Python Direct Runner doesn't support both streaming & non streaming sources

Please see Stack Overflow discussion:

[https://stackoverflow.com/questions/68125864/transform-node-appliedptransform-was-not-replaced-as-expected-error-with-the-dir](https://stackoverflow.com/questions/68125864/transform-node-appliedptransform-was-not-replaced-as-expected-error-with-the-dir)

When I create a GCS source & a Pub Source and try to flatten both, there is an error because of some incompatible transformation done by the direct runner.

Code example:
```

gcsEventsColl = p | "Read from GCS" >> beam.io.ReadFromText("gs://sample_events_for_beam/*.log") \

| 'convert to dict' >> beam.Map(lambda x: json.loads(x))
liveEventsColl = p | "Read
from Pubsub" >> beam.io.ReadFromPubSub(topic="projects/axxxx/topics/input_topic") \

| 'convert to dict2' >> beam.Map(lambda x: json.loads(x))

input_rec = (gcsEventsColl, liveEventsColl)
| 'flatten' >> beam.Flatten()

```

Error:
```

File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 564, in run
return self.runner.run_pipeline(self, self._options)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/runners/direct/direct_runner.py",
line 131, in run_pipeline
return runner.run_pipeline(pipeline, options)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/runners/direct/direct_runner.py",
line 529, in run_pipeline
pipeline.replace_all(_get_transform_overrides(options))
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 504, in replace_all
self._check_replacement(override)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 478, in _check_replacement
self.visit(ReplacementValidator())
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 611, in visit
self._root_transform().visit(visitor, self, visited)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 1195, in visit
part.visit(visitor, pipeline, visited)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 1195, in visit
part.visit(visitor, pipeline, visited)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 1195, in visit
part.visit(visitor, pipeline, visited) [Previous line repeated 4 more times]

File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 1198, in visit
visitor.visit_transform(self)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/apache_beam/pipeline.py",
line 476, in visit_transform
transform_node) RuntimeError: Transform node AppliedPTransform(Read
from GCS/Read/SDFBoundedSourceReader/ParDo(SDFBoundedSourceDoFn)/ProcessKeyedElements/GroupByKey/GroupByKey,

_GroupByKeyOnly) was not replaced as expected.

```

The direct runner corrupts the pipeline when it rewrites the transforms.

Imported from Jira [BEAM-12586](https://issues.apache.org/jira/browse/BEAM-12586). Original Jira may contain additional context.
Reported by: rodriguezc.

Reproduce the mixed GCS ReadFromText and Pub/Sub ReadFromPubSub pipeline with Flatten, then inspect the replacement path in apache_beam/runners/direct/direct_runner.py and validation in apache_beam/pipeline.py. Done means the Direct Runner handles this pipeline without the AppliedPTransform replacement error and includes coverage for the case.

Written by the indexing model from the issue text.