mpkocher

Arch Overview

Core Nouns of the PacBio System

1. Run (often created/edited from SMRT Link RunDesign, stored as XML)
2. CollectionMetadata a Run has a list of Collection (Primary Analysis will convert a CollectionMetadata to a SubreadSet)
3. PacBio DataSets SubreadSet, ReferenceSet, etc... These are thin-ish XML files that have general metadata as well as pointers to 'external resources' (e.g., BAM, Fasta files) and their companion index files.
4. SMRT Link Job A general (async) unit of work to perform operations on PacBio DataSets
5. ** DataStoreFile** a container for output files from a SMRT Link Job and contains metadata, such as file type, size, path. A list of DataStore Files is called a DataStore. This is the core output of SMRT Link Job.
6. ** Report** a Report is general model to capture Report metrics (also referred to as 'Attributes'), Report Tables and Report Plot Groups. A Report is a specific type of DataStoreFile and are used to communicate details of

mpkocher

@ import akka.http.scaladsl.model.Uri 
import akka.http.scaladsl.model.Uri

@ val u = Uri("http://smrtlink-bihourly:8081") 
u: Uri = Uri("http", Authority(NamedHost("smrtlink-bihourly"), 8081, ""), , None, None)

@ val p1 = Uri.Path("root") / "alpha" / "beta" 
p1: Uri.Path = Segment("root", Slash(Segment("alpha", Slash(Segment("beta", )))))

@ val p2 =  p1 / "gamma" 

mpkocher

Manual creation of sending TS

1. Get Failed Job By Id
2. Use pbservice to create a TS failed job request
3. Manually download the TGZ file from the Job UI page or curl
4. Manulally send TGZ file using `tech-support-uploader'

From SL beta.

mpkocher

#!/usr/bin/env python
import logging
import sys

from pbcommand.services import ServiceAccessLayer as S
from pbcore.io.dataset import SubreadSet

log = logging.getLogger(__name__)

mpkocher

#!/usr/bin/env python
import json
import sys
import argparse
import os
import operator


def extract_table_values(dt, column_id):
    for column_d in dt['columns']:

mpkocher

#!/usr/bin/env python
"""Tool for Scrapping Jobs and DataSets from a SMRT Link instance"""
import argparse
import base64
import datetime
import sys
import json
import os
import time
import functools

mpkocher

SMRT Link Dependencies

DOT Legend

Shape (and Color)	Description
RECT DOTTED	Third party dependency
OVAL GREEN	Build Output
RECT	BitBucket Repo

mpkocher

09:33 $ python /Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py log
(pbsmrtpipe_test) ✔ ~/scratch_pad/verify-bugs/SL-1512 
09:33 $ python /Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py dir-that-does-not-exist
ls: cannot access 'dir-that-does-not-exist': No such file or directory
Traceback (most recent call last):
  File "/Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py", line 19, in <module>
    sys.exit(main(argv=sys.argv[1:]))
  File "/Users/mkocher/repos/pbcommand/extras/validation_argparse_option_example.py", line 14, in main
    p.parse_args(argv)
  File "/Users/mkocher/miniconda2/envs/pbsmrtpipe_test/lib/python2.7/argparse.py", line 1701, in parse_args

mpkocher

#!/bin/bash

declare -a packages=("devtools" "knitr" "ggplot2" "mplot" "googleVis" "data.table" "caret" "pRoc" "sqldf" "glmnet")
declare -a ghpackages=("ramnathv/rCharts")

for i in "${packages[$@]}"; do
  echo "Attempting to install '${i}'"
  R -e "install.packages('${i}', repos = 'http://cran.us.r-project.org')"
done

mpkocher

import hashlib
import hmac
import math
import datetime
import base64


def to_h(secret, method, segment, t=None):
    """
    Example: