text: from flask import request
  from sqlalchemy import tuple_
  from vardb.datamodel import sample, genotype, allele
  
  from api import ApiError, ConflictError
  from api.util.util import request_json, authenticate, rest_filter, paginate
  from api.v1.resource import LogRequestResource
  
  from . import helpers
  from datalayer import queries
  from vardb.datamodel.workflow import AnalysisInterpretationSnapshot, AnalysisInterpretation
  from vardb.datamodel.sample import Analysis
  from api.schemas.analysisinterpretations import AnalysisInterpretationSnapshotSchema
  from api.schemas.filterconfigs import FilterConfigSchema
  
  
  class AnalysisStatsResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, user=None):
  
          # Number of alleles
          allele_count = (
              session.query(allele.Allele.id)
              .join(genotype.Genotype.alleles, sample.Sample)
              .filter(sample.Sample.analysis_id == analysis_id)
              .count()
          )
  
          stats = {"allele_count": allele_count}
  
          return stats
  
  
  class AnalysisGenepanelResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, gp_name, gp_version, user=None):
          """
          Returns genepanel for analysis, only including relevant transcripts and phenotypes.
          """
          allele_ids = request.args.get("allele_ids", "")
          if not allele_ids:
              allele_ids = []
          else:
              allele_ids = allele_ids.split(",")
          return helpers.load_genepanel_for_allele_ids(session, allele_ids, gp_name, gp_version)
  
  
  class AnalysisInterpretationAllelesListResource(LogRequestResource):
      @authenticate()
      @paginate
      def get(self, session, analysis_id, interpretation_id, user=None, page=None, per_page=None):
          if (
              not session.query(AnalysisInterpretation)
              .filter(
                  AnalysisInterpretation.id == interpretation_id,
                  AnalysisInterpretation.analysis_id == analysis_id,
              )
              .count()
          ):
              raise ApiError(
                  "Interpretation id {} is not part of analysis with id {}".format(
                      interpretation_id, analysis_id
                  )
              )
          allele_ids = request.args.get("allele_ids").split(",")
          current = request.args.get("current", "").lower() == "true"
          filterconfig_id = request.args.get("filterconfig_id")
          if filterconfig_id is not None:
              filterconfig_id = int(filterconfig_id)
          return (
              helpers.get_alleles(
                  session,
                  allele_ids,
                  user.group.genepanels,
                  analysisinterpretation_id=interpretation_id,
                  current_allele_data=current,
                  filterconfig_id=filterconfig_id,
              ),
              len(allele_ids),
          )
  
  
  class AnalysisInterpretationResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, interpretation_id, user=None):
          """
          Returns analysisinterpretation for analysis.
          ---
          summary: Get analysis interpretation
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
            - name: interpretation_id
              in: path
              type: integer
              description: AnalysisInterpretation id
          responses:
            200:
              schema:
                title: AnalysisInterpretation
                allOf:
                  - $ref: '#/definitions/AnalysisInterpretation'
                  - properties:
                      allele_ids:
                        title: Allele ids
                        type: array
                        description: Allele ids
                        items:
                          type: integer
                      excluded_allele_ids:
                        title: ExcludedAlleles
                        type: object
                        description: Filtered allele ids
                        properties:
                          frequency:
                            type: array
                            items:
                              type: integer
                          region:
                            type: array
                            items:
                              type: integer
                          gene:
                            type: array
                            items:
                              type: integer
  
              description: Interpretation object
          """
          return helpers.get_interpretation(
              session, user.group.genepanels, user.id, analysisinterpretation_id=interpretation_id
          )
  
      @authenticate()
      @request_json(["id"], allowed=["state", "user_state"])
      def patch(self, session, analysis_id, interpretation_id, data=None, user=None):
          """
          Updates the current interpretation inplace.
  
          **Only allowed for interpretations that are `Ongoing`**
          ---
          summary: Update interpretation
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
            - data:
              in: body
              required: true
              schema:
                title: AnalysisInterpretation data
                type: object
                properties:
                  state:
                    description: State data
                    type: object
                  user_state:
                    description: User state data
                    type: object
          responses:
            200:
              type: null
              description: OK
          """
          helpers.update_interpretation(
              session, user.id, data, analysisinterpretation_id=interpretation_id
          )
          session.commit()
  
          return None, 200
  
  
  class AnalysisInterpretationListResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, user=None):
          """
          Returns all interpretations for analysis.
          ---
          summary: Get interpretations
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
          responses:
            200:
              schema:
                type: array
                items:
                  $ref: '#/definitions/AnalysisInterpretation'
  
              description: AnalysisInterpretation objects
          """
          return helpers.get_interpretations(
              session, user.group.genepanels, user.id, analysis_id=analysis_id
          )
  
  
  class AnalysisActionOverrideResource(LogRequestResource):
      @authenticate()
      def post(self, session, analysis_id, user=None):
          """
          Lets an user take over an analysis, by replacing the
          analysis' current interpretation's user_id with the authenticated user_id.
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Assign analysis to another user
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.override_interpretation(session, user.id, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionStartResource(LogRequestResource):
      @authenticate()
      def post(self, session, analysis_id, user=None):
          """
          Starts an analysisinterpretation.
  
