kdaily

---
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,

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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,

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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:]

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"""Linked list.

"""

from collections.abc import Sequence
import logging

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

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"""Bootstrap the components of a project to be used with the GENIE framework.

"""

import synapseclient
import genie
import pandas
import random
import tempfile

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"""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

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

import logging

import synapseclient
import genie.config

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

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library(tidyr)
library(dplyr)
library(readr)
library(synapser)
synLogin()

id <- 'syn19034850'

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

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# 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