@mantra-ai/core 0.1.0

package/dist/types/paper/types.d.ts

@@ -0,0 +1,41 @@
+export type PaperSource = {
+    name: string;
+    url: string;
+};
+export interface Paper {
+    id: string;
+    doi?: string;
+    title: string;
+    license?: string;
+    source: PaperSource;
+}
+export type SectionName = "introduction" | "methods" | "results" | "discussion" | string;
+export interface Section {
+    name: SectionName;
+    title?: string;
+    text: string;
+    path: string[];
+}
+export interface TableMeta {
+    id: string;
+    label?: string;
+    caption?: string;
+}
+export interface TableJSON {
+    id: string;
+    caption?: string;
+    rows: (string | null)[][];
+}
+export interface FigureMeta {
+    id: string;
+    label?: string;
+    caption?: string;
+    sizes?: string[];
+    src?: Record<string, string>;
+}
+export interface StatusSnapshot {
+    license: any;
+    crossmark?: any;
+    retractions?: any[];
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/types/paper/types.d.ts.map

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package/dist/types/paper/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/types/paper/types.js.map

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+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/types/paper/types.ts"],"names":[],"mappings":""}

package/dist/types/results-types.d.ts

@@ -0,0 +1,122 @@
+export interface ThematicBlock {
+    block_id: string;
+    objective_summary: string;
+    findings_main_text: string;
+    doi: string;
+    block_order_in_paper: number;
+    source_section: string;
+    word_count: number;
+    explicit_references: string[];
+    hypotheses: string[];
+    key_entities_mentioned?: string[];
+}
+export interface Parameter {
+    name: string;
+    value: string | number;
+    unit?: string;
+    context?: string;
+    source_text_snippet?: string;
+}
+export interface ObservationQuantification {
+    metric: string;
+    value: string;
+    condition?: string;
+    comparison?: string;
+    significance?: string;
+    source_text_snippet?: string;
+}
+export interface MentionedEntity {
+    name: string;
+    type: string;
+    role_in_method?: string;
+    role_in_finding?: string;
+    identifier?: string;
+}
+export interface MethodFindingUnit {
+    unit_id: string;
+    linking_narrative: string;
+    explicit_references: string[];
+    full_text_verbatim: string;
+    method_description: string;
+    method_text_verbatim: string;
+    finding_description: string;
+    finding_text_verbatim: string;
+}
+export interface ProtocolFindingOutput {
+    method_finding_units: MethodFindingUnit[];
+}
+export interface MethodResultUnit {
+    original_block_id: string;
+    order_in_block?: number;
+    processed_data: ProtocolFindingOutput | null;
+    error?: string;
+}
+export declare enum DataType {
+    RAW_SEQUENCE_READS = "raw_sequence_reads",
+    ALIGNED_READS_BAM = "aligned_reads_bam",
+    GENE_COUNT_MATRIX = "gene_count_matrix",
+    NORMALIZED_COUNT_MATRIX = "normalized_count_matrix",
+    DIFFERENTIAL_EXPRESSION_RESULTS = "differential_expression_results",
+    PLOT_DATA_CSV = "plot_data_csv",
+    IMAGE_FILE = "image_file",
+    TABULAR_DATA_CSV = "tabular_data_csv",
+    PARAMETER_SET_JSON = "parameter_set_json",
+    TEXT_REPORT = "text_report",
+    UNKNOWN = "unknown"
+}
+export interface DataArtifact {
+    artifact_id: string;
+    description: string;
+    data_type: DataType;
+    format_details?: string;
+    source_asu_id?: string;
+    is_input_to_asu_ids?: string[];
+    storage_location_placeholder?: string;
+    original_data_source_description?: string;
+    is_publicly_available?: boolean;
+    access_url?: string;
+}
+export interface SoftwareDependency {
+    name: string;
+    version_constraint?: string;
+    installation_method?: string;
+}
+export interface CodeSpec {
+    language: "python" | "r" | "bash" | "pseudocode" | "proprietary_simulation" | "unknown";
+    script_placeholder?: string;
+    entry_point?: string;
+    simulation_config_placeholder?: string;
+    simulator_name?: string;
+}
+export interface ParameterValue {
+    name: string;
+    value: any;
+    unit?: string;
+    is_configurable?: boolean;
+}
+export interface ExpectedOutcome {
+    description: string;
+    metric?: string;
+    expected_value_range?: string;
+    qualitative_statement?: string;
+    supporting_figure_table?: string;
+}
+export interface AnalysisStepUnit {
+    asu_id: string;
+    source_mfu_id: string;
+    order_in_paper_workflow: number;
+    short_description: string;
+    input_data_artifacts: DataArtifact[];
+    output_data_artifacts: DataArtifact[];
+    software_dependencies: SoftwareDependency[];
+    computational_parameters: ParameterValue[];
+    code_spec: CodeSpec;
+    expected_outcomes: ExpectedOutcome[];
+    depends_on_asu_ids?: string[];
+    generates_input_for_asu_ids?: string[];
+    execution_status?: "pending" | "running" | "completed_success" | "completed_error" | "skipped";
+    generated_results_summary?: any;
+    verification_status?: "unverified" | "matches_claim" | "partially_matches_claim" | "contradicts_claim" | "error_in_replication";
+    verification_notes?: string;
+}
+//# sourceMappingURL=results-types.d.ts.map

package/dist/types/results-types.d.ts.map

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package/dist/types/results-types.js

@@ -0,0 +1,17 @@
+///////////////////////////////////////////////////////////////////////////
+export var DataType;
+(function (DataType) {
+    DataType["RAW_SEQUENCE_READS"] = "raw_sequence_reads";
+    DataType["ALIGNED_READS_BAM"] = "aligned_reads_bam";
+    DataType["GENE_COUNT_MATRIX"] = "gene_count_matrix";
+    DataType["NORMALIZED_COUNT_MATRIX"] = "normalized_count_matrix";
+    DataType["DIFFERENTIAL_EXPRESSION_RESULTS"] = "differential_expression_results";
+    DataType["PLOT_DATA_CSV"] = "plot_data_csv";
+    DataType["IMAGE_FILE"] = "image_file";
+    DataType["TABULAR_DATA_CSV"] = "tabular_data_csv";
+    DataType["PARAMETER_SET_JSON"] = "parameter_set_json";
+    DataType["TEXT_REPORT"] = "text_report";
+    // ... more specific data types
+    DataType["UNKNOWN"] = "unknown";
+})(DataType || (DataType = {}));
+//# sourceMappingURL=results-types.js.map

package/dist/types/results-types.js.map

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package/dist/types/supp-types.d.ts

@@ -0,0 +1,6 @@
+export interface MethodologicalDetail {
+    category: string;
+    methodological_item_name: string;
+    description: string;
+}
+//# sourceMappingURL=supp-types.d.ts.map

package/dist/types/supp-types.d.ts.map

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package/dist/types/supp-types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=supp-types.js.map

package/dist/types/supp-types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"supp-types.js","sourceRoot":"","sources":["../../src/types/supp-types.ts"],"names":[],"mappings":""}