Merge branch 'master' into stable

brsynth · Jun 23, 2022 · 7f45eaf · 7f45eaf
2 parents 0d516a2 + ed51b6f
commit 7f45eaf
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diff --git a/docsource/_autosummary/rptools.rpranker.Args.add_arguments.rst b/docsource/_autosummary/rptools.rpranker.Args.add_arguments.rst
@@ -1,6 +1,6 @@
-rptools.rpranker.Args.add\_arguments
+rptools.rprank.Args.add\_arguments
 ====================================
 
-.. currentmodule:: rptools.rpranker.Args
+.. currentmodule:: rptools.rprank.Args
 
 .. autofunction:: add_arguments
diff --git a/docsource/_autosummary/rptools.rpranker.Args.rst b/docsource/_autosummary/rptools.rpranker.Args.rst
@@ -1,7 +1,7 @@
-rptools.rpranker.Args
+rptools.rprank.Args
 =====================
 
-.. automodule:: rptools.rpranker.Args
+.. automodule:: rptools.rprank.Args
 
 
 

diff --git a/docsource/_autosummary/rptools.rpranker.rpRanker.rank.rst b/docsource/_autosummary/rptools.rpranker.rpRanker.rank.rst
@@ -1,6 +1,6 @@
-rptools.rpranker.rpRanker.rank
+rptools.rprank.rprank.rank
 ==============================
 
-.. currentmodule:: rptools.rpranker.rpRanker
+.. currentmodule:: rptools.rprank.rprank
 
 .. autofunction:: rank
diff --git a/docsource/_autosummary/rptools.rpranker.rpRanker.rst b/docsource/_autosummary/rptools.rpranker.rpRanker.rst
@@ -1,7 +1,7 @@
-rptools.rpranker.rpRanker
+rptools.rprank.rprank
 =========================
 
-.. automodule:: rptools.rpranker.rpRanker
+.. automodule:: rptools.rprank.rprank
 
 
 

diff --git a/docsource/_autosummary/rptools.rpranker.rst b/docsource/_autosummary/rptools.rpranker.rst
@@ -1,7 +1,7 @@
-rptools.rpranker
+rptools.rprank
 ================
 
-.. automodule:: rptools.rpranker
+.. automodule:: rptools.rprank
 
 
 
@@ -26,7 +26,7 @@ rptools.rpranker
    :template: custom-module-template.rst
    :recursive:
 
-   rptools.rpranker.Args
-   rptools.rpranker.rpRanker
+   rptools.rprank.Args
+   rptools.rprank.rprank
 
 
diff --git a/docsource/_autosummary/rptools.rst b/docsource/_autosummary/rptools.rst
@@ -31,7 +31,7 @@
    rptools.rpextractsink
    rptools.rpfba
    rptools.rplibs
-   rptools.rpranker
+   rptools.rprank
    rptools.rpreport
    rptools.rpscore
    rptools.rpthermo

diff --git a/environment.yaml b/environment.yaml
@@ -4,8 +4,6 @@ channels:
 dependencies:
   - python
   - brs_utils # rpcompletion, rpfba, Args
-  - requests # rpcompletion, rpfba, rplibs
-  - urllib3 # rpcompletion, rpfba
   - cobra # rpfba, rpextractsink, rplibs
   - timeout-decorator # rpextractsink
   - rdkit # rpextractsink, rplibs
@@ -14,7 +12,6 @@ dependencies:
   - pandas # rplibs, rpthermo
   - scipy # rpthermo
   - equilibrator-api # rpthermo
-  - equilibrator-pathway # rpthermo
   - openbabel # rpthermo (equilibrator-assets)
   - colored # rplibs
   - networkx >=2.5 # rplibs

diff --git a/rptools/rpfba/rpFBA.py b/rptools/rpfba/rpFBA.py
@@ -171,8 +171,10 @@ def runFBA(
     )
     if rpsbml_merged is None:
         return None
-    logger.debug('rpsbml_merged: ' + str(rpsbml_merged))
-    logger.debug('reactions_in_both: ' + str(reactions_in_both))
+    logger.debug(f'rpsbml_merged: {rpsbml_merged}')
+    logger.debug(f'reactions_in_both: {reactions_in_both}')
+    logger.debug(f'missing_species: {missing_species}')
+
     cobra_rpsbml_merged = rpSBML.cobraize(rpsbml_merged)
 
     ## MEDIUM
@@ -235,11 +237,14 @@ def runFBA(
             logger=logger
         )
     else: hidden_species = []
-    
+
     # NOTE: reactions is organised with key being the rpsbml reaction and value being the rpsbml_gem value`
     # BUG: when merging the rxn_sink (very rare cases) can be recognised if another reaction contains the same species as a reactant
     ## under such as scenario the algorithm will consider that they are the same -- TODO: overwrite it
-    if objective_rxn_id in reactions_in_both:
+    if (
+        reactions_in_both is not None and
+        objective_rxn_id in reactions_in_both
+    ):
         logger.warning(
             'The target_reaction ('+str(objective_rxn_id)+') ' \
           + 'has been detected in model ' + str(gem_sbml_path.getName()) + ', ' \
@@ -278,6 +283,7 @@ def runFBA(
             medium=df_medium,
             logger=logger
         )
+
         results['biomass'] = results_biomass
 
