        modules?: Array<string>;
+        container?: string;
+        artifacts?: Array<string>;
+        checkpoint?: string;
+    };
+    path?: never;
+    query?: never;
+    url: "/settings/compute/jobs";
+};
+export type SettingsComputeJobsStartErrors = {
+    /**
+     * Bad request
+     */
+    400: BadRequestError;
+};
+export type SettingsComputeJobsStartError = SettingsComputeJobsStartErrors[keyof SettingsComputeJobsStartErrors];
+export type SettingsComputeJobsStartResponses = {
+    /**
+     * Started job
+     */
+    200: {
+        id: string;
+        name: string;
+        command: string;
+        cwd?: string;
+        target: {
+            kind: "local";
+        } | {
+            kind: "ssh";
+            host_id: string;
+        };
+        target_label: string;
+        scheduler: "none" | "slurm" | "pbs";
+        status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted";
+        created_at: string;
+        started_at?: string;
+        completed_at?: string;
+        exit_code?: number | null;
+        pid?: number;
+        error?: string;
+        resources?: {
+            cpus?: number;
+            gpus?: number;
+            memory_gb?: number;
+            time_minutes?: number;
+            partition?: string;
+        };
+        modules?: Array<string>;
+        container?: string;
+        artifact_patterns?: Array<string>;
+        artifacts?: Array<{
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        }>;
+        checkpoint_path?: string;
+        checkpoint?: {
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        };
+        reproducibility?: {
+            captured_at: string;
+            command: string;
+            cwd: string;
+            platform: string;
+            arch: string;
+            bun: string;
+            node: string;
+            python?: string;
+            git?: {
+                branch?: string;
+                commit?: string;
+                dirty: boolean;
+            };
+            lockfiles: Array<{
+                path: string;
+                size: number;
+                sha256: string;
+                modified_at: string;
+            }>;
+            resources?: {
+                cpus?: number;
+                gpus?: number;
+                memory_gb?: number;
+                time_minutes?: number;
+                partition?: string;
+            };
+        };
+        capture_error?: string;
+    };
+};
+export type SettingsComputeJobsStartResponse = SettingsComputeJobsStartResponses[keyof SettingsComputeJobsStartResponses];
+export type SettingsComputeJobsClearData = {
+    body?: never;
+    path?: never;
+    query?: never;
+    url: "/settings/compute/jobs/completed";
+};
+export type SettingsComputeJobsClearResponses = {
+    /**
+     * Number cleared
+     */
+    200: {
+        cleared: number;
+    };
+};
+export type SettingsComputeJobsClearResponse = SettingsComputeJobsClearResponses[keyof SettingsComputeJobsClearResponses];
+export type SettingsComputeJobsLogData = {
+    body?: never;
+    path: {
+        id: string;
+    };
+    query?: never;
+    url: "/settings/compute/jobs/{id}/log";
+};
+export type SettingsComputeJobsLogErrors = {
+    /**
+     * Not found
+     */
+    404: NotFoundError;
+};
+export type SettingsComputeJobsLogError = SettingsComputeJobsLogErrors[keyof SettingsComputeJobsLogErrors];
+export type SettingsComputeJobsLogResponses = {
+    /**
+     * Job output
+     */
+    200: {
+        log: string;
+    };
+};
+export type SettingsComputeJobsLogResponse = SettingsComputeJobsLogResponses[keyof SettingsComputeJobsLogResponses];
+export type SettingsComputeJobsCancelData = {
+    body?: never;
+    path: {
+        id: string;
+    };
+    query?: never;
+    url: "/settings/compute/jobs/{id}/cancel";
+};
+export type SettingsComputeJobsCancelErrors = {
+    /**
+     * Not found
+     */
+    404: NotFoundError;
+};
+export type SettingsComputeJobsCancelError = SettingsComputeJobsCancelErrors[keyof SettingsComputeJobsCancelErrors];
+export type SettingsComputeJobsCancelResponses = {
+    /**
+     * Cancelled job
+     */
+    200: {
+        id: string;
+        name: string;
+        command: string;
+        cwd?: string;
+        target: {
+            kind: "local";
+        } | {
+            kind: "ssh";
+            host_id: string;
+        };
+        target_label: string;
+        scheduler: "none" | "slurm" | "pbs";
+        status: "queued" | "running" | "succeeded" | "failed" | "cancelled" | "interrupted";
+        created_at: string;
+        started_at?: string;
+        completed_at?: string;
+        exit_code?: number | null;
+        pid?: number;
+        error?: string;
+        resources?: {
+            cpus?: number;
+            gpus?: number;
+            memory_gb?: number;
+            time_minutes?: number;
+            partition?: string;
+        };
+        modules?: Array<string>;
+        container?: string;
+        artifact_patterns?: Array<string>;
+        artifacts?: Array<{
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        }>;
+        checkpoint_path?: string;
+        checkpoint?: {
+            path: string;
+            size: number;
+            sha256: string;
+            modified_at: string;
+        };
+        reproducibility?: {
+            captured_at: string;
