check_setup.template.json

{
    "item_counts_by_type": {
        "title": "Item counts by type",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "indexing_progress": {
        "title": "Indexing progress",
        "group": "Elasticsearch Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "status_of_elasticsearch_indices": {
        "title": "Status of elasticsearch indices",
        "group": "Elasticsearch Checks",
        "conditions": [
            "put_env"
        ],
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "indexing_records": {
        "title": "Indexing records",
        "group": "Elasticsearch Checks",
        "conditions": [
            "put_env"
        ],
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "change_in_item_counts": {
        "title": "Change in item counts",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "page_children_routes": {
        "title": "Pages with bad routes",
        "group": "Audit Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "workflow_properties": {
        "title": "Workflows with missing or duplicate steps properties",
        "group": "Audit Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "check_validation_errors": {
        "title": "Search for Validation Errors",
        "group": "Audit Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "check_suggested_enum_values": {
        "title": "Check fields with suggested enum",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "ingest_vcf_status": {
        "title": "d) CGAP trigger VCF ingestion",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "elastic_search_space": {
        "title": "ES Disk Space Check",
        "group": "Elasticsearch Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "elasticsearch_s3_count_diff": {
        "title": "S3/ES Check Count Differential",
        "group": "Elasticsearch Checks",
        "schedule": {
            "morning_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        }
    },
    "clean_s3_es_checks": {
        "title": "Wipe Checks Older Than One Month",
        "group": "System Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "core_project_status": {
        "title": "Ensure CGAP Core project items are shared",
        "group": "Metadata Checks",
        "schedule": {
            "morning_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "item_type": [
                            "VariantSample",
                            "Case",
                            "Family",
                            "Individual",
                            "WorkflowRun",
                            "FileFastq",
                            "FileProcessed",
                            "Sample",
                            "SampleProcessing",
                            "Report",
                            "QualityMetric",
                            "FilterSet"
                        ]
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "workflow_run_has_deleted_input_file": {
        "title": "WorkflowRun linked to deleted Files",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "update_variant_genelist": {
        "title": "Add gene lists to variants/variant samples",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    }
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "long_running_wfrs_status": {
        "title": "x) Long Running Runs",
        "group": "Pipeline Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "ecs_status": {
        "title": "ECS Status",
        "group": "ECS Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "update_ecs_application_versions": {
        "title": "Update ECS Cluster Application Versions",
        "group": "ECS Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "metawfrs_to_run": {
        "title": "Metawfrs_to_run",
        "group": "Pipeline Checks",
        "schedule": {
            "fifteen_min_checks_3": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "metawfrs_to_checkstatus": {
        "title": "Metawfrs to check status",
        "group": "Pipeline Checks",
        "schedule": {
            "fifteen_min_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "failed_metawfrs": {
        "title": "Failed Metawfrs",
        "group": "Pipeline Checks",
        "schedule": {
            "fifteen_min_checks_2": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "spot_failed_metawfrs": {
        "title": "Spot-failed Metawfrs",
        "group": "Pipeline Checks",
        "schedule": {
            "fifteen_min_checks_2": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "metawfrs_to_patch_samples": {
        "title": "Metawfrs to patch samples with processed files",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks_2": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "SNV_metawfrs_to_patch_sample_processing": {
        "title": "SNV metawfrs to patch sample processing with processed files",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks_2": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "SV_metawfrs_to_patch_sample_processing": {
        "title": "SV metawfrs to patch sample processing with processed files",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks_2": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "metawfrs_to_check_linecount": {
        "title": "Metawfrs to run line count qc",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true,
                        "queue_action": "prod"
                    },
                    "dependencies": []
                }
            }
        }
    },
    "md5runCGAP_status": {
        "title": "a) md5 runs",
        "group": "Pipeline Checks",
        "schedule": {
            "hourly_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        }
    },
    "get_metadata_for_cases_to_clone": {
        "title": "Get Clone Case Metadata",
        "group": "Metadata Checks",
        "schedule": {
            "manual_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    },
    "snapshot_rds": {
        "title": "Snapshot RDS",
        "group": "System Checks",
        "schedule": {
            "monthly_checks": {
                "<env-name>": {
                    "kwargs": {
                        "primary": true
                    },
                    "dependencies": []
                }
            }
        },
        "display": [
            "<env-name>"
        ]
    }
}