cbare

## follow redirects, including rePOSTing, with the requests library.
######################################################################

import requests

## authentication with no redirects
ans = requests.post(url=endp_prod + "/session", data=json.dumps(d), headers=h)

## results in a successful login
ans.status_code

cbare

## first, let's dump some data into a file
python generate_random_data.py > data.txt

## Create a project in synapse
synapse create -name "provenance test project" Project

## Add a couple of entities to our project, first a Data entity...
synapse add -parentid syn1661878 -name "data.txt" -description "My randomly generated data" data.txt

## ...and a Code entity that holds the script

cbare

## Loading with files in the R synapse client
##################################################

## If you haven't already, install the synapse R client
# source('http://depot.sagebase.org/CRAN.R')
# pkgInstall(c("synapseClient"))

library(synapseClient)

## list the files in a project

cbare

##
## upload a file with the synapse fileHandle service
############################################################

## import the synapse library and sign in
import synapseclient
syn = synapseclient.Synapse()
syn.login('[email protected]', 'secret')

## the file we're going to upload

cbare

class Dynamic(dict):
  """Dynamic objects are just bags of properties, some of which may happen to be functions"""
  def __init__(self, **kwargs):
    self.__dict__ = self
    self.update(kwargs)

  def __setattr__(self, name, value):
    import types    
    if isinstance(value, types.FunctionType):
      self[name] = types.MethodType(value, self)

cbare

import synapseclient
import re, sys
import requests

syn = synapseclient.Synapse()
syn.login('[email protected]', 'secret')

repoEndPoint = 'https://repo-prod.prod.sagebase.org/repo/v1'

headers = {'Accept': 'application/json', 'sessionToken': syn.sessionToken}

cbare

##
## example session with the python synapse client
## Note: You'll have to insert your credentials and a project ID
######################################################################

## import the synapse library and sign in
import synapseclient
syn = synapseclient.Synapse()
syn.login('[email protected]', 'secret')

cbare

## An example of regular expressions using capture groups
## in R. See:
## http://stackoverflow.com/questions/14700799/r-regex-gsub-extract-part-of-pattern/14714370#14714370
############################################################

# example data
data <-
"Station       lat        lon
1940    K01R    31-08N    092-34W
1941    K01T    28-08N    094-24W

cbare

Playing with Earthquake Data
========================================================

This is a little example inspired by Jeff Leek's [Data analysis class](https://class.coursera.org/dataanalysis-001/). Jeff pointed us towards some data from the [US Geological Survey](http://www.usgs.gov/) on earthquakes. I believe these are the earthquakes for the last 7 days. I decided to see what I could do with it.

```{r}
fileUrl <- "http://earthquake.usgs.gov/earthquakes/catalogs/eqs7day-M1.txt"
download.file(fileUrl,destfile="./data/earthquake_7day.csv",method="curl")
eq <- read.csv("./data/earthquake_7day.csv")
```

cbare

import collections


class DictObject(collections.MutableMapping):
    def __init__(self, *args, **kwargs):
        for arg in args:
            if isinstance(arg, collections.Mapping):
                self.__dict__.update(arg)
        self.__dict__.update(kwargs)