Implemented a Streamflow Executor

Modified the CWL executor so that it's Streamflow/RO-Crate friendly
Updated Dockerfiles (images have been pushed)
Minor fixes here and there

Author: henricasanova

pyproject.toml

@@ -26,6 +26,7 @@ license = {text = "GNU General Public License v3 (GPLv3)"}
 dependencies = [
     "jsonschema",
     "matplotlib",
+    "pygraphviz",
     "networkx",
     "numpy",
     "pandas",

tests/translators_loggers/Dockerfile.airflow

@@ -1,5 +1,5 @@
-# docker build -t wfcommons-dev -f Dockerfile.airflow .
-# docker run -it --rm -v .:/home/wfcommons/mount wfcommons-dev /bin/bash
+# docker build -t wfcommons-dev-airflow -f Dockerfile.airflow .
+# docker run -it --rm -v .:/home/wfcommons/mount wfcommons-dev-airflow /bin/bash
 
 FROM amd64/ubuntu:noble
 
@@ -21,12 +21,14 @@ RUN apt-get -y install cmake-data
 RUN apt-get -y install sudo 
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
+RUN apt-get -y install graphviz libgraphviz-dev
+
 #RUN apt-get -y install gcc-multilib
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 

tests/translators_loggers/Dockerfile.bash

@@ -22,12 +22,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.cwl

@@ -1,5 +1,5 @@
-# docker build --platform amd64 -t wfcommons-dev-dask -f Dockerfile.dask .
-# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-dask /bin/bash
+# docker build --platform amd64 -t wfcommons-dev-cwl -f Dockerfile.cwl .
+# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-cwl /bin/bash
 
 FROM amd64/ubuntu:noble
 
@@ -22,12 +22,13 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.dask

@@ -22,12 +22,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.makeflow

@@ -1,5 +1,5 @@
-# docker build --platform amd64 -t wfcommons-dev -f Dockerfile.parsl .
-# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev /bin/bash
+# docker build --platform amd64 -t wfcommons-dev-makeflow -f Dockerfile.makeflow .
+# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-makeflow /bin/bash
 
 FROM amd64/ubuntu:noble
 
@@ -23,12 +23,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.nextflow

@@ -23,12 +23,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN pip install --break-system-packages pathos pandas filelock 
-RUN pip install --break-system-packages networkx scipy matplotlib
+RUN pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.parsl

@@ -1,5 +1,5 @@
-# docker build --platform amd64 -t wfcommons-dev -f Dockerfile.parsl .
-# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev /bin/bash
+# docker build --platform amd64 -t wfcommons-dev-parsl -f Dockerfile.parsl .
+# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-parsl /bin/bash
 
 FROM amd64/ubuntu:noble
 
@@ -22,12 +22,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.pegasus

@@ -1,5 +1,5 @@
-# docker build --platform amd64 -t wfcommons-dev-dask -f Dockerfile.dask .
-# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-dask /bin/bash
+# docker build --platform amd64 -t wfcommons-dev-pegasus -f Dockerfile.pegasus .
+# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-pegasus /bin/bash
 
 FROM amd64/ubuntu:noble
 
@@ -22,12 +22,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install --break-system-packages pathos pandas filelock
-RUN python3 -m pip install --break-system-packages networkx scipy matplotlib
+RUN python3 -m pip install --break-system-packages networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install --break-system-packages pyyaml jsonschema requests
 RUN python3 -m pip install --break-system-packages --upgrade setuptools
 

tests/translators_loggers/Dockerfile.pycompss

@@ -1,5 +1,5 @@
-# docker build --platform amd64 -t wfcommons-dev-dask -f Dockerfile.dask .
-# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-dask /bin/bash
+# docker build --platform amd64 -t wfcommons-dev-pycompss -f Dockerfile.pycompss .
+# docker run -it --rm -v `pwd`:/home/wfcommons wfcommons-dev-pycompss /bin/bash
 
 FROM compss/pycompss
 
@@ -22,12 +22,14 @@ RUN apt-get -y install sudo
 RUN apt-get -y install vim --fix-missing
 RUN apt-get -y install gcc 
 RUN apt-get -y install gcc-multilib
+RUN apt-get -y install graphviz libgraphviz-dev
+
 
 # Python stuff
 RUN apt-get -y install python3 python3-pip
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
 RUN python3 -m pip install pathos pandas filelock
-RUN python3 -m pip install networkx scipy matplotlib
+RUN python3 -m pip install networkx scipy matplotlib pygraphviz
 RUN python3 -m pip install pyyaml jsonschema requests
 #RUN python3 -m pip install --upgrade setuptools
 #RUN python3 -m pip install --upgrade wheels