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leoschwarz committed Oct 16, 2024
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![unitTests](https://github.com/fgcz/bfabricPy/workflows/unit%20tests/badge.svg)
[![PR Checks](https://github.com/fgcz/bfabricPy/actions/workflows/run_unit_tests.yml/badge.svg)](https://github.com/fgcz/bfabricPy/actions/workflows/run_unit_tests.yml)
[![Nightly Integration Tests](https://github.com/fgcz/bfabricPy-tests/actions/workflows/nightly_tests.yml/badge.svg)](https://github.com/fgcz/bfabricPy-tests/actions/workflows/nightly_tests.yml)
[![EDBT'10](https://img.shields.io/badge/EDBT-10.1145%2F1739041.1739135-brightgreen)](https://doi.org/10.1145/1739041.1739135)
[![JIB](https://img.shields.io/badge/JIB-10.1515%2Fjib.2022.0031-brightgreen)](https://doi.org/10.1515/jib-2022-0031)

Expand All @@ -10,262 +11,6 @@ For more advanced users the *bfabricPy* package also provides a powerful query i

You can find the up-to-date documentation at [https://fgcz.github.io/bfabricPy](https://fgcz.github.io/bfabricPy).

## CheatSheet

### Read

```{bash}
bfabric_read.py storage
bfabric_read.py application
```

Simple database query examples

```{bash}
bfabric_read.py user login cpanse
bfabric_read.py project id 3000
bfabric_read.py workunit id 199387
bfabric_read.py sample name autoQC4L
bfabric_read.py workunit status processing
bfabric_read.py workunit status pending
bfabric_read.py workunit status failed
# list empty resources
bfabric_read.py resource filechecksum d41d8cd98f00b204e9800998ecf8427e
```

Using the Python API:

```{py}
from bfabric import Bfabric
client = Bfabric.from_config()
user = client.read(endpoint = 'user', obj={'login': 'cpanse'})
resource = client.read(endpoint = 'resource', obj={'id': 550327 })
```

### save

```{bash}
bfabric_save_workunit_attribute.py 199387 status available
```

```{python}
import json
rv = client.save('workunit', {'id': 254063, 'status': 'available'})
print(json.dumps(rv.to_list_dict(), indent=2))
```

### Command line code snippet

Find empty resource files in bfabric

```{bash}
bfabric_read.py resource filechecksum `md5sum < /dev/null | cut -c-32` \
| cat -n \
| tail
```

