Moving From DAX3 to DAX4

Changes:

moved from camelCase to snake_case for functions
job.uses(file, link=Link.INPUT) is now job.uses(file, type=LinkType.INPUT)
job.uses(file, type=LinkType.INPUT, transfer=True, register=True) is now job.uses(file, type=LinkType.INPUT, stage_out=True, register_replica=True
add_PFN(PFN("uri", "site_name")) is now just add_pfn(*uris, site="local"))
add_profile(Profile(namespace, key, value)) is now just add_profile(namespace, key, value)
job.uses(....) is now split up into job.add_inputs(*inputs) and job.add_outputs(*outputs, stage_out=True, register_replica=True) (stage_out and register_replica would apply to all of *outputs, and so this can be called multiple times if different values of stage_out and register_replica must be set for some subset of *outputs)
transformation.uses(exec) is now transformation.uses(*execs)
obj.metadata(key, value) is now obj.add_metadata(key, value)
dag.depends(parent=some_parent, child=some_child) is now dag.add_dependency(parent, *children)

Given what we have in DAX4 (middle column below), we could rewrite it to be something like what we have in the right most column below. Functionality it is the same. At least in this example, it looks a little less cluttered and simpler to read than the middle column while saving a few lines in the process...

DAX3 Black Diamond

#!/usr/bin/env python

from Pegasus.DAX3 import *

# Create a DAX
diamond = ADAG("diamond")

# Add some metadata
diamond.metadata("name", "diamond")
diamond.metadata("createdby", "Gideon Juve")

# Add input file to the DAX-level replica catalog
a = File("f.a")
a.addPFN(PFN("gsiftp://site.com/inputs/f.a","site"))
a.metadata("size", "1024")
diamond.addFile(a)

# Add executables to the DAX-level replica catalog
e_preprocess = Executable(namespace="diamond", name="preprocess", version="4.0", os="linux", arch="x86_64")
e_preprocess.metadata("size", "2048")
e_preprocess.addPFN(PFN("gsiftp://site.com/bin/preprocess","site"))
diamond.addExecutable(e_preprocess)

e_findrange = Executable(namespace="diamond", name="findrange", version="4.0", os="linux", arch="x86_64")
e_findrange.addPFN(PFN("gsiftp://site.com/bin/findrange","site"))
diamond.addExecutable(e_findrange)

e_analyze = Executable(namespace="diamond", name="analyze", version="4.0", os="linux", arch="x86_64")
e_analyze.addPFN(PFN("gsiftp://site.com/bin/analyze","site"))
diamond.addExecutable(e_analyze)

# Add a preprocess job
preprocess = Job(e_preprocess)
preprocess.addProfile(Profile(Namespace.DAGMAN, "RETRY", 0))
preprocess.metadata("time", "60")
b1 = File("f.b1")
b2 = File("f.b2")
preprocess.addArguments("-a preprocess","-T60","-i",a,"-o",b1,b2)
preprocess.uses(a, link=Link.INPUT)
preprocess.uses(b1, link=Link.OUTPUT, transfer=True)
preprocess.uses(b2, link=Link.OUTPUT, transfer=True)
diamond.addJob(preprocess)

# Add left Findrange job
frl = Job(e_findrange)
frl.metadata("time", "60")
c1 = File("f.c1")
frl.addArguments("-a findrange","-T60","-i",b1,"-o",c1)
frl.uses(b1, link=Link.INPUT)
frl.uses(c1, link=Link.OUTPUT, transfer=True)
diamond.addJob(frl)

# Add right Findrange job
frr = Job(e_findrange)
frr.metadata("time", "60")
c2 = File("f.c2")
frr.addArguments("-a findrange","-T60","-i",b2,"-o",c2)
frr.uses(b2, link=Link.INPUT)
frr.uses(c2, link=Link.OUTPUT, transfer=True)
diamond.addJob(frr)

