From 654f4257cddd5914049e0d9a468e6ec43b008c58 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nina=20Ro=C3=9Fbach?=
 <167868803+niinina@users.noreply.github.com>
Date: Thu, 22 Aug 2024 10:33:34 +0200
Subject: [PATCH] small updates #8

---
 src/specimen/cmpb/workflow.py                   | 17 ++++++++++-------
 src/specimen/hqtb/core/refinement/annotation.py |  3 ++-
 src/specimen/hqtb/core/refinement/extension.py  |  3 ++-
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/src/specimen/cmpb/workflow.py b/src/specimen/cmpb/workflow.py
index ac376a1..c5cb253 100644
--- a/src/specimen/cmpb/workflow.py
+++ b/src/specimen/cmpb/workflow.py
@@ -22,7 +22,7 @@
 from refinegems.analysis import growth
 from refinegems.analysis.investigate import plot_rea_sbo_single
 from refinegems.classes.reports import ModelInfoReport
-from refinegems.utility.entities import test_biomass_presence
+from refinegems.utility.util import test_biomass_presence
 from refinegems.curation.biomass import check_normalise_biomass
 from refinegems.curation.charges import correct_charges_modelseed
 from refinegems.curation.curate import resolve_duplicates
@@ -120,10 +120,6 @@ def between_analysis(model: Model, cfg:dict, step:str):
     else:
         config = validate_config(configpath, 'cmpb') 
 
-    if not config['general']['save_all_models']:
-        only_modelpath = Path(dir,'cmpb_out','model.xml') # @TODO Use model ID here...
-                                                          # model might not exist here ...
-
     # create directory structure
     # --------------------------
 
@@ -139,6 +135,12 @@ def between_analysis(model: Model, cfg:dict, step:str):
     Path(dir,"cmpb_out",'misc', 'kegg_pathway').mkdir(parents=True, exist_ok=False)   #      |- kegg_pathways
     Path(dir,"cmpb_out",'misc', 'auxotrophy').mkdir(parents=True, exist_ok=False)     #      |- auxothrophy
 
+    # save modelpath
+    # --------------
+    if not config['general']['save_all_models']:
+        only_modelpath = Path(dir,'cmpb_out','models','model.xml') # @TODO Use model ID here...
+                                                          # model might not exist here ...
+
     # create log
     # ----------
     today = date.today().strftime("%Y%m%d")
@@ -314,8 +316,8 @@ def between_analysis(model: Model, cfg:dict, step:str):
     current_libmodel = load_model(str(current_modelpath),'libsbml')
     if config['general']['save_all_models']:
         current_libmodel = run_SBOannotator(current_libmodel)
-        write_model_to_file(current_libmodel, str(Path(dir,'cmpb_out','models', 'SBOannotated.xml')))
-        current_modelpath = Path(dir,'cmpb_out','models', 'SBOannotated.xml')
+        write_model_to_file(current_libmodel, str(Path(dir,'cmpb_out','models', f'{current_libmodel.getId()}_SBOannotated.xml')))
+        current_modelpath = Path(dir,'cmpb_out','models', f'{current_libmodel.getId()}_SBOannotated.xml')
     else:
         current_libmodel = run_SBOannotator(current_libmodel)
         write_model_to_file(current_libmodel, str(current_modelpath))
@@ -416,6 +418,7 @@ def between_analysis(model: Model, cfg:dict, step:str):
     
     # MCC
     # ---
+    Path(dir,"cmpb_out",'misc','mcc').mkdir(parents=True, exist_ok=False)
     current_model = perform_mcc(current_model, Path(dir,'cmpb_out','misc','mcc'),apply=True)
 
     # save the final model
diff --git a/src/specimen/hqtb/core/refinement/annotation.py b/src/specimen/hqtb/core/refinement/annotation.py
index 788bf33..d1ea683 100644
--- a/src/specimen/hqtb/core/refinement/annotation.py
+++ b/src/specimen/hqtb/core/refinement/annotation.py
@@ -17,8 +17,9 @@
 import urllib.error
 
 # refinegems
-from refinegems.utility.io import load_model, kegg_reaction_parser, write_model_to_file
+from refinegems.utility.io import load_model, write_model_to_file
 from refinegems.utility.connections import run_memote, run_SBOannotator
+from refinegems.utility.db_access import kegg_reaction_parser
 
 ################################################################################
 # functions
diff --git a/src/specimen/hqtb/core/refinement/extension.py b/src/specimen/hqtb/core/refinement/extension.py
index 3136984..3628672 100644
--- a/src/specimen/hqtb/core/refinement/extension.py
+++ b/src/specimen/hqtb/core/refinement/extension.py
@@ -30,9 +30,10 @@
 from Bio.KEGG import REST
 from Bio.KEGG import Enzyme, Compound
 
-from refinegems.utility.io import kegg_reaction_parser, load_a_table_from_database
+from refinegems.utility.io import load_a_table_from_database
 from refinegems.utility.entities import create_random_id, get_reaction_annotation_dict, match_id_to_namespace
 from refinegems.utility.connections import run_memote
+from refinegems.utility.db_access import kegg_reaction_parser
 
 # further required programs:
 #        - DIAMOND, tested with version 0.9.14 (works only for certain sensitivity mode)