## Examples \[outdated\]

### bash script generated by the yaml wrapper creator / submitter

externaljobid-45939_executableid-15312.bash listing:

```bash
#!/bin/bash
#
# $HeadURL: http://fgcz-svn.uzh.ch/repos/scripts/trunk/linux/bfabric/apps/python/README.md $
# $Id: README.md 2535 2016-10-24 08:49:17Z cpanse $
# Christian Panse <[email protected]> 2007-2015

# Grid Engine Parameters
#$ -q PRX@fgcz-c-071
#$ -e /home/bfabric/sgeworker/logs/workunitid-134923_resourceid-203236.err
#$ -o /home/bfabric/sgeworker/logs/workunitid-134923_resourceid-203236.out


set -e
set -o pipefail

export EXTERNALJOBID=45938
export RESSOURCEID_OUTPUT=203238
export RESSOURCEID_STDOUT_STDERR="203237 203238"
export OUTPUT="[email protected]:/srv/www/htdocs//p1000/bfabric/Proteomics/gerneric_yaml/2015/2015-09/2015-09-02//workunit_134923//203236.zip"

# job configuration set by B-Fabrics wrapper_creator executable
_OUTPUT=`echo $OUTPUT | cut -d"," -f1`
test $? -eq 0 && _OUTPUTHOST=`echo $_OUTPUT | cut -d":" -f1`
test $? -eq 0 && _OUTPUTPATH=`echo $_OUTPUT | cut -d":" -f2`
test $? -eq 0 && _OUTPUTPATH=`dirname $_OUTPUTPATH`
test $? -eq 0 && ssh $_OUTPUTHOST "mkdir -p $_OUTPUTPATH"

if [ $? -eq 1 ];
then
echo "writting to output url failed!";
exit 1;
fi

cat > /tmp/yaml_config.$$ <<EOF
application:
input:
mascot_dat:
- [email protected]//usr/local/mascot/:/data/20150807/F221967.dat
- [email protected]//usr/local/mascot/:/data/20150807/F221973.dat
output:
- [email protected]:/srv/www/htdocs//p1000/bfabric/Proteomics/gerneric_yaml/2015/2015-09/2015-09-02//workunit_134923//203236.zip
parameters:
gelcms: 'true'
mudpit: 'false'
qmodel: None
xtandem: 'false'
protocol: scp
job_configuration:
executable: /usr/local/fgcz/proteomics/bin/fgcz_scaffold.bash
external_job_id: 45938
input:
mascot_dat:
- 201919
- 201918
output:
protocol: scp
resource_id: 203238
ssh_args: -o StrictHostKeyChecking=no -c arcfour -2 -l bfabric -x
stderr:
protocol: file
resource_id: 203237
url: /home/bfabric/sgeworker/logs/workunitid-134923_resourceid-203236.err
stdout:
protocol: file
resource_id: 203238
url: /home/bfabric/sgeworker/logs/workunitid-134923_resourceid-203236.out
workunit_id: 134923
EOF

# debug / host statistics
hostname
uptime
echo $0
pwd

# run the application
test -f /tmp/yaml_config.$$ && /usr/local/fgcz/proteomics/bin/fgcz_scaffold.bash /tmp/yaml_config.$$

if [ $? -eq 0 ];
then
/home/bfabric/.python/fgcz_bfabric_setResourceStatus_available.py $RESSOURCEID_OUTPUT
/home/bfabric/.python/fgcz_bfabric_setExternalJobStatus_done.py $EXTERNALJOBID
else
echo "application failed"
/home/bfabric/.python/fgcz_bfabric_setResourceStatus_available.py $RESSOURCEID_STDOUT_STDERR $RESSOURCEID;
exit 1;
fi


# Should be available also as zero byte files

/home/bfabric/.python/fgcz_bfabric_setResourceStatus_available.py $RESSOURCEID_STDOUT_STDERR

exit 0
```

### curl example

```{bash}
#!/bin/bash
query(){
url=$1 \
&& curl \
${url} \
-v \
--header "Content-Type: text/xml;charset=UTF-8" \
--header "SOAPAction: read" \
-d '
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:end="http://endpoint.webservice.component.bfabric.org/">
<soapenv:Header/>
<soapenv:Body>
<end:read>
<parameters>
<login>XXX</login>
<password>XXX</password>
<query>
<id>482</id>
</query>
</parameters>
</end:read>
</soapenv:Body>
</soapenv:Envelope>'
}
for url in https://fgcz-bfabric.uzh.ch/bfabric/user?wsdl https://fgcz-bfabric-test.uzh.ch/bfabric/user?wsdl;
do
echo
echo "==== ${url} === "
query ${url}
done
echo $?
```

### Example usage

remove accidentally inserted mgf files

```
bfabric_read.py importresource \
| grep mgf$ \
| awk '{print $1}' \
| tee /tmp/$$.log \
| while read i;
do
bfabric_delete.py importresource $i ;
done
```

## Send an E-mail \[outdated\]

```
# by CT,CP
# not implemented yet 2022-10-19 ,
rv = B.save_object(endpoint = 'mail',
obj={'subject': "TEST",
'recipientemail': '[email protected]',
'message': "TEST; ignore that email",
'parentId': 482,
'parentClassName': 'user'})
# shown as mail for user id 482
```

## See also

- [bfabric documentation](https://fgcz-bfabric.uzh.ch/wiki/HomePage)
- [FAQ](faq.md)
- [wsdl4BFabric](http://fgcz-intranet.uzh.ch/tiki-index.php?page=wsdl4BFabric) wiki page
- WSDL Interface to B-Fabric [endpoints](http://fgcz-bfabric.uzh.ch/bfabric/workunit?wsdl)

## FAQ

### How to resolve `<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed`?

on macOSX

```
cd /Applications/Python 3.12 && ./Install\ Certificates.command
```

### How is the version numbering working?

X.Y.Z

X is used for major changes, that contain breaking changes

Y should be the current bfabric release

Z is increased for feature releases, that should not break the API

### Howto cite?
# Howto cite?

Panse, Christian, Trachsel, Christian and Türker, Can. "Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences" Journal of Integrative Bioinformatics, 2022, pp. 20220031. [doi: 10.1515/jib-2022-0031](https://doi.org/10.1515/jib-2022-0031).
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