+            command: string;
+            cwd: string;
+            platform: string;
+            arch: string;
+            bun: string;
+            node: string;
+            python?: string;
+            git?: {
+                branch?: string;
+                commit?: string;
+                dirty: boolean;
+            };
+            lockfiles: Array<{
+                path: string;
+                size: number;
+                sha256: string;
+                modified_at: string;
+            }>;
+            resources?: {
+                cpus?: number;
+                gpus?: number;
+                memory_gb?: number;
+                time_minutes?: number;
+                partition?: string;
+            };
+        };
+        capture_error?: string;
+    };
+};
+export type SettingsComputeJobsCancelResponse = SettingsComputeJobsCancelResponses[keyof SettingsComputeJobsCancelResponses];
 export type SettingsPermissionsGetData = {
     body?: never;
     path?: never;
@@ -4635,6 +5016,242 @@ export type FileWriteResponses = {
     200: FileContent;
 };
 export type FileWriteResponse = FileWriteResponses[keyof FileWriteResponses];
+export type FileInspectData = {
+    body?: never;
+    path?: never;
+    query: {
+        directory?: string;
+        path: string;
+    };
+    url: "/file/inspect";
+};
+export type FileInspectResponses = {
+    /**
+     * Scientific file inspection
+     */
+    200: {
+        format: "bam" | "cram" | "h5ad" | "loom";
+        name: string;
+        size: number;
+        modified: number;
+        signature: boolean;
+        index?: string;
+        tool: {
+            name: string;
+            available: boolean;
+            detail?: string;
+        };
+        details: {
+            [key: string]: unknown;
+        };
+    };
+};
+export type FileInspectResponse = FileInspectResponses[keyof FileInspectResponses];
+export type FileRawData = {
+    body?: never;
+    path?: never;
+    query: {
+        directory?: string;
+        path: string;
+    };
+    url: "/file/raw";
+};
+export type FileRawResponses = {
+    /**
+     * Raw file contents
+     */
+    200: unknown;
+};
+export type FileArtifactsData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/artifacts";
+};
+export type FileArtifactsResponses = {
+    /**
+     * Research artifacts
+     */
+    200: Array<{
+        name: string;
+        path: string;
+        kind: "notebook" | "dataset" | "figure" | "report" | "structure" | "sequence" | "genomics" | "spectrum" | "model" | "archive";
+        format: string;
+        size: number;
+        modified: number;
+    }>;
+};
+export type FileArtifactsResponse = FileArtifactsResponses[keyof FileArtifactsResponses];
+export type FileProvenanceData = {
+    body?: never;
+    path?: never;
+    query: {
+        directory?: string;
+        path: string;
+    };
+    url: "/file/provenance";
+};
+export type FileProvenanceResponses = {
+    /**
+     * Local provenance
+     */
+    200: {
+        path: string;
+        tracked: boolean;
+        dirty: boolean;
+        status: "clean" | "modified" | "added" | "deleted" | "untracked" | "local";
+        branch?: string;
+        commit?: {
+            sha: string;
+            author: string;
+            email: string;
+            date: string;
+            message: string;
+        };
+    };
+};
+export type FileProvenanceResponse = FileProvenanceResponses[keyof FileProvenanceResponses];
+export type FileReproducibilityData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/reproducibility";
+};
+export type FileReproducibilityResponses = {
+    /**
+     * Project reproducibility audit
+     */
+    200: {
+        generated_at: string;
+        score: number;
+        status: "ready" | "warnings" | "blocked";
+        git?: {
+            branch?: string;
+            commit?: string;
+            dirty: boolean;
+        };
+        lockfiles: Array<string>;
+        environments: Array<string>;
+        notebooks: {
+            total: number;
+            valid: number;
+            invalid: Array<string>;
+        };
+        artifacts: {
+            total: number;
+            nonempty: number;
+            bytes: number;
+        };
+        checks: Array<{
+            id: string;
+            label: string;
+            status: "pass" | "warn" | "fail";
+            detail: string;
+            weight: number;
+        }>;
+    };
+};
+export type FileReproducibilityResponse = FileReproducibilityResponses[keyof FileReproducibilityResponses];
+export type FileManifestData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/manifest";
+};
+export type FileManifestResponses = {
+    /**
+     * Artifact checksum manifest
+     */
+    200: {
+        format: "openscience.artifact-manifest.v1";
+        generated_at: string;
+        digest: string;
+        artifacts: Array<{
+            name: string;
+            path: string;
+            kind: "notebook" | "dataset" | "figure" | "report" | "structure" | "sequence" | "genomics" | "spectrum" | "model" | "archive";
+            format: string;
+            size: number;
+            modified: number;
+            sha256: string;
+        }>;
+    };
+};
+export type FileManifestResponse = FileManifestResponses[keyof FileManifestResponses];
+export type FileStarterData = {
+    body?: {
+        template: "single-cell" | "dose-response" | "protein-structure";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/starters";
+};
+export type FileStarterResponses = {
+    /**
+     * Created starter files
+     */
+    200: {
+        template: "single-cell" | "dose-response" | "protein-structure";
+        directory: string;
+        files: Array<string>;
+        notebook: string;
+        readme: string;
+    };
+};
+export type FileStarterResponse = FileStarterResponses[keyof FileStarterResponses];
+export type FilePublicationCapabilitiesData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/publication/capabilities";
+};
+export type FilePublicationCapabilitiesResponses = {
+    /**
+     * Available local publication formats
+     */
+    200: {
+        pandoc: boolean;
+        pdf_engine?: string;
+        formats: {
+            [key: string]: boolean;
+        };
+    };
+};
+export type FilePublicationCapabilitiesResponse = FilePublicationCapabilitiesResponses[keyof FilePublicationCapabilitiesResponses];
+export type FilePublicationData = {
+    body?: {
+        path: string;
+        format: "html" | "pdf" | "docx" | "latex" | "pptx";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/file/publication";
+};
+export type FilePublicationResponses = {
+    /**
+     * Created publication artifact
+     */
+    200: {
+        path: string;
+        format: "html" | "pdf" | "docx" | "latex" | "pptx";
+        size: number;
+        created_at: string;
+        engine: string;
+    };
+};
+export type FilePublicationResponse = FilePublicationResponses[keyof FilePublicationResponses];
 export type FileStatusData = {
     body?: never;
     path?: never;
@@ -4650,6 +5267,186 @@ export type FileStatusResponses = {
     200: Array<File>;
 };
 export type FileStatusResponse = FileStatusResponses[keyof FileStatusResponses];
+export type NotebookExecuteData = {
+    body?: {
+        id: string;
+        language: "python" | "r";
+        code: string;
+        timeout?: number;
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/notebook/execute";
+};
+export type NotebookExecuteResponses = {
+    /**
+     * Jupyter-compatible cell outputs
+     */
+    200: unknown;
+};
+export type NotebookStatusData = {
+    body?: never;
+    path?: never;
+    query: {
+        directory?: string;
+        id: string;
+        language: "python" | "r";
+    };
+    url: "/notebook/status";
+};
+export type NotebookStatusResponses = {
+    /**
+     * Kernel state
+     */
+    200: unknown;
+};
+export type NotebookRestartData = {
+    body?: {
+        id: string;
+        language: "python" | "r";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/notebook/restart";
+};
+export type NotebookRestartResponses = {
+    /**
+     * Kernel state
+     */
+    200: unknown;
+};
+export type NotebookInterruptData = {
+    body?: {
+        id: string;
+        language: "python" | "r";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/notebook/interrupt";
+};
+export type NotebookInterruptResponses = {
+    /**
+     * Kernel state
+     */
+    200: unknown;
+};
+export type ProvenanceListData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/provenance";
+};
+export type ProvenanceListResponses = {
+    /**
+     * Project provenance graph
+     */
+    200: unknown;
+};
+export type ProvenanceRecordData = {
+    body?: {
+        kind: "artifact" | "run" | "source" | "claim";
+        label: string;
+        artifact_type?: string;
+        path?: string;
+        content_hash?: string;
+        size?: number;
+        tool?: string;
+        status?: "ok" | "error";
+        meta?: {
+            [key: string]: unknown;
+        };
+        derived_from?: string;
+        relation?: "produced" | "consumed" | "derived-from" | "supports" | "refutes";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/provenance/nodes";
+};
+export type ProvenanceRecordErrors = {
+    /**
+     * Invalid link target
+     */
+    400: unknown;
+};
+export type ProvenanceRecordResponses = {
+    /**
+     * Recorded node
+     */
+    200: unknown;
+};
+export type ProvenanceReviewData = {
+    body?: {
+        target: string;
+        claim: string;
+        issue: string;
+        severity: "blocking" | "major" | "minor" | "info";
+        evidence: string;
+        verdict?: "refutes" | "supports";
+    };
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/provenance/reviews";
+};
+export type ProvenanceReviewErrors = {
+    /**
+     * Invalid target
+     */
+    400: unknown;
+};
+export type ProvenanceReviewResponses = {
+    /**
+     * Recorded finding
+     */
+    200: unknown;
+};
+export type ProvenanceExportData = {
+    body?: never;
+    path?: never;
+    query?: {
+        directory?: string;
+    };
+    url: "/provenance/export";
+};
+export type ProvenanceExportResponses = {
+    /**
+     * Portable JSON audit packet
+     */
+    200: unknown;
+};
+export type ProvenanceTraceData = {
+    body?: never;
+    path: {
+        id: string;
+    };
+    query?: {
+        directory?: string;
+    };
+    url: "/provenance/{id}";
+};
+export type ProvenanceTraceErrors = {
+    /**
+     * Node not found
+     */
+    404: unknown;
+};
+export type ProvenanceTraceResponses = {
+    /**
+     * Connected lineage
+     */
+    200: unknown;
+};
 export type McpStatusData = {
     body?: never;
     path?: never;