agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/api-spec.openapi.yaml

@@ -1,1258 +0,0 @@
-openapi: 3.0.3
-info:
-  title: CRISPR-Cas13 Bioinformatics Pipeline API
-  version: 1.0.0
-  description: |
-    RESTful API for CRISPR-Cas13 RNA-targeting experiments in primate models.
-
-    **Features:**
-    - FASTQ data ingestion
-    - Automated QC and alignment pipelines
-    - Off-target prediction
-    - Innate immune response analysis
-    - Real-time job monitoring via WebSocket
-    - W3C PROV-O provenance tracking
-
-    **Authentication:** API Key (Header: `X-API-Key`) or OAuth2 Bearer token
-
-  contact:
-    name: Bioinformatics Core
-    email: support@crispr-pipeline.org
-  license:
-    name: MIT
-    url: https://opensource.org/licenses/MIT
-
-servers:
-  - url: https://api.crispr-pipeline.org/v1
-    description: Production server
-  - url: https://staging-api.crispr-pipeline.org/v1
-    description: Staging server
-  - url: http://localhost:8000/v1
-    description: Local development server
-
-security:
-  - ApiKeyAuth: []
-  - OAuth2: [read, write]
-
-tags:
-  - name: Experiments
-    description: Experiment metadata management
-  - name: Sequencing
-    description: FASTQ data upload and management
-  - name: Jobs
-    description: Processing job submission and monitoring
-  - name: Results
-    description: Analysis results retrieval
-  - name: References
-    description: Reference genome management
-  - name: Users
-    description: User account management
-  - name: System
-    description: System health and configuration
-
-paths:
-  /experiments:
-    get:
-      summary: List experiments
-      description: Retrieve paginated list of experiments with optional filtering
-      tags: [Experiments]
-      parameters:
-        - name: page
-          in: query
-          schema:
-            type: integer
-            default: 1
-            minimum: 1
-        - name: per_page
-          in: query
-          schema:
-            type: integer
-            default: 20
-            minimum: 1
-            maximum: 100
-        - name: species
-          in: query
-          schema:
-            type: string
-            enum: [rhesus_macaque, cynomolgus_macaque, human_cell_line]
-        - name: cas13_variant
-          in: query
-          schema:
-            type: string
-            enum: [Cas13a, Cas13b, Cas13c, Cas13d]
-        - name: experimenter
-          in: query
-          schema:
-            type: string
-        - name: date_from
-          in: query
-          schema:
-            type: string
-            format: date-time
-        - name: date_to
-          in: query
-          schema:
-            type: string
-            format: date-time
-        - name: sort_by
-          in: query
-          schema:
-            type: string
-            enum: [date_performed, created_at, title]
-            default: created_at
-        - name: sort_order
-          in: query
-          schema:
-            type: string
-            enum: [asc, desc]
-            default: desc
-      responses:
-        '200':
-          description: Successful response
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  data:
-                    type: array
-                    items:
-                      $ref: '#/components/schemas/Experiment'
-                  pagination:
-                    $ref: '#/components/schemas/Pagination'
-        '401':
-          $ref: '#/components/responses/Unauthorized'
-        '500':
-          $ref: '#/components/responses/InternalServerError'
-
-    post:
-      summary: Create new experiment
-      description: Submit new experiment metadata
-      tags: [Experiments]
-      requestBody:
-        required: true
-        content:
-          application/json:
-            schema:
-              $ref: '#/components/schemas/ExperimentCreate'
-      responses:
-        '201':
-          description: Experiment created successfully
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/Experiment'
-        '400':
-          $ref: '#/components/responses/BadRequest'
-        '401':
-          $ref: '#/components/responses/Unauthorized'
-        '422':
-          $ref: '#/components/responses/ValidationError'
-
-  /experiments/{experiment_id}:
-    get:
-      summary: Get experiment details
-      tags: [Experiments]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      responses:
-        '200':
-          description: Successful response
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/Experiment'
-        '404':
-          $ref: '#/components/responses/NotFound'
-
-    put:
-      summary: Update experiment
-      tags: [Experiments]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      requestBody:
-        required: true
-        content:
-          application/json:
-            schema:
-              $ref: '#/components/schemas/ExperimentUpdate'
-      responses:
