Merge pull request #229 from dianakolusheva/gromet

EMMAA to GroMEt

.github/workflows/tests.yml

@@ -56,6 +56,10 @@ jobs:
         cd ../indralab_web_templates
         pip install .
         cd ../..
+        git clone https://github.com/ml4ai/automates.git
+        cd automates
+        git checkout claytonm/gromet
+        cd ..
         pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage moto[iam] sqlalchemy_utils termcolor flask-cors
         pip install --no-dependencies .
         pip install -U sqlalchemy==1.3.23
@@ -69,7 +73,7 @@ jobs:
         export AWS_DEFAULT_REGION='us-east-1'
         export NOSEATTR="!notravis"
         export NOSEATTR=$(if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then echo $NOSEATTR,!nonpublic; else echo $NOSEATTR; fi)
-        export PYTHONPATH=$PYTHONPATH:`pwd`/covid-19:`pwd`/kappy:`pwd`/indra_world
+        export PYTHONPATH=$PYTHONPATH:`pwd`/covid-19:`pwd`/kappy:`pwd`/indra_world:`pwd`/automates/scripts
         export BNGPATH=`pwd`/BioNetGen-2.4.0
         export INDRA_WM_CACHE="."
         nosetests -v -a $NOSEATTR emmaa/tests/test_s3.py

.gitignore

@@ -113,3 +113,4 @@ emmaa/tests/test_query_delta.html
 emmaa/tests/new_test_query_delta.txt
 emmaa/tests/trips_output.xml
 trips_output.xml
+emmaa/tests/gromet_test.json

Dockerfile

@@ -29,6 +29,12 @@ RUN git clone https://github.com/pagreene/pgcopy.git && \
 # Install covid-19
 RUN git clone https://github.com/indralab/covid-19.git
 
+# Install automates
+RUN git clone https://github.com/ml4ai/automates.git && \
+    cd automates && \
+    git checkout claytonm/gromet && \
+    cd ..
+
 # Clone and install EMMAA
 RUN pip install git+https://github.com/indralab/indra_db.git[misc] && \
     pip install git+https://github.com/sorgerlab/bioagents.git && \

doc/model_config.rst

@@ -78,7 +78,7 @@ First level fields of config.json
 
 - `export_formats` : list[str], optional
     A list of formats the model can be exported to. Accepted values include:
-    `indranet`, `pybel`, `sbml`, `kappa`, `kappa_im`, `kappa_cm`,
+    `indranet`, `pybel`, `sbml`, `kappa`, `kappa_im`, `kappa_cm`, `gromet`,
     `bngl`, `sbgn`, `pysb_flat`, `kappa_ui`. Note that `kappa_ui` option does
     not generate a separate export file but adds a link to Kappa interactive
     UI that uses model's kappa export (generated if `kappa` is in this list).

