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MedBook Platform for Cancer Data Capture, Analysis and Sharing

Project description

MedBookLib provides a python interface to MedBook (R version should come next).

PYTHON

MedBookConnection(<name optional>, <password optional>)
You begin the conversation by creating a MedBook Connection object which will be used

MedBookConnection("ted@soe.ucsc.edu", "test1234");

or using the MedBook environment variables: MEDBOOKUSER, MEDBOOKPASSWORD

medbook = MedBookConnection();

This will throw an exception object if it does not make authenticated connection to the MedBook server.

`
MedBookConnection.find(<collection required>, <mongo query optional>, <keyword querys optional>)

The simplest find command will return all of the data objects in a collection. For example

data = medbook.find("Clinical_Info");



Some tables such as Expression2 are very large and if just need one gene from one study, you can do this by simply doing:

data = medbook.find("Expression2", { "Study_ID": "prad_wcdt", "gene": "BRCA1" });


This can be more easily expressed using the python keyword idiom:

data = medbook.find("Expression2", Study_ID="prad_wcdt", gene="BRCA1");


But use the mongo syntax to express complicated queriess,

data = medbook.find("Expression2", { "Study_ID": {"$in": [ "prad_tcga", "prad_wcdt"] }, "gene": { "$in": ["EGFR","BRCA1"]}});


You cannot combine keyword queries and mongo queries.



OPTIONAL ENVIRONEMNT VARIABLE CREDENTIALS
You must provide credentials to MedBook in the form of a name and password. There are two ways
to do this:

Preferred way: Set the MEDBOOKUSER and MEDBOOKPASSWORD environment variables. For exmaple:
export MEDBOOKUSER=ted@soe.ucsc.edu
export MEDBOOKPASSWORD=test1234


There is also a MEDBOOKSERVER environment variable. If no server is specificed
The default server is https://medbook.ucsc.edu. But you can also set the server to be your laptop.

Common ones are:

export MEDBOOKSERVER=https://su2c-dev.ucsc.edu/

export MEDBOOKSERVER=http://su2c-dev.ucsc.edu:20012/

export MEDBOOKSERVER=http://localhost:20012/

Alternatively, you can provide the name and password in the parameters of the MedBookConnection object (see above).



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