-        '200':
-          description: Experiment updated
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/Experiment'
-        '404':
-          $ref: '#/components/responses/NotFound'
-
-    delete:
-      summary: Delete experiment
-      description: Delete experiment and all associated data (requires admin role)
-      tags: [Experiments]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      responses:
-        '204':
-          description: Experiment deleted
-        '403':
-          $ref: '#/components/responses/Forbidden'
-        '404':
-          $ref: '#/components/responses/NotFound'
-
-  /experiments/{experiment_id}/provenance:
-    get:
-      summary: Get experiment provenance
-      description: Retrieve W3C PROV-O provenance graph
-      tags: [Experiments]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-        - name: format
-          in: query
-          schema:
-            type: string
-            enum: [json-ld, turtle, rdf-xml]
-            default: json-ld
-      responses:
-        '200':
-          description: Provenance graph
-          content:
-            application/ld+json:
-              schema:
-                type: object
-            text/turtle:
-              schema:
-                type: string
-
-  /sequencing-data:
-    post:
-      summary: Upload FASTQ files
-      description: Upload raw sequencing data (FASTQ format)
-      tags: [Sequencing]
-      requestBody:
-        required: true
-        content:
-          multipart/form-data:
-            schema:
-              type: object
-              required:
-                - experiment_id
-                - sample_id
-                - sequencing_platform
-                - read_type
-                - file_r1
-              properties:
-                experiment_id:
-                  type: string
-                  format: uuid
-                sample_id:
-                  type: string
-                sequencing_platform:
-                  type: string
-                  enum: [Illumina_NovaSeq_6000, Illumina_NextSeq_2000, Illumina_MiSeq]
-                read_type:
-                  type: string
-                  enum: [single_end, paired_end]
-                read_length:
-                  type: integer
-                file_r1:
-                  type: string
-                  format: binary
-                  description: "FASTQ file (R1 or single-end)"
-                file_r2:
-                  type: string
-                  format: binary
-                  description: "FASTQ file (R2, required for paired-end)"
-      responses:
-        '201':
-          description: Upload successful
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/SequencingRun'
-        '400':
-          description: Invalid file format or missing required fields
-        '413':
-          description: File too large (>50GB)
-
-  /sequencing-data/{run_id}:
-    get:
-      summary: Get sequencing run details
-      tags: [Sequencing]
-      parameters:
-        - name: run_id
-          in: path
-          required: true
-          schema:
-            type: string
-            format: uuid
-      responses:
-        '200':
-          description: Sequencing run details
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/SequencingRun'
-
-  /sequencing-data/{run_id}/qc:
-    get:
-      summary: Get QC results
-      description: Retrieve FastQC quality control metrics
-      tags: [Sequencing]
-      parameters:
-        - name: run_id
-          in: path
-          required: true
-          schema:
-            type: string
-            format: uuid
-      responses:
-        '200':
-          description: QC metrics
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/QualityControl'
-
-  /jobs:
-    get:
-      summary: List jobs
-      description: List all processing jobs for the authenticated user
-      tags: [Jobs]
-      parameters:
-        - name: status
-          in: query
-          schema:
-            type: string
-            enum: [queued, running, completed, failed, cancelled, all]
-            default: all
-        - name: job_type
-          in: query
-          schema:
-            type: string
-            enum: [qc_only, alignment, full_pipeline, off_target_prediction]
-        - name: experiment_id
-          in: query
-          schema:
-            type: string
-            format: uuid
-        - name: page
-          in: query
-          schema:
-            type: integer
-            default: 1
-        - name: per_page
-          in: query
-          schema:
-            type: integer
-            default: 20
-      responses:
-        '200':
-          description: Job list
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  data:
-                    type: array
-                    items:
-                      $ref: '#/components/schemas/ProcessingJob'
-                  pagination:
-                    $ref: '#/components/schemas/Pagination'
-
-    post:
-      summary: Submit processing job
-      description: Submit a new bioinformatics pipeline job
-      tags: [Jobs]
-      requestBody:
-        required: true
-        content:
-          application/json:
-            schema:
-              $ref: '#/components/schemas/JobSubmission'
-      responses:
-        '201':
-          description: Job submitted
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ProcessingJob'
-        '400':
-          $ref: '#/components/responses/BadRequest'
-
-  /jobs/{job_id}:
-    get:
-      summary: Get job status
-      description: Get detailed job status and progress
-      tags: [Jobs]
-      parameters:
-        - name: job_id
-          in: path
-          required: true
-          schema:
-            type: string
-            format: uuid
-      responses:
-        '200':
-          description: Job status
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ProcessingJob'
-        '404':
-          $ref: '#/components/responses/NotFound'
-
-    delete:
-      summary: Cancel job
-      description: Cancel a running or queued job
-      tags: [Jobs]
-      parameters:
-        - name: job_id
-          in: path
-          required: true
-          schema:
-            type: string
-            format: uuid
-      responses:
-        '200':
-          description: Job cancelled
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ProcessingJob'
-        '400':
-          description: Job cannot be cancelled (already completed)
-
-  /jobs/{job_id}/logs:
-    get:
-      summary: Get job logs
-      description: Retrieve stdout/stderr logs for debugging
-      tags: [Jobs]
-      parameters:
-        - name: job_id
-          in: path
-          required: true
-          schema:
-            type: string
-            format: uuid
-        - name: log_type
-          in: query
-          schema:
-            type: string
-            enum: [stdout, stderr, both]
-            default: both
-        - name: tail
-          in: query
-          schema:
-            type: integer
-            description: "Number of lines from end of log"
-            default: 100
-      responses:
-        '200':
-          description: Job logs
-          content:
-            text/plain:
-              schema:
-                type: string
-            application/json:
-              schema:
-                type: object
-                properties:
-                  stdout:
-                    type: string
-                  stderr:
-                    type: string
-
-  /results/{experiment_id}:
-    get:
-      summary: Get experiment results
-      description: Retrieve all analysis results for completed experiment
-      tags: [Results]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-        - name: include
-          in: query
-          schema:
-            type: string
-            description: "Comma-separated list: qc,alignment,target,offtargets,immune"
-            default: "qc,alignment,target"
-      responses:
-        '200':
-          description: Experiment results
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ExperimentResults'
-
-  /results/{experiment_id}/target-analysis:
-    get:
-      summary: Get target analysis results
-      description: On-target knockdown efficiency and statistics
-      tags: [Results]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      responses:
-        '200':
-          description: Target analysis
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/TargetAnalysis'
-
-  /results/{experiment_id}/off-targets:
-    get:
-      summary: Get off-target predictions
-      description: Ranked list of predicted off-target sites
-      tags: [Results]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-        - name: top_n
-          in: query
-          schema:
-            type: integer
-            default: 100
-            maximum: 1000
-        - name: min_score
-          in: query
-          schema:
-            type: number
-            default: 0.5
-            minimum: 0.0
-            maximum: 1.0
-      responses:
-        '200':
-          description: Off-target sites
-          content:
-            application/json:
-              schema:
-                type: array
-                items:
-                  $ref: '#/components/schemas/OffTargetSite'
-
-  /results/{experiment_id}/immune-response:
-    get:
-      summary: Get immune response analysis
-      description: Innate immune pathway activation metrics
-      tags: [Results]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      responses:
-        '200':
-          description: Immune response
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ImmuneResponse'
-
-  /results/{experiment_id}/files:
-    get:
-      summary: List result files
-      description: Get download URLs for result files (BAM, VCF, TSV, etc.)
-      tags: [Results]
-      parameters:
-        - $ref: '#/components/parameters/ExperimentId'
-      responses:
-        '200':
-          description: File list with pre-signed URLs
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  files:
-                    type: array
-                    items:
-                      type: object
-                      properties:
-                        file_type:
-                          type: string
-                          enum: [bam, bai, vcf, tsv, html, bed]
-                        file_name:
-                          type: string
-                        file_size:
-                          type: integer
-                        download_url:
-                          type: string
-                          format: uri
-                          description: "Pre-signed URL (expires in 1 hour)"
-                        md5_checksum:
-                          type: string
-
-  /references/genomes:
-    get:
-      summary: List reference genomes
-      description: Available reference genomes and their indices
-      tags: [References]
-      responses:
-        '200':
-          description: Reference genome list
-          content:
-            application/json:
-              schema:
-                type: array
-                items:
-                  $ref: '#/components/schemas/ReferenceGenome'
-
-    post:
-      summary: Upload custom reference genome
-      description: Add custom reference genome (requires admin role)
-      tags: [References]
-      requestBody:
-        required: true
-        content:
-          multipart/form-data:
-            schema:
-              type: object
-              required: [species, assembly_name, genome_fasta, annotation_gtf]
-              properties:
-                species:
-                  type: string
-                assembly_name:
-                  type: string
-                genome_fasta:
-                  type: string
-                  format: binary
-                annotation_gtf:
-                  type: string
-                  format: binary
-      responses:
-        '201':
-          description: Reference genome uploaded
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/ReferenceGenome'
-
-  /users/me:
-    get:
-      summary: Get current user profile
-      tags: [Users]
-      responses:
-        '200':
-          description: User profile
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/User'
-
-    patch:
-      summary: Update user profile
-      tags: [Users]
-      requestBody:
-        content:
-          application/json:
-            schema:
-              type: object
-              properties:
-                full_name:
-                  type: string
-                institution:
-                  type: string
-                notification_email:
-                  type: string
-                  format: email
-      responses:
-        '200':
-          description: Profile updated
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/User'
-
-  /users/me/api-key:
-    post:
-      summary: Generate new API key
-      description: Generate new API key (invalidates old key)
-      tags: [Users]
-      responses:
-        '201':
-          description: New API key generated
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  api_key:
-                    type: string
-                    description: "SAVE THIS! It will not be shown again."
-                  created_at:
-                    type: string
-                    format: date-time
-
-  /system/health:
-    get:
-      summary: System health check
-      description: Check API and database connectivity
-      tags: [System]
-      security: []  # No authentication required
-      responses:
-        '200':
-          description: System healthy
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  status:
-                    type: string
-                    enum: [healthy, degraded, unhealthy]
-                  timestamp:
-                    type: string
-                    format: date-time
-                  components:
-                    type: object
-                    properties:
-                      api:
-                        type: string
-                        enum: [up, down]
-                      database:
-                        type: string
-                        enum: [up, down]
-                      storage:
-                        type: string
-                        enum: [up, down]
-                      queue:
-                        type: string
-                        enum: [up, down]
-                  version:
-                    type: string
-                    example: "1.0.0"
-
-  /system/stats:
-    get:
-      summary: System statistics
-      description: Overall system usage statistics (admin only)
-      tags: [System]
-      responses:
-        '200':
-          description: System stats
-          content:
-            application/json:
-              schema:
-                type: object
-                properties:
-                  total_experiments:
-                    type: integer
-                  total_sequencing_runs:
-                    type: integer
-                  total_jobs:
-                    type: object
-                    properties:
-                      queued:
-                        type: integer
-                      running:
-                        type: integer
-                      completed:
-                        type: integer
-                  storage_used_tb:
-                    type: number
-                  active_users:
-                    type: integer
-
-# WebSocket endpoint (not OpenAPI standard, documented separately)
-# ws://api.crispr-pipeline.org/v1/ws/jobs/{job_id}
-
-components:
-  securitySchemes:
-    ApiKeyAuth:
-      type: apiKey
-      in: header
-      name: X-API-Key
-      description: "API key authentication. Obtain from /users/me/api-key"
-
-    OAuth2:
-      type: oauth2