          If no analysisinterpretations exists for given analysis id, one is created.
          ---
          summary: Start analysis
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.start_interpretation(session, user.id, {}, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionMarkNotReadyResource(LogRequestResource):
      @authenticate()
      @request_json(
          ["alleleassessment_ids", "annotation_ids", "custom_annotation_ids", "allelereport_ids"]
      )
      def post(self, session, analysis_id, data=None, user=None):
          """
          Marks an analysis as Not ready.
  
          This sets the analysis' current interpretation's status to `Done` and creates
          a new current interpretation with status `Not started` in `Not ready` state.
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Mark analysis as Not ready
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.marknotready_interpretation(session, data, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionMarkInterpretationResource(LogRequestResource):
      @authenticate()
      @request_json(
          ["alleleassessment_ids", "annotation_ids", "custom_annotation_ids", "allelereport_ids"]
      )
      def post(self, session, analysis_id, data=None, user=None):
          """
          Marks an analysis for interpretation.
  
          This sets the analysis' current interpretation's status to `Done` and creates
          a new current interpretation with status `Not started` in `Interpretation` state.
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Mark analysis for interpretation
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.markinterpretation_interpretation(session, data, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionMarkReviewResource(LogRequestResource):
      @authenticate()
      @request_json(
          ["alleleassessment_ids", "annotation_ids", "custom_annotation_ids", "allelereport_ids"]
      )
      def post(self, session, analysis_id, data=None, user=None):
          """
          Marks an analysis for review.
  
          This sets the analysis' current interpretation's status to `Done` and creates
          a new current interpretation with status `Not started` in `Review` state.
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Mark analysis for review
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.markreview_interpretation(session, data, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionMarkMedicalReviewResource(LogRequestResource):
      @authenticate()
      @request_json(
          ["alleleassessment_ids", "annotation_ids", "custom_annotation_ids", "allelereport_ids"]
      )
      def post(self, session, analysis_id, data=None, user=None):
          """
          Marks an analysis for medical review.
  
          This sets the analysis' current interpretation's status to `Done` and creates
          a new current interpretation with status `Not started` in `Medical review` state.
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Mark analysis for medical review
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.markmedicalreview_interpretation(session, data, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionReopenResource(LogRequestResource):
      @authenticate()
      def post(self, session, analysis_id, user=None):
          """
          Reopens an analysis workflow that has previously been finalized.
  
          This creates a new current interpretation for the analysis,
          with status set to `Not started`.
  
  
          **Only works for analyses with a `Ongoing` current interpretation**
          ---
          summary: Reopen analysis workflow
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          helpers.reopen_interpretation(session, workflow_analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisActionFinalizeAlleleResource(LogRequestResource):
      @authenticate(user_config=True)
      @request_json(jsonschema="workflowActionFinalizeAllelePost.json")
      def post(self, session, analysis_id, user_config=None, data=None, user=None):
          """
          Finalizes a single allele within an analysis.
  
          This will create any [alleleassessment|referenceassessment|allelereport] objects for the provided allele id.
  
          **Only works for analyses with a `Ongoing` current interpretation**
  
          ---
          summary: Finalize allele in analysis
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
            - name: data
              in: body
              required: true
              type: object
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          result = helpers.finalize_allele(
              session, user.id, user.group.id, data, user_config, workflow_analysis_id=analysis_id
          )
          session.commit()
  
          return result, 200
  
  
  class AnalysisActionFinalizeResource(LogRequestResource):
      @authenticate(user_config=True)
      @request_json(
          [
              "alleleassessment_ids",
              "allelereport_ids",
              "annotation_ids",
              "custom_annotation_ids",
              "notrelevant_allele_ids",
              "technical_allele_ids",
          ]
      )
      def post(self, session, analysis_id, user_config=None, data=None, user=None):
          """
          Finalizes an analysis workflow.
  