     # print(cobra_results.objective_value)
@@ -409,10 +415,12 @@ def check_SBML_compartment(
 
     # Check model compartment ID
     # Set new compartment ID in case it exists under another ID
-    has_compartment = rpsbml.has_compartment(compartment_id)
-    if has_compartment:
-        logger.debug(f'Compartment \'{compartment_id}\' found in the model \'{rpsbml.getName()}\'')
-        return compartment_id
+    compartment = rpsbml.has_compartment(compartment_id)
+    if compartment is not None:
+        logger.debug(f'Compartment \'{compartment_id}\' found in the model \'{rpsbml.getName()}\' as {compartment.getId()}')
+        if compartment_id != compartment.getId():
+            logger.warning(f'Compartment \'{compartment_id}\' has been replaced by {compartment.getId()}')
+        return compartment.getId()
     else:
         logger.error(f'Compartment \'{compartment_id}\' not found in the model \'{rpsbml.getName()}\'')
         logger.error(
@@ -846,10 +854,6 @@ def get_annot_objective(
         if fbc_obj_annot is None:
             logger.error('No annotation available for: '+str(biomass_objective_id))
 
-    # print(cobra_results.objective_value)
-    # rpsbml.write_to_file('joan.xml')
-    # exit()
-
     flux = float(
         fbc_obj_annot.getChild(
             'RDF'
@@ -864,26 +868,15 @@ def get_annot_objective(
         )
     )
 
-    # exit()
-    # # TODO: add another to check if the objective id exists
-    # logger.debug('FBA source flux ('+str(src_rxn_id)+') is: '+str(source_flux))
-    # if not objective_id:
-    #     objective_id = 'obj_'+str(tgt_rxn_id)+'__restricted_'+str(src_rxn_id)
-
     objective_id = rpsbml.find_or_create_objective(
         rxn_id=objective_rxn_id,
         obj_id=f'brs_obj_{objective_rxn_id}',
     )
-    # objective_id = rpsbml.find_or_create_objective(
-    #     reactions = [tgt_rxn_id],
-    #     coefficients = [tgt_coeff],
-    #     is_max = is_max,
-    #     objective_id = objective_id
-    # )
+    logger.debug(f'objective_id: {objective_id}')
 
-    logger.debug('Optimising the objective: '+str(biomass_rxn_id))
-    logger.debug('     Setting upper bound: '+str(flux*fraction_coeff))
-    logger.debug('     Setting lower bound: '+str(flux*fraction_coeff))
+    logger.debug(f'Optimising the objective: {biomass_rxn_id}')
+    logger.debug(f'     Setting upper bound: {flux*fraction_coeff}')
+    logger.debug(f'     Setting lower bound: {flux*fraction_coeff}')
 
     old_upper_bound, old_lower_bound = rpsbml.getReactionConstraints(biomass_rxn_id)
     rpsbml.setReactionConstraints(
@@ -906,21 +899,6 @@ def get_annot_objective(
     if cobra_results is None:
         return results_biomass, None, objective_id, minimal_medium
 
-    # # rxn>scores>fba>fraction = cobra_results.fluxes('rxn_X')
-    # # scores>fba>fraction = cobra_results.objective_value
-    # results[sim_type] = cobra_results
-
-    # # Write results for merged model
-    # write_results_to_rpsbml(
-    #     rpsbml=rpsbml,
-    #     objective_id=objective_id,
-    #     sim_type=sim_type,
-    #     cobra_results=cobra_results,
-    #     pathway_id=pathway_id,
-    #     logger=logger
-    # )
-
-    # rpsbml.write_to_file('joan.xml')
     ##### print the biomass results ######
     logger.debug('Biomass: '+str(cobra_results.fluxes.get(biomass_objective_id)))
     logger.debug(' Target: '+str(cobra_results.fluxes.get(objective_id)))
@@ -983,6 +961,10 @@ def runCobra(
         logger.debug(cobraModel.medium)
 
     cobra_results = None
+    # cobraModel.objective = {
+    #     cobraModel.reactions.get_by_id('BIOMASS_Ec_iML1515_core_75p37M'): 1,
+    #     cobraModel.reactions.get_by_id('PYRt2'): 2
+    # }
     if sim_type.lower() == 'pfba':
         cobra_results = pfba(cobraModel, fraction_coeff)
     else:
@@ -1016,6 +998,8 @@ def build_cobra_model(
     """
 
     rpsbml.logger.info('Creating Cobra object from rpSBML...')
+    logger.debug(f'objective_id: {objective_id}')
+    logger.debug(f'missing_species: {hidden_species}')
 
     rpsbml.activateObjective(
         objective_id = objective_id,