-      flows:
-        authorizationCode:
-          authorizationUrl: https://auth.crispr-pipeline.org/oauth/authorize
-          tokenUrl: https://auth.crispr-pipeline.org/oauth/token
-          scopes:
-            read: Read access to experiments and results
-            write: Submit jobs and create experiments
-            admin: Administrative access
-
-  parameters:
-    ExperimentId:
-      name: experiment_id
-      in: path
-      required: true
-      schema:
-        type: string
-        format: uuid
-      description: Unique experiment identifier
-
-  schemas:
-    Experiment:
-      type: object
-      required:
-        - experiment_id
-        - title
-        - species
-        - cas13_variant
-        - guide_rna
-      properties:
-        experiment_id:
-          type: string
-          format: uuid
-        title:
-          type: string
-        description:
-          type: string
-        species:
-          type: string
-          enum: [rhesus_macaque, cynomolgus_macaque, human_cell_line]
-        tissue_type:
-          type: string
-        cas13_variant:
-          type: string
-          enum: [Cas13a, Cas13b, Cas13c, Cas13d]
-        guide_rna:
-          $ref: '#/components/schemas/GuideRNA'
-        delivery_method:
-          type: string
-        timepoint_hours:
-          type: integer
-        replicate_number:
-          type: integer
-        control_type:
-          type: string
-          nullable: true
-        experimenter:
-          type: string
-        institution:
-          type: string
-        date_performed:
-          type: string
-          format: date-time
-        created_at:
-          type: string
-          format: date-time
-        updated_at:
-          type: string
-          format: date-time
-
-    ExperimentCreate:
-      type: object
-      required:
-        - title
-        - species
-        - cas13_variant
-        - guide_rna
-        - date_performed
-      properties:
-        title:
-          type: string
-          minLength: 10
-          maxLength: 200
-        description:
-          type: string
-        species:
-          type: string
-          enum: [rhesus_macaque, cynomolgus_macaque, human_cell_line]
-        tissue_type:
-          type: string
-        cas13_variant:
-          type: string
-        guide_rna:
-          $ref: '#/components/schemas/GuideRNA'
-        delivery_method:
-          type: string
-        timepoint_hours:
-          type: integer
-        replicate_number:
-          type: integer
-        experimenter:
-          type: string
-        institution:
-          type: string
-        date_performed:
-          type: string
-          format: date-time
-
-    ExperimentUpdate:
-      type: object
-      properties:
-        title:
-          type: string
-        description:
-          type: string
-        metadata:
-          type: object
-
-    GuideRNA:
-      type: object
-      required:
-        - sequence
-        - target_gene
-      properties:
-        sequence:
-          type: string
-          pattern: "^[ACGTU]{22,30}$"
-        target_gene:
-          type: string
-        target_transcript_id:
-          type: string
-        protospacer_coordinates:
-          type: object
-        gc_content:
-          type: number
-        off_target_potential:
-          type: string
-          enum: [low, medium, high]
-
-    SequencingRun:
-      type: object
-      properties:
-        run_id:
-          type: string
-          format: uuid
-        experiment_id:
-          type: string
-          format: uuid
-        sample_id:
-          type: string
-        sequencing_platform:
-          type: string
-        read_type:
-          type: string
-        read_length:
-          type: integer
-        total_reads:
-          type: integer
-        read_files:
-          type: array
-          items:
-            $ref: '#/components/schemas/FastqFile'
-        created_at:
-          type: string
-          format: date-time
-
-    FastqFile:
-      type: object
-      properties:
-        file_id:
-          type: string
-          format: uuid
-        file_path:
-          type: string
-          format: uri
-        file_name:
-          type: string
-        read_pair:
-          type: string
-          enum: [R1, R2, single]
-        file_size:
-          type: integer
-        md5_checksum:
-          type: string
-
-    QualityControl:
-      type: object
-      properties:
-        qc_id:
-          type: string
-          format: uuid
-        sequencing_run_id:
-          type: string
-          format: uuid
-        status:
-          type: string
-          enum: [pass, warn, fail]
-        total_sequences:
-          type: integer
-        mean_quality_score:
-          type: number
-        gc_content:
-          type: number
-        duplication_rate:
-          type: number
-        report_html:
-          type: string
-          format: uri
-
-    ProcessingJob:
-      type: object
-      properties:
-        job_id:
-          type: string
-          format: uuid
-        job_type:
-          type: string
-        status:
-          type: string
-          enum: [queued, running, completed, failed, cancelled]
-        priority:
-          type: string
-        progress:
-          type: number
-        current_stage:
-          type: string
-        eta_seconds:
-          type: integer
-          nullable: true
-        started_at:
-          type: string
-          format: date-time
-        completed_at:
-          type: string
-          format: date-time
-        error_message:
-          type: string
-          nullable: true
-
-    JobSubmission:
-      type: object
-      required:
-        - job_type
-        - sequencing_run_id
-        - reference_genome
-      properties:
-        job_type:
-          type: string
-          enum: [qc_only, alignment, full_pipeline, off_target_prediction]
-        sequencing_run_id:
-          type: string
