With the Partek Flow REST API, you can create custom solutions to query or drive your server. Below are some common use cases for the REST API:
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A complete list of all the commands available reference for the API can be found on the REST API Command List. The public key and Python libraries or by visiting [server]/api/v1/servlets
The referenced Python library can be downloaded here.
Generate an authentication token
An access token can be generated from the System information section of the settings page.
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Alternatively, GetToken.py will generate a token:
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python GetToken.py --server localhost:8080 --user admin |
Example output:
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TOKEN: cUOWY0VvkSFagrDUANVtM7A8SPal8Gx0cf0ee24bfa9fe68e2b5564dab2b6a27e1fb525e5... |
you will be prompted to enter your password.
This token can be specified as the --password parameter for the Python API. If the token is not supplied, then the Python API will prompt for the password and encrypt it.When accessing the API directly, the encrypt parameter must be specified with the RSA value to use the token: token parameter.
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curl --form username=admin --form encrypt=RSA --form password=token=cUOWY0VvkSFagr... http://localhost:8080/flow/api/v1/users/list |
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curl -X POST --form username=admin --form encrypt=RSA --form password=token=$FLOW_TOKEN --form project="My Project" http://localhost:8080/flow/api/v1/projects |
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python UploadSamples.py --verbose --user admin --password token $FLOW_TOKEN --server http://localhost:8080 --project "My Project" \
--files ~/MoreData/REST/sample1.fastq.gz ~/MoreData/REST/sample2.fastq.gz ~/MoreData/REST/sample3.fastq.gz ~/MoreData/REST/sample4.fastq.gz |
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python AddAttribute.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --project_name "My Project" --sample_name sample1 --attribute Type --value Case
python AddAttribute.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --project_name "My Project" --sample_name sample2 --attribute Type --value Case
python AddAttribute.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --project_name "My Project" --sample_name sample3 --attribute Type --value Control
python AddAttribute.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --project_name "My Project" --sample_name sample4 --attribute Type --value Control
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python RunPipeline.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --project_id 0 --pipeline AlignAndQuantify --inputs 102,103 |
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python UploadSamples.py -v --server http://localhost:8080 --user admin --password token $FLOW_TOKEN --files ~/sampleA.fastq.gz ~/sampleB.fastq.gz --project NewProject --pipeline AlignAndQuantify --inputs 102,103 |
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curl -X PUT "http://localhost:8080/flow/api/v1/projects?project=ProjectName&collaborator=user1&role=Collaborator&username=admin&encrypt=RSA&password=[url encoded token]token=$FLOW_TOKEN" |
Monitor a folder and upload files as they are created
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#!/bin/bash
inotifywait -m $PATH_TO_MONITOR -e create -e moved_to |
while read path action file; do
if [[ $file == *.fastq.gz ]]; then
echo "Uploading $file"
python UploadSamples.py -v --server $SERVER --usertoken $USER$FLOW_TOKEN --password $TOKEN --files $path/$file --project "$PROJECT"
fi
done |
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#!/bin/bash
while true; do
result=`python QueueStatistics.py --server $SERVER --user $USER --password token $TOKEN --max_waiting $MAX_WAITING`
if [ $? -eq 1 ]; then
/usr/bin/notify-send $result
exit 1
fi
sleep $INTERVAL
done |
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