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taigapy
Library for reading from taiga in python
See here for installing taigr, the library for reading from taiga in R
Token set up
First, you need to get your authorization token so the client library can make requests on your behalf. Go to https://cds.team/taiga/token/ and click on the "Copy" button to copy your token. Paste your token in a file at ~/.taiga/token
.
mkdir ~/.taiga/
echo YOUR_TOKEN_HERE > ~/.taiga/token
Installing Taigapy
If you are only using Taigapy and not making modifications to it, run
pip install taigapy
If you are developing Taigapy, check out the repo and run
python setup.py develop
Use Taigapy
You can now fetch from taiga in python.
Main methods
Download
- If you need a specific file (table or matrix) from a specific dataset version, use
.get
method - If you need all the files from a specific dataset version, use
.get_all
method - If you need a raw file, we will give you the path to it with
.download_to_cache
method since we don't know what the format of your file is
Example:
from taigapy import TaigaClient
tc = TaigaClient() # These two steps could be merged in one with `from taigapy import default_tc as tc`
# fetch by ID a full dataset
df = tc.get(id='6d9a6104-e2f8-45cf-9002-df3bcedcb80b')
# fetch by name a full version of a dataset
df1 = tc.get(name='achilles-v2-4-6', version=4)
# fetch a specific data file
# If Raw file, use download_to_cache, which will give you the path of the file
raw_path = tc.download_to_cache(name='taigr-data-40f2', version=3, file="raw_file")
# Else, if CSV convertible
df = tc.get(name='taigr-data-40f2', version=1, file="tiny_table")
# name and version can serve as the id using name.version
df = tc.get(id='achilles-v2-4-6.4')
# the file can also be specified in the id using name.version/file
# id/file (as in 6d9a6104-e2f8-45cf-9002-df3bcedcb80b/tiny_table) is also not supported in either
df = tc.get(id='taigr-data-40f2.1/tiny_table')
Upload
You can also upload data into taiga (see below for available formats). Methods are:
- Create a dataset with
create_dataset
- Update a dataset with
update_dataset
Example:
- Create a new dataset in folder public (you can find the folder_id in the url of Taiga web)
from taigapy import TaigaClient
tc = TaigaClient()
# Create a new dataset in public
tc.create_dataset(dataset_name='My Dataset Name',
dataset_description='My Dataset Description',
upload_file_path_dict={'file_one_path': 'format'}, folder_id='public')
- Update a dataset with new files, interactively, in public folder (default)
from taigapy import TaigaClient
tc = TaigaClient()
tc.update_dataset(dataset_id=dataset_id, upload_file_path_dict={'file_updated_or_new_path': 'format'},
dataset_description="Interactive test")
- Update a dataset with new files, keeping all previous files, in a specific folder:
from taigapy import TaigaClient
tc = TaigaClient()
tc.update_dataset(dataset_id=dataset_id, upload_file_path_dict={'file_new_path': 'format'},
dataset_description="Force Keep",
force_keep=True)
- Update a dataset with new files, removing all previous files, in a specific folder:
from taigapy import TaigaClient
tc = TaigaClient()
tc.update_dataset(dataset_id=dataset_id, upload_file_path_dict={'file_updated_or_new_path': 'format'},
dataset_description="Force Remove",
force_remove=True)
- Update a dataset with new files, based on its permaname and version
from taigapy import TaigaClient
tc = TaigaClient()
tc.update_dataset(dataset_permaname=dataset_permaname, dataset_version=2,
upload_file_path_dict={'file_updated_or_new_path': 'format'},
dataset_description="Update a specific version")
- Update a dataset with new files, based on its permaname only (will update from the latest version)
from taigapy import TaigaClient
tc = TaigaClient()
tc.update_dataset(dataset_permaname=dataset_permaname,
upload_file_path_dict={'file_updated_or_new_path': 'format'},
dataset_description="Update from latest")
Virtual dataset creation and update
Requires version 2.8.1 of taigapy
from taigapy import TaigaClient
tc = TaigaClient()
# To create a virtual dataset
tc.create_virtual_dataset(name="internal_19Q2", description="The DepMap internal 19Q2 release", aliases=[
("CCLE_gene_cn", "segmented-cn-wes-prioritzed-7fe1.24/CCLE_internal_19q2_gene_cn"),
("CCLE_segmented_cn", "segmented-cn-wes-prioritzed-7fe1.24/CCLE_internal_19q2_segmented_cn")
], folder_id="21eeb52951984bfa9219b2c251c27df3")
# To add to a virtual dataset
tc.update_virtual_dataset('internal-19q2-9504', new_aliases=[
('CCLE_gene_cn', 'segmented-cn-wes-prioritzed-7fe1.25/CCLE_internal_19q2_gene_cn')
]
)
# To remove from a virtual dataset
# can simultaneously be provided with new_aliases
tc.update_virtual_dataset('internal-19q2-9504', names_to_drop=['CCLE_gene_cn'])
Available formats
Formats available currently are:
- NumericMatrixCSV
- NumericMatrixTSV
- TableCSV
- TableTSV
- GCT
- Raw
Running Taigapy via Command line
Run python -m taigapy -h
to have an up to date help.
Create a new dataset
python -m taigapy create -n dataset_name -f {'file_path_one': 'format', ...}
Update an existing dataset
python -m taigapy update -p dataset_permaname -v dataset_version -f {'file_path_one': 'format', ...}
Get a dataset from Taiga
python -m taigapy get -p dataset_permaname -v dataset_version -f file_name -t format
[Important] Please choose a format available for this specific file in taiga Web UI
Publish Taigapy on pypi
pip install twine
(not to be confused with the interactive fiction software called twine)
Execute: publish_new_taigapy_pypi.sh
which will do the following:
rm -r dist/
python setup.py bdist_wheel --universal
twine upload dist/*
More Taigapy information:
Confluence: https://confluence.broadinstitute.org/display/CPDS/Taiga
Running tests:
pytest
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