-          format: uuid
-        reference_genome:
-          type: string
-        priority:
-          type: string
-          enum: [low, normal, high, urgent]
-          default: normal
-        parameters:
-          type: object
-          description: "Job-specific parameters"
-        notification_email:
-          type: string
-          format: email
-
-    ExperimentResults:
-      type: object
-      properties:
-        experiment_id:
-          type: string
-          format: uuid
-        status:
-          type: string
-        qc_metrics:
-          type: object
-        alignment_metrics:
-          type: object
-        target_analysis:
-          $ref: '#/components/schemas/TargetAnalysis'
-        off_targets:
-          type: array
-          items:
-            $ref: '#/components/schemas/OffTargetSite'
-        immune_response:
-          $ref: '#/components/schemas/ImmuneResponse'
-        files:
-          type: object
-
-    TargetAnalysis:
-      type: object
-      properties:
-        analysis_id:
-          type: string
-          format: uuid
-        target_gene:
-          type: string
-        knockdown_efficiency:
-          type: number
-        fold_change:
-          type: number
-        p_value:
-          type: number
-        control_expression_tpm:
-          type: number
-        treated_expression_tpm:
-          type: number
-
-    OffTargetSite:
-      type: object
-      properties:
-        offtarget_id:
-          type: string
-          format: uuid
-        rank:
-          type: integer
-        confidence_score:
-          type: number
-        gene_symbol:
-          type: string
-        transcript_id:
-          type: string
-        genomic_coordinates:
-          type: object
-        mismatch_count:
-          type: integer
-        expression_level:
-          type: number
-
-    ImmuneResponse:
-      type: object
-      properties:
-        immune_id:
-          type: string
-          format: uuid
-        overall_immune_score:
-          type: number
-        interferon_score:
-          type: number
-        activated_pathways:
-          type: array
-          items:
-            type: string
-        differential_genes:
-          type: array
-          items:
-            type: object
-
-    ReferenceGenome:
-      type: object
-      properties:
-        genome_id:
-          type: string
-          format: uuid
-        species:
-          type: string
-        assembly_name:
-          type: string
-        source:
-          type: string
-        total_genome_size:
-          type: integer
-        gene_count:
-          type: integer
-
-    User:
-      type: object
-      properties:
-        user_id:
-          type: string
-          format: uuid
-        email:
-          type: string
-          format: email
-        username:
-          type: string
-        full_name:
-          type: string
-        institution:
-          type: string
-        role:
-          type: string
-        storage_quota_gb:
-          type: integer
-        storage_used_gb:
-          type: number
-        created_at:
-          type: string
-          format: date-time
-
-    Pagination:
-      type: object
-      properties:
-        page:
-          type: integer
-        per_page:
-          type: integer
-        total_items:
-          type: integer
-        total_pages:
-          type: integer
-
-    Error:
-      type: object
-      properties:
-        error:
-          type: string
-        message:
-          type: string
-        details:
-          type: object
-        timestamp:
-          type: string
-          format: date-time
-
-  responses:
-    BadRequest:
-      description: Bad request
-      content:
-        application/json:
-          schema:
-            $ref: '#/components/schemas/Error'
-          example:
-            error: "BAD_REQUEST"
-            message: "Invalid input parameters"
-            timestamp: "2025-10-12T00:15:30Z"
-
-    Unauthorized:
-      description: Unauthorized
-      content:
-        application/json:
-          schema:
-            $ref: '#/components/schemas/Error'
-          example:
-            error: "UNAUTHORIZED"
-            message: "Invalid or missing API key"
-
-    Forbidden:
-      description: Forbidden
-      content:
-        application/json:
-          schema:
-            $ref: '#/components/schemas/Error'
-          example:
-            error: "FORBIDDEN"
-            message: "Insufficient permissions"
-
-    NotFound:
-      description: Resource not found
-      content:
-        application/json:
-          schema:
-            $ref: '#/components/schemas/Error'
-          example:
-            error: "NOT_FOUND"
-            message: "Experiment not found"
-
-    ValidationError:
-      description: Validation error
-      content:
-        application/json:
-          schema:
-            allOf:
-              - $ref: '#/components/schemas/Error'
-              - type: object
-                properties:
-                  details:
-                    type: object
-                    properties:
-                      field_errors:
-                        type: array
-                        items:
-                          type: object
-                          properties:
-                            field:
-                              type: string
-                            message:
-                              type: string
-          example:
-            error: "VALIDATION_ERROR"
-            message: "Input validation failed"
-            details:
-              field_errors:
-                - field: "guide_rna.sequence"
-                  message: "Must be 22-30 nucleotides"
-
-    InternalServerError:
-      description: Internal server error
-      content:
-        application/json:
-          schema:
-            $ref: '#/components/schemas/Error'
-          example:
-            error: "INTERNAL_SERVER_ERROR"
-            message: "An unexpected error occurred"