mpkocher

import spray.http.HttpMethods._
import spray.http.{HttpResponse, HttpMethod, HttpMethods, AllOrigins}
import spray.http.HttpHeaders.{`Access-Control-Allow-Methods`, `Access-Control-Max-Age`, `Access-Control-Allow-Headers`, `Access-Control-Allow-Origin`}
import spray.routing._
import spray.routing.directives.BasicDirectives

/**
 * Forked from
 *
 * https://gist.github.com/joseraya/176821d856b43b1cfe19

mpkocher

from pbcore.io import FastaReader, BamReader

def to_records(reader_klass, transform_func, file_name):
    with reader_klass(file_name) as r:
        for record in r:
            yield transform_func(record)

def bam_record_to_fasta_record(b_record):
    # fill me in here
    return b_record

mpkocher

"""Simple CLI dev app for testing"""

import logging
import sys

from pbsystem.common.cmdline.core2 import (get_default_parser,
                                           pacbio_args_or_contract_runner,
                                           add_resolved_tool_contract_option)
from pbsystem.common.utils import setup_log
from pbsystem.common.validators import validate_file

mpkocher

// This is all write by hand and probably has typos. 
// The general idea is to show how it composes and how other
// system that extend the core services can choose which implementations
// of the coreservice DAOs to use
trait CoreServiceDaos {
  val logDao: LogDao
  val healthDao: HealthDao
}

mpkocher

import json
import logging

from pbcommand.models import TaskTypes, FileTypes, get_default_contract_parser

log = logging.getLogger(__name__)

TOOL_ID = "pbcommand.tools.dev_mixed_app"
__version__ = "0.2.0"

mpkocher

from pbcommand.models import get_default_contract_parser, TaskTypes, ResourceTypes, FileTypes
from pbcommand.validators import validate_file

def get_pbparser():
    driver_exe = "my-exe"
    p = get_default_contract_parser("pbexample.tasks.my_tool", "My Tool Desc", "0.1.0", driver_exe, TaskTypes.LOCAL, 1, ())
    return p

def add_common(p):
    p.add_input_file_type(FileTypes.DS_BAM, "algn_ds", "Alignment DataSet", "Alignment Set Desc")

mpkocher

library(methods)

#' @export
ExampleRegistry <- setRefClass("ExampleRegistry", fields=list(namespace="character", driver="character", rtcRunners="list", toolContracts="list"))


registerFunc <- function(r, funcId, func) {
  r$rtcRunners[[funcId]] <- func
  return(r)
}

mpkocher

pbcommand High Level Overview

Full Docs

Note the APIs are still in flux. WIP.

PacBio library for common utils, models, and tools to interface with pbsmrtpipe workflow engine.

mpkocher

import os
import re
import abc
import logging
import h5py
import json
import collections
import gzip
from tarfile import TarFile
from xml.etree.ElementTree import ElementTree

mpkocher

class InValidMetricError(Exception):
    pass

class TestReportMetric(TestBase):
    REPORT_ID = ""
    DEFAULT_VALUES = {}
    # this will be populated via metaclass or @monkey_metrics model
    RULES = []
    
    def _apply_rules(self, rules):