# Add Analyze job
analyze = Job(e_analyze)
analyze.metadata("time", "60")
d = File("f.d")
analyze.addArguments("-a analyze","-T60","-i",c1,c2,"-o",d)
analyze.uses(c1, link=Link.INPUT)
analyze.uses(c2, link=Link.INPUT)
analyze.uses(d, link=Link.OUTPUT, transfer=True, register=True)
diamond.addJob(analyze)

# Add dependencies
diamond.depends(parent=preprocess, child=frl)
diamond.depends(parent=preprocess, child=frr)
diamond.depends(parent=frl, child=analyze)
diamond.depends(parent=frr, child=analyze)

# Write the DAX to stdout
import sys
diamond.writeXML(sys.stdout)

# Write the DAX to a file
f = open("diamond.dax","w")
diamond.writeXML(f)
f.close()

DAX4 Black Diamond

#!/usr/bin/env python

from Pegasus.DAX4 import *

# Create a DAX
diamond = Workflow("diamond")

# Add some metadata
diamond.add_metadata("name", "diamond")
diamond.add_metadata("createdby", "Gideon Juve")

# Add input file to the DAX-level replica catalog
a = File("f.a")
a.add_PFN("gsiftp://site.com/inputs/f.a","site")
a.add_metadata("size", "1024")
diamond.add_file(a)

# Add executables to the DAX-level replica catalog
e_preprocess = Transformation(namespace="diamond", name="preprocess", version="4.0", os="linux", arch="x86_64")
e_preprocess.add_metadata("size", "2048")
e_preprocess.add_PFN("gsiftp://site.com/bin/preprocess","site")
diamond.add_transformation(e_preprocess)

e_findrange = Transformation(namespace="diamond", name="findrange", version="4.0", os="linux", arch="x86_64")
e_findrange.add_PFN("gsiftp://site.com/bin/findrange","site")
diamond.add_transformation(e_findrange)

e_analyze = Transformation(namespace="diamond", name="analyze", version="4.0", os="linux", arch="x86_64")
e_analyze.add_PFN("gsiftp://site.com/bin/analyze","site")
diamond.add_transformation(e_analyze)

# Add a preprocess job
preprocess = Job(e_preprocess)
preprocess.add_profile(Namespace.DAGMAN, "RETRY", 0)
preprocess.add_metadata("time", "60")
b1 = File("f.b1")
b2 = File("f.b2")
preprocess.add_arguments("-a preprocess","-T60","-i",a,"-o",b1,b2)
preprocess.add_inputs(a)
preprocess.add_outputs(b1, b2, stage_out=True, register_replica=False)
diamond.add_job(preprocess)

# Add left Findrange job
frl = Job(e_findrange)
frl.add_metadata("time", "60")
c1 = File("f.c1")
frl.add_arguments("-a findrange","-T60","-i",b1,"-o",c1)
frl.add_inputs(b1)
frl.add_outputs(c1, stage_out=True)
diamond.add_job(frl)

# Add right Findrange job
frr = Job(e_findrange)
frr.add_metadata("time", "60")
c2 = File("f.c2")
frr.add_arguments("-a findrange","-T60","-i",b2,"-o",c2)
frr.add_inputs(b2)
frr.add_outputs(c3, stage_out=True)
diamond.add_job(frr)

# Add Analyze job
analyze = Job(e_analyze)
analyze.add_metadata("time", "60")
d = File("f.d")
analyze.add_arguments("-a analyze","-T60","-i",c1,c2,"-o",d)
analyze.add_inputs(c1, c2)
analyze.add_outputs(d, stage_out=True, register_replica=True)
diamond.add_job(analyze)

# Add dependencies
diamond.add_dependency(preprocess, frl, frr) # Workflow.add_dependency(parent, *children)
diamond.add_dependency(frl, analyze) # Workflow.add_dependency(parent, *children)
diamond.add_dependency(frr, analyze) # Workflow.add_dependency(parent, *children)

# Write the DAX to stdout
import sys
diamond.write_yaml(sys.stdout)

# Write the DAX to a file
f = open("diamond.yml","w")
diamond.write_yaml(f)
f.close()

DAX4 Black Diamond, catalogs included

'''
------- Catalogs -------
Pegasus.DAX4.SiteCatalog
- add_site(name)
- get_site(name)
- has_site(name)
- write_catalog(path)
...

Pegasus.DAX4.ReplicaCatalog
- add_replica(lfn, iri, site, regex=false)
- get_replica(lfn)
- has_replica(lfn)
- remove_replica(lfn)
- write_catalog(path)
...

Pegasus.DAX4.TransformationCatalog
- add_transformation(namespace, name, version, os, arch, ...)
- get_transformation(namespace, name, version, os, arch, ...)
- has_transformation(namespace, name, version, os, arch, ...)
- remove_transformation(namespace, name, version, os, arch, ...)
- write_catalog(path)
...

------- Workflow -------
Pegasus.DAX4.Workflow <------ requires only 'pegasus' (version), 'name', and 'jobs' (jobs and parent-child dependencies)
- add_job(transformation, *args)
- add_dependency(parent, *children)
- add_site_catalog(sc)            # add inline OR iri if string is given
- add_replica_catalog(rc)         # add inline
- add_transformation_catalog(tc)  # add inline
...

'''


#!/usr/bin/env python

from Pegasus.DAX4 import *

# Create a DAX
diamond = Workflow("diamond")

# Add some metadata
diamond.add_metadata("name", "diamond")\
    .add_metadata("createdby", "Gideon Juve")

# Add input file to the replica_catalog
rc = ReplicaCatalog()
a = rc.add_file("f.a", "gsiftp://site.com/inputs/f.a", "site", regex=False)\
        .add_metadata("size", "1024")

# Add executables to the transformation catalog
tc = TransformationCatalog()
e_preprocess = tc.add_transformation(namespace="diamond", name="preprocess", version="4.0", os="linux", arch="x86_64")\
                .add_metadata("size", "2048")\
                .add_site(site="site", uri="gsiftp://site.com/bin/preprocess", type="installed")

e_findrange = tc.add_transformation(namespace="diamond", name="findrange", version="4.0", os="linux", arch="x86_64")\
                .add_site(site="site", uri="gsiftp://site.com/bin/findrange", type="installed")

e_analyze = tc.add_transformation(namespace="diamond", name="analyze", version="4.0", os="linux", arch="x86_64")\
                .add_site(site="site", uri="gsiftp://site.com/bin/analyze", type="installed")

# Add a preprocess job
b1 = File("f.b1")
b2 = File("f.b2")
preprocess = diamond.add_job(e_preprocess, "-a preprocess", "-T60", "-i", a, "-o", b1, b2)\ # ADAG.add_job(exec, *args)
                .add_profile(Namespace.DAGMAN, "RETRY", 0)\
                .add_metadata("time", "60")\
                .add_inputs(a)\
                .add_outputs(b1, b2, stage_out=True, register_replica=False) # job.add_outputs(*lfns, stage_out=True, register_replica=False)

# Add left Findrange job
c1 = File("f.c1")
frl = diamond.add_job(e_findrange, "-a findrange", "-T60", "-i", b1, "-o", c1)\ # ADAG.add_job(exec, *args)
        .add_metadata("time", "60")\
        .add_inputs(b1)\
        .add_outputs(c1, stage_out=True)

# Add right Findrange job
c2 = File("f.c2")
frr = diamond.add_job(e_findrange, "-a findrange", "-T60", "-i", b2, "-o", c2)\ # ADAG.add_job(exec, *args)
        .add_metadata("time", "60")\
        .add_inputs(b2)\
        .add_outputs(c2, stage_out=True)\

# Add Analyze job
d = File("f.d")
analyze = diamond.add_job(e_analyze, *["-a analyze", "-T60", "-i", c1, c2, "-o", d])\ # ADAG.add_job(exec, *args)
            .add_metadata("time", "60")\
            .add_inputs(c1, c2)\
            .add_outputs(d, stage_out=True, register_replica=True)

# Add dependencies
diamond.add_dependency(preprocess, frl, frr)\
    .add_dependency(frl, analyze)\
    .add_dependency(frr, analyze)


If you wanted the catalogs inline, then:
diamond.add_replica_catalog(rc)
diamond.add_transformation_catalog(tc)
diamond.add_site_catalog(sc) # not defined above, but if it was


# Write the DAX to a file
f = open("diamond.yml","w")
diamond.write_yaml(f)
f.close()

'''
# Additionally, we could use contextlib and rewrite like the following:
with ReplicaCatalog("rc.yml") as rc, \
     SiteCatalog("sc.yml") as sc, \
     TransformationCatalog("tc.yml") as tc, \
     Workflow("diamond") as wf:

     # do stuff

# with block ends and all the catalogs + workflow are written to separate files
'''

DAX3 Invokes

from Pegasus.DAX3 import *

# Create a DAX
adag = ADAG("workflow")

# Add invoke
adag.addInvoke(Invoke("start", "/usr/bin/echo hello"))
# adag.invoke("start", "/usr/bin/echo hello")

DAX4 Hooks

from Pegasus.DAX4 import *

# Create a DAX
adag = Workflow("workflow")

# Add shell hook
adag.add_shell_hook("start", "/usr/bin/echo hello")

# Add web hook hook
adag.add_webhook_hook("start", ...)

DAX3 Transformations

from Pegasus.DAX3 import *

# Create a DAX
adag = ADAG("workflow")

# Create some executables
e1 = Executable("executable_1")
e2 = Executable("executable_2")
e3 = Executable("executable_3")

# Create a transformation
t = Transformation(e3)
t.uses(e1)
t.uses(e2)
t.uses(e3)

DAX4 Transformations

from Pegasus.DAX4 import *

# Create a DAX
adag = Workflow("workflow")

# Create some transformations
e1 = Transformation("executable_1")
e2 = Transformation("executable_2")


# Create a transformation that requires other transformations
t = Transformation("executable_3")
t.requires(e1, e2)

Jobs

'''
Trying to be declarative, but then workflow.add(...) might need to be
workflow.jobs(Job(...)) to be consistent. Don't like how the function names
aren't verbs.
'''
job = workflow.add(Job(transformation, arguments))\
    .profiles(namespace, "key", "value")\
    .metadata({"time": "60"})\
    .metadata({"key": "value"})\
    .hooks(ShellHook(args))\
    .inputs(a)\
    .outputs(b1, b2, stage_out=True)

'''
Verbose, explicitly stating operations on job.
The following two assignments are the same.
'''
job = workflow.add_job(transformation, arguments...)\
    .add_profile(namespace, "key", "value")\
    .add_metadata(**{"time": "60", "key": "value"})\
    .add_shell_hook(args)\
    .add_inputs(a)\
    .add_outputs(b1, b2, stage_out=True)

job = workflow.add_job(Job(transformation, args))\
    .add_profile(Profile(namespace, "key", "value"))\
    .add_metadata(*[Metadata("time", "60"), Metadata("key", "value")])\
    .add_shell_hook(args)\
    .add_inputs(a)\
    .add_outputs(b1, b2, stage_out=True)

'''
List/Set semantics.Can't chain as job.<member>.add(something) won't
return back a ref to the job (unless we make it but that would look awkward)
'''
job = workflow.add(Job(transformation, arguments))
# List semantics for (job.args)
job.arguments.append("A") 
job.arguments.extend( ["A", "B"] )
# Set semantics for (job.profiles)
job.profiles.add(namespace, "key", "value")
# Dict semantics for job.{<namespace>,metadata}.*
job.env.key = "value"
job.env["key"] = "value" 
job.env.update( {"key1": "value1", "key2": "value2"} )
job.metadata.add({"time": "60"})
job.metadata.add({"key": "value"})
job.hooks.add(ShellHook(args))
job.inputs.add(a)
job.outputs.add(b1, b2, stage_out=True)

Child pages

Moving From DAX3 to DAX4