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Alternatively, GetToken.py will generate a token:
| Code Block | ||
|---|---|---|
| ||
python GetToken.py --server localhost:8080 --user admin |
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When accessing the API directly, the encrypt parameter must be specified with the RSA value to use the token:
| Code Block | ||
|---|---|---|
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curl --form username=admin --form encrypt=RSA --form password=cUOWY0VvkSFagr... http://localhost:8080/flow/api/v1/users/list |
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Use UploadSamples.py to upload the samples and launch the pipeline:
| Code Block | ||
|---|---|---|
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python UploadSamples.py -v --server http://localhost:8080 --user admin --password [access token] --files ~/sample1.fastq.gz ~/sample2.fastq.gz --project ProjectName --pipeline AlignAndQuantify --inputs 28061,145855 |
Use AddAttribute.py to add sample attributes:
| Code Block | ||
|---|---|---|
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python AddAttribute.py -v --server http://localhost:8080 --user admin --password [access token] --project_name ProjectName --sample_name sample1 --attribute Type --value Case |
Add a collaborator to a project
To add a collaborator to a project:
| Code Block | ||
|---|---|---|
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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]" |
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Monitor a folder and upload files as they are created
| Code Block | ||
|---|---|---|
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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 --user $USER --password $TOKEN --files $path/$file --project "$PROJECT"
fi
done |
Monitor the queue and send a notification if there are too many waiting tasks:
| Code Block | ||
|---|---|---|
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#!/bin/bash
while true; do
result=`python QueueStatistics.py --server $SERVER --user $USER --password $TOKEN --max_waiting $MAX_WAITING`
if [ $? -eq 1 ]; then
/usr/bin/notify-send $result
exit 1
fi
sleep $INTERVAL
done |
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