emmaa/model.py

@@ -4,6 +4,7 @@
 import datetime
 import pybel
 from botocore.exceptions import ClientError
+from sqlalchemy.sql.functions import mode
 from indra.databases import ndex_client
 from indra.literature import pubmed_client, elsevier_client, biorxiv_client
 from indra.assemblers.cx import CxAssembler
@@ -542,10 +543,14 @@ def assemble_pysb(self, mode='local', bucket=EMMAA_BUCKET_NAME):
         if mode == 's3':
             for exp_f in self.export_formats:
                 if exp_f not in {'sbml', 'kappa', 'kappa_im', 'kappa_cm',
-                                 'bngl', 'sbgn', 'pysb_flat'}:
+                                 'bngl', 'sbgn', 'pysb_flat', 'gromet'}:
                     continue
-                fname = f'{exp_f}_{self.date_str}.{exp_f}'
-                pa.export_model(exp_f, fname)
+                elif exp_f == 'gromet':
+                    fname = f'gromet_{self.date_str}.json'
+                    pysb_to_gromet(pysb_model, self.name, fname)
+                else:
+                    fname = f'{exp_f}_{self.date_str}.{exp_f}'
+                    pa.export_model(exp_f, fname)
                 logger.info(f'Uploading {fname}')
                 client = get_s3_client(unsigned=False)
                 client.upload_file(fname, bucket,
@@ -922,3 +927,121 @@ def load_custom_grounding_map(model, bucket=EMMAA_BUCKET_NAME):
 def get_search_term_names(model, bucket=EMMAA_BUCKET_NAME):
     config = load_config_from_s3(model, bucket=bucket)
     return [st['name'] for st in config['search_terms']]
+
+
+def pysb_to_gromet(pysb_model, model_name, fname=None):
+    """Convert PySB model to GroMEt object and save it to a JSON file.
+
+    Parameters
+    ----------
+    pysb_model : pysb.Model
+        PySB model object.
+    model_name : str
+        A name of EMMAA model.
+    fname : Optional[str]
+        If given, the GroMEt will be dumped into JSON file.
+
+    Returns
+    -------
+    g : automates.script.gromet.gromet.Gromet
+        A GroMEt object built from PySB model.
+    """
+    from gromet.gromet import Gromet, gromet_to_json, \
+        Junction, Wire, UidJunction, UidType, UidWire, Relation, \
+        UidBox, UidGromet, Literal, Val
+    from pysb import Parameter
+    from pysb.bng import generate_equations
+
+    generate_equations(pysb_model)
+
+    junctions = []
+    wires = []
+    # Get all species values
+    species_values = {}
+    for initial in pysb_model.initials:
+        ix = pysb_model.get_species_index(initial.pattern)
+        if initial.value:
+            species_values[ix] = Literal(
+                uid=None, type=UidType("T:Integer"),
+                value=Val(initial.value.value),
+                name=None, metadata=None)
+    # Store species names to refer later
+    species_nodes = [str(sp) for sp in pysb_model.species]
+    # Add all species junctions (uid and name are the same for now)
+    for ix, sp in enumerate(species_nodes):
+        junctions.append(Junction(uid=UidJunction(sp),
+                                  type=UidType('State'),
+                                  name=sp,
+                                  value=species_values.get(ix),
+                                  value_type=UidType('T:Integer'),
+                                  metadata=None))
+    # Add all rate junctions (uid and name are the same for now)
+    junctions += [Junction(uid=UidJunction(par.name),
+                           type=UidType('Rate'),
+                           name=par.name,
+                           value=Literal(uid=None,
+                                         type=UidType("T:Float"),
+                                         value=Val(par.value),
+                                         name=None,
+                                         metadata=None),
+                           value_type=UidType('T:Float'),
+                           metadata=None)
+                  for par in pysb_model.parameters]
+    # Add wires for each reaction
+    for rxn in pysb_model.reactions:
+        rate_params = [rate_term for rate_term in rxn['rate'].args
+                       if isinstance(rate_term, Parameter)]
+        assert len(rate_params) == 1
+        rate_node = rate_params[0].name
+        # Add wires from reactant to rate
+        for reactant_ix in rxn['reactants']:
+            reactant = species_nodes[reactant_ix]
+            wires.append(Wire(uid=UidWire(f'{reactant}_{rate_node}'),
+                              type=None,
+                              value_type=None,
+                              name=None,
+                              value=None,
+                              metadata=None,
+                              src=UidJunction(reactant),
+                              tgt=UidJunction(rate_node)))
+        # Add wires from rate to product
+        for prod_ix in rxn['products']:
+            prod = species_nodes[prod_ix]
+            wires.append(Wire(uid=UidWire(f'{rate_node}_{prod}'),
+                              type=None,
+                              value_type=None,
+                              name=None,
+                              value=None,
+                              metadata=None,
+                              src=UidJunction(rate_node),
+                              tgt=UidJunction(prod)))
+    # Create relation
+    pnc = Relation(uid=UidBox(model_name),
+                   type=UidType("PetriNetClassic"),
+                   name=model_name,
+                   ports=None,
+                   # contents
+                   junctions=[j.uid for j in junctions],
+                   wires=[w.uid for w in wires],
+                   boxes=None,
+                   metadata=None)
+    boxes = [pnc]
+    # Create Gromet object
+    g = Gromet(
+        uid=UidGromet(f'{model_name}_pnc'),
+        name=model_name,
+        type=UidType("PetriNetClassic"),
+        root=pnc.uid,
+        types=None,
+        literals=None,
+        junctions=junctions,
+        ports=None,
+        wires=wires,
+        boxes=boxes,
+        variables=None,
+        metadata=None
+    )
+    # Optionally save Gromet to JSON file
+    if fname:
+        gromet_to_json(g, fname)
+    return g

emmaa/tests/test_model.py

@@ -1,7 +1,7 @@
 import datetime
 from indra.statements import Activation, ActivityCondition, Phosphorylation, \
     Agent, Evidence
-from emmaa.model import EmmaaModel
+from emmaa.model import EmmaaModel, pysb_to_gromet
 from emmaa.priors import SearchTerm
 from emmaa.statements import EmmaaStatement
 
@@ -135,3 +135,23 @@ def test_papers():
     # Add more paper_ids from reading
     emmaa_model.add_paper_ids({'4567', '5678'}, id_type='TRID')
     assert len(emmaa_model.paper_ids) == 5
+
+
+def test_pysb_to_gromet():
+    from gromet.gromet import Gromet
+    emmaa_model = create_model()
+    pysb_model = emmaa_model.assemble_pysb()
+    gromet = pysb_to_gromet(pysb_model, 'test_model', 'gromet_test.json')
+    assert isinstance(gromet, Gromet)
+    # Test PySB properties are correctly represented in GroMEt
+    # Model species and parameters match junctions
+    assert len(pysb_model.species) == 5
+    assert len(pysb_model.parameters) == 5
+    assert len(gromet.junctions) == 10
+    assert len([j for j in gromet.junctions if j.type == 'State']) == 5
+    assert len([j for j in gromet.junctions if j.type == 'Rate']) == 5
+    # Number of wires match total number of reactants and products in reactions
+    assert len(pysb_model.reactions) == 2
+    assert sum([len(r['reactants']) + len(r['products'])
+                for r in pysb_model.reactions]) == 8
+    assert len(gromet.wires) == 8