Kenneth Daily kdaily

## semi-annual-usage-report.Rmd
---
title: "AMP-AD Semi-Annual Report"
author: "Kenneth Daily"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE,
                      message = FALSE,

## fastq-to-bam-add-provenance.R
library(synapseClient)
synapseLogin()

table_id <- "syn7871084"
fileview_df <- synTableQuery(sprintf('select * from %s', table_id))@values

fastq2bam <- fileview_df %>%
    filter(fileFormat %in% c("fastq", "bam")) %>% # keep fastq and bam
    # group for cases where there are multiple files per file format
    group_by(sample_id_biorepository,

## mergesort.py
class Counter(object):
    value = 0

def mergeSort(myList):
    if len(myList) > 1:
        depth.value += 1

        mid = (len(myList) + 1) // 2
        left = myList[:mid]
        right = myList[mid:]

## linkedlist.py
"""Linked list.

"""

from collections.abc import Sequence
import logging

logging.basicConfig()
logger = logging.getLogger(__name__)
logger.setLevel(level=logging.INFO)

## bootstrap-genie-project.py
"""Bootstrap the components of a project to be used with the GENIE framework.

"""

import synapseclient
import genie
import pandas
import random
import tempfile

## batch_file_request_download.py
"""Example code for using Synapse pre-signed URLs to download directly.

This only uses the Synapse Python client to perform the POST operation to get
the pre-signed URLs and generate signed headers. The `requests` library is used
to fetch the file.

"""

import synapseclient
import json

## remove_veoibd_submissions.py
"""Script to remove all artifacts of submissionf for a center.
"""

import logging

import synapseclient
import genie.config

logging.basicConfig()
logger = logging.getLogger(__name__)

## dog.jpg

      
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                kdaily
                / dog.jpg
            
            
              Created
              July 7, 2019 22:12
            
              
                Test upload of two dog pictures, one JPG and one PNG
              
          
## filter-missing-size-md5.R
library(tidyr)
library(dplyr)
library(readr)
library(synapser)
synLogin()

id <- 'syn19034850'

obj <- synGet(id)
d <- readr::read_csv(obj$path)

## validate_syn18486863.sh
# Uses https://gist.github.com/kdaily/fea5b0f72fac1264048e39e6c4d04647#file-query_to_json-py
query_to_json.py "select assay,Level,CellLine,DataType from syn18486863" > /tmp/syn18486863_file_annotations.json

# uses ajv-cli - https://github.com/jessedc/ajv-cli
ajv validate -s file_annotations_file_schema.json -r file_annotation.json -d /tmp/syn18486863_file_annotations.json --errors=line
	---
	title: "AMP-AD Semi-Annual Report"
	author: "Kenneth Daily"
	date: "`r format(Sys.time(), '%B %d, %Y')`"
	output: html_document
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = FALSE,
	message = FALSE,
	library(synapseClient)
	synapseLogin()

	table_id <- "syn7871084"
	fileview_df <- synTableQuery(sprintf('select * from %s', table_id))@values

	fastq2bam <- fileview_df %>%
	filter(fileFormat %in% c("fastq", "bam")) %>% # keep fastq and bam
	# group for cases where there are multiple files per file format
	group_by(sample_id_biorepository,
	class Counter(object):
	value = 0

	def mergeSort(myList):
	if len(myList) > 1:
	depth.value += 1

	mid = (len(myList) + 1) // 2
	left = myList[:mid]
	right = myList[mid:]
	"""Linked list.

	"""

	from collections.abc import Sequence
	import logging

	logging.basicConfig()
	logger = logging.getLogger(__name__)
	logger.setLevel(level=logging.INFO)
	"""Bootstrap the components of a project to be used with the GENIE framework.

	"""

	import synapseclient
	import genie
	import pandas
	import random
	import tempfile
	"""Example code for using Synapse pre-signed URLs to download directly.

	This only uses the Synapse Python client to perform the POST operation to get
	the pre-signed URLs and generate signed headers. The `requests` library is used
	to fetch the file.

	"""

	import synapseclient
	import json
	"""Script to remove all artifacts of submissionf for a center.
	"""

	import logging

	import synapseclient
	import genie.config

	logging.basicConfig()
	logger = logging.getLogger(__name__)
	library(tidyr)
	library(dplyr)
	library(readr)
	library(synapser)
	synLogin()

	id <- 'syn19034850'

	obj <- synGet(id)
	d <- readr::read_csv(obj$path)
	# Uses https://gist.github.com/kdaily/fea5b0f72fac1264048e39e6c4d04647#file-query_to_json-py
	query_to_json.py "select assay,Level,CellLine,DataType from syn18486863" > /tmp/syn18486863_file_annotations.json

	# uses ajv-cli - https://github.com/jessedc/ajv-cli
	ajv validate -s file_annotations_file_schema.json -r file_annotation.json -d /tmp/syn18486863_file_annotations.json --errors=line