updated fix for worker

biosimulators · Sep 23, 2024 · 4be6820 · 4be6820
1 parent c086668
commit 4be6820
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Showing 4 changed files with 37 additions and 25 deletions.
diff --git a/compose_worker/Dockerfile-compose_worker b/compose_worker/Dockerfile-compose_worker
@@ -33,8 +33,12 @@ COPY . /app/worker
 RUN /app/assets/install_deps.sh /app/worker/requirements.worker.txt
 
 # add deps with extras
-RUN poetry add pysces --extras=sbml \
-    && poetry add biosimulators-utils --extras=logging
+RUN yes | poetry cache clear PyPI --all \
+    && poetry add biosimulators-utils@^0.1.188 --extras=logging \
+    && poetry add pysces --extras=sbml
+
+# RUN poetry add pysces --extras=sbml \
+#     && poetry add biosimulators-utils --extras=logging
 
 WORKDIR /app/worker
 

diff --git a/compose_worker/output_data.py b/compose_worker/output_data.py
@@ -138,6 +138,9 @@ def get_sbml_species_mapping(sbml_fp: str):
     # parse and handle names/ids
     sbml_species_ids = []
     for spec in sbml_model_object.getListOfSpecies():
+        spec_name = spec.name
+        if not spec_name:
+            spec.name = spec.getId()
         if not spec.name == "":
             sbml_species_ids.append(spec)
     names = list(map(lambda s: s.name, sbml_species_ids))
@@ -204,8 +207,10 @@ def run_sbml_pysces(sbml_fp: str, start, dur, steps):
 
 def run_sbml_tellurium(sbml_fp: str, start, dur, steps):
     simulator = te.loadSBMLModel(sbml_fp)
-    floating_species_list = simulator.getFloatingSpeciesIds()
-    sbml_species_names = list(get_sbml_species_mapping(sbml_fp).keys())
+    floating_species_list = simulator.getFloatingSpeciesIds()  # SBML IDS
+    mapping = get_sbml_species_mapping(sbml_fp)
+    sbml_species_names = list(mapping.keys())  # SBML NAMES
+    sbml_species_ids = list(mapping.values())
 
     try:
         # in the case that the start time is set to a point after the simulation begins
@@ -218,7 +223,10 @@ def run_sbml_tellurium(sbml_fp: str, start, dur, steps):
         for index, row in enumerate(result.transpose()):
             if not index == 0:
                 for i, name in enumerate(floating_species_list):
-                    outputs[sbml_species_names[i]] = row
+                    spec_index = sbml_species_ids.index(name)
+                    spec_name = sbml_species_names[spec_index]
+                    if spec_index == index:
+                        outputs[spec_name] = row
 
         return outputs
     except:

diff --git a/compose_worker/requirements.worker.txt b/compose_worker/requirements.worker.txt
@@ -1,5 +1,6 @@
 meson-python
-meson ninja
+meson
+ninja
 biosimulators-amici
 biosimulators-copasi
 biosimulators-pysces

diff --git a/compose_worker/supervisor.py b/compose_worker/supervisor.py
@@ -157,34 +157,33 @@ async def _check(self):
                 # run job again
                 try:
                     # check: run simulations
+
                     if job_id.startswith('simulation-execution'):
                         worker = SimulationRunWorker(job=pending_job)
                     # check: verifications
                     elif job_id.startswith('verification'):
-                        # otherwise: create new worker with job
                         worker = VerificationWorker(job=pending_job)
                     # check: files
                     elif job_id.startswith('files'):
                         worker = FilesWorker(job=pending_job)
-
                     # check: composition
-                    if job_id.startswith('composition-run'):
-                        worker = CompositionWorker(job=pending_job)
-                        await worker.run(conn=self.db_connector)
-                        # result_data = worker.job_result
-                        # await self.db_connector.insert_job_async(
-                        #     collection_name=DatabaseCollections.COMPLETED_JOBS.value,
-                        #     job_id=job_id,
-                        #     timestamp=self.db_connector.timestamp(),
-                        #     status=JobStatus.COMPLETED.value,
-                        #     source=source_name,
-                        #     simulator=simulator,
-                        #     results=result_data['data']
-                        # )
-                    else:
-                        # when worker completes, dismiss worker (if in parallel)
-                        await worker.run()
-
+                    # elif job_id.startswith('composition-run'):
+                    #     worker = CompositionWorker(job=pending_job)
+                    #     await worker.run(conn=self.db_connector)
+                    #     result_data = worker.job_result
+                    #     simulator = pending_job.get('simulator', 'copasi')
+                    #     await self.db_connector.insert_job_async(
+                    #         collection_name=DatabaseCollections.COMPLETED_JOBS.value,
+                    #         job_id=job_id,
+                    #         timestamp=self.db_connector.timestamp(),
+                    #         status=JobStatus.COMPLETED.value,
+                    #         source=source_name,
+                    #         simulator=simulator,
+                    #         results=result_data['data']
+                    #     )
+
+                    # when worker completes, dismiss worker (if in parallel)
+                    await worker.run()
                     # create new completed job using the worker's job_result
                     result_data = worker.job_result
                     await self.db_connector.insert_job_async(