          ---
          summary: Finalize analysis workflow
          tags:
            - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
            - name: data
              in: body
              required: true
              type: object
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
  
          result = helpers.finalize_workflow(
              session, user.id, data, user_config, workflow_analysis_id=analysis_id
          )
          session.commit()
  
          return result, 200
  
      @authenticate()
      def get(self, session, analysis_id, user=None):
          f = (
              session.query(AnalysisInterpretationSnapshot)
              .filter(
                  Analysis.id == analysis_id,
                  tuple_(Analysis.genepanel_name, Analysis.genepanel_version).in_(
                      (gp.name, gp.version) for gp in user.group.genepanels
                  ),
              )
              .join(AnalysisInterpretation, Analysis)
              .all()
          )
  
          result = AnalysisInterpretationSnapshotSchema(strict=True).dump(f, many=True).data
          return result
  
  
  class AnalysisCollisionResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, user=None):
  
          allele_ids = request.args.get("allele_ids")
          if allele_ids is None:
              raise ApiError("Missing required arg allele_ids")
  
          if not allele_ids:
              return []
  
          allele_ids = [int(i) for i in allele_ids.split(",")]
  
          return helpers.get_workflow_allele_collisions(session, allele_ids, analysis_id=analysis_id)
  
  
  class AnalysisInterpretationFinishAllowedResource(LogRequestResource):
      @authenticate()
      @rest_filter
      def get(self, session, analysis_id, interpretation_id, rest_filter=None, data=None, user=None):
          sample_ids = (
              session.query(sample.Sample.id).filter(sample.Sample.analysis_id == analysis_id).all()
          )
          sample_ids = [s[0] for s in sample_ids]
  
          if not sample_ids == rest_filter["sample_ids"]:
              raise ConflictError(
                  "Can not finish interpretation. Additional data have been added to this analysis. Please refresh."
              )
          else:
              return None, 200
  
  
  class AnalysisInterpretationLogListResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id, user=None):
          """
          Get all interpreation log entries for an analysis workflow.
  
          ---
          summary: Get interpretation log
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
          logs = helpers.get_interpretationlog(session, user.id, analysis_id=analysis_id)
  
          return logs, 200
  
      @authenticate()
      @request_json([], allowed=["warning_cleared", "priority", "message", "review_comment"])
      def post(self, session, analysis_id, data=None, user=None):
          """
          Create a new interpretation log entry for an analysis workflow.
  
          ---
          summary: Create interpretation log
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
          helpers.create_interpretationlog(session, user.id, data, analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisInterpretationLogResource(LogRequestResource):
      @authenticate()
      @request_json(["message"])
      def patch(self, session, analysis_id, log_id, data=None, user=None):
          """
          Patch an interpretation log entry.
  
          ---
          summary: Patch interpretation log
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
          helpers.patch_interpretationlog(
              session, user.id, log_id, data["message"], analysis_id=analysis_id
          )
          session.commit()
  
          return None, 200
  
      @authenticate()
      def delete(self, session, analysis_id, log_id, user=None):
          """
          Delete an interpretation log entry.
  
          ---
          summary: Create interpretation log
          tags:
              - Workflow
          parameters:
            - name: analysis_id
              in: path
              type: integer
              description: Analysis id
            - name: interpretationlog_id
              in: path
              type: integer
              description: Interpretation log id
  
          responses:
            200:
              description: Returns null
            500:
              description: Error
          """
          helpers.delete_interpretationlog(session, user.id, log_id, analysis_id=analysis_id)
          session.commit()
  
          return None, 200
  
  
  class AnalysisInterpretationFilteredAlleles(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id=None, interpretation_id=None, user=None):
          interpretation = (
              session.query(AnalysisInterpretation)
              .filter(AnalysisInterpretation.id == interpretation_id)
              .one()
          )
  
          filterconfig_id = request.args.get("filterconfig_id")
          if filterconfig_id is not None:
              filterconfig_id = int(filterconfig_id)
  
          allele_ids, excluded_allele_ids = helpers.get_filtered_alleles(
              session, interpretation, filter_config_id=filterconfig_id
          )
          result = {"allele_ids": allele_ids, "excluded_allele_ids": excluded_allele_ids}
  
          return result
  
  
  class AnalysisFilterConfigResource(LogRequestResource):
      @authenticate()
      def get(self, session, analysis_id=None, user=None):
          filterconfigs = queries.get_valid_filter_configs(
              session, user.group_id, analysis_id=analysis_id
          ).all()
          if not filterconfigs:
              raise ApiError("Unable to find filter config matching analysis {}".format(analysis_id))
          return FilterConfigSchema().dump(filterconfigs, many=True).data
  