gsrap 0.9.0__tar.gz → 0.10.1__tar.gz

{gsrap-0.9.0 → gsrap-0.10.1}/PKG-INFO

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: gsrap
-Version: 0.9.0
+Version: 0.10.1
 Summary: 
 License: GNU General Public License v3.0
+License-File: LICENSE.txt
 Author: Gioele Lazzari
 Requires-Python: >=3.9
 Classifier: License :: Other/Proprietary License
@@ -12,9 +13,11 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: biopython (>=1.80)
 Requires-Dist: cobra (>=0.29)
 Requires-Dist: colorlog (>=6.9.0)
+Requires-Dist: escher (>=1.8.1)
 Requires-Dist: gdown (>=5.2.0)
 Requires-Dist: gempipe (>=1.38.1)
 Requires-Dist: matplotlib (>=3.9.0)

{gsrap-0.9.0 → gsrap-0.10.1}/pyproject.toml

@@ -1,24 +1,24 @@
 [tool.poetry]
 name = "gsrap"
-version = "0.9.0"
+version = "0.10.1"
 description = ""
 authors = ["Gioele Lazzari"]
 license = "GNU General Public License v3.0"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.9"
-cobra = ">=0.29"
-memote = ">=0.17.0"
-pandas = ">=2.0.0"
-openpyxl = ">=3.1.0"
-biopython = ">=1.80"
+python = ">=3.9" 
+cobra = ">=0.29" 
+memote = ">=0.17.0" 
+pandas = ">=2.0.0" 
+openpyxl = ">=3.1.0" 
+biopython = ">=1.80" 
 gempipe = ">=1.38.1"  
-gdown = ">=5.2.0"
-colorlog = ">=6.9.0"
-matplotlib = ">=3.9.0"
-xlsxwriter = ">=3.1.0"
-
+gdown = ">=5.2.0" 
+colorlog = ">=6.9.0" 
+matplotlib = ">=3.9.0" 
+xlsxwriter = ">=3.1.0" 
+escher = ">=1.8.1"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/.ipynb_checkpoints/__init__-checkpoint.py

@@ -162,11 +162,12 @@ def main():
     
     
     # print the full command line:
-    command_line = '' 
-    for arg, value in vars(args).items():
-        if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
-        else: command_line = command_line + f"--{arg} {value} "
-    logger.info('Inputted command line: "' + command_line.rstrip() + '".\n')
+    if args.verbose:
+        command_line = '' 
+        for arg, value in vars(args).items():
+            if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
+            else: command_line = command_line + f"--{arg} {value} "
+        logger.info('Inputted command line: "' + command_line.rstrip() + '".\n')
     
     
     

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/__init__.py

@@ -162,11 +162,12 @@ def main():
     
     
     # print the full command line:
-    command_line = '' 
-    for arg, value in vars(args).items():
-        if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
-        else: command_line = command_line + f"--{arg} {value} "
-    logger.info('Inputted command line: "' + command_line.rstrip() + '".\n')
+    if args.verbose:
+        command_line = '' 
+        for arg, value in vars(args).items():
+            if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
+            else: command_line = command_line + f"--{arg} {value} "
+        logger.info('Inputted command line: "' + command_line.rstrip() + '".\n')
     
     
     

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py

@@ -160,6 +160,9 @@ def get_precursors_to_pathway():
 def introduce_universal_biomass(logger, dbexp, universe): 
     
     
+    logger.debug("Introducing universal biomass reaction...")
+    
+    
     biomass_dict = get_biomass_dict(logger, universe, dbexp)
     
     

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py

@@ -5,6 +5,7 @@ import time
 import tempfile
 import json
 import glob
+import sys
 
 
 import gdown
@@ -12,6 +13,30 @@ import pandas as pnd
 
 
 
+
+class SimpleLoadingWheel():
+    # a simple endless loading wheel
+    
+    msg = ''
+    wheel_figures = ['|', '/', '-', '\\']
+    wheel_cnt = 0
+    
+    def __init__(self, msg='Please wait... '):
+        self.msg = msg
+    
+    def proceed(self):
+        print(f"{self.msg}{self.wheel_figures[self.wheel_cnt]}", file=sys.stderr, end='\r')
+        self.wheel_cnt += 1
+        if self.wheel_cnt == 4: self.wheel_cnt = 0
+        time.sleep(0.5)
+        
+    def clear(self):
+        clear_str = ''.join([' ' for i in range(len(self.msg)+1)])
+        print(f'{clear_str}', file=sys.stderr, end='\r')
+        wheel_cnt = 0
+    
+
+
 def get_dbuni(logger):
     
     
@@ -29,7 +54,7 @@ def get_dbuni(logger):
     
     # check table presence
     sheet_names = exceldb.sheet_names
-    for i in ['T', 'R', 'M', 'authors']: 
+    for i in ['T', 'R', 'M', 'curators']: 
         if i not in sheet_names:
             logger.error(f"Sheet '{i}' is missing!")
             return 1
@@ -40,15 +65,15 @@ def get_dbuni(logger):
     dbuni['T'] = exceldb.parse('T')
     dbuni['R'] = exceldb.parse('R')
     dbuni['M'] = exceldb.parse('M')
-    dbuni['authors'] = exceldb.parse('authors')
+    dbuni['curators'] = exceldb.parse('curators')
     
     
     # check table headers
     headers = {}
-    headers['T'] = ['rid', 'rstring', 'kr', 'gpr_manual', 'name', 'author', 'notes']
-    headers['R'] = ['rid', 'rstring', 'kr', 'gpr_manual', 'name', 'author', 'notes']
-    headers['M'] = ['pure_mid', 'formula', 'charge', 'kc', 'name', 'inchikey', 'author', 'notes']
-    headers['authors'] = ['username', 'first_name', 'last_name', 'role', 'mail']
+    headers['T'] = ['rid', 'rstring', 'kr', 'gpr_manual', 'name', 'curator', 'notes']
+    headers['R'] = ['rid', 'rstring', 'kr', 'gpr_manual', 'name', 'curator', 'notes']
+    headers['M'] = ['pure_mid', 'formula', 'charge', 'kc', 'name', 'inchikey', 'curator', 'notes']
+    headers['curators'] = ['username', 'first_name', 'last_name', 'role', 'mail']
     for i in dbuni.keys(): 
         if set(dbuni[i].columns) != set(headers[i]):
             logger.error(f"Sheet '{i}' is missing the columns {set(headers[i]) - set(dbuni[i].columns)}.")
@@ -136,40 +161,141 @@ def get_dbexp(logger):
 
 
 
-def get_eschermap(logger):
-    
-    
+def get_eschermap(logger, map_id):
+    
+    
+    dict_escher_maps = {
+        'gr_other_reactions': '1un4Nqpc7l-U3k8iX67osIqM_I6AntWDy',
+        'gr_sinks_demands':   '1lKS2_kXhdBWTFY_vsABRBfPUH3SidgQK',
+        'gr_unsaturates_w7':  '1jh5quSsiqJ6PecvlWRRp00s9Uj-96SBK',
+        'gr_transport':    '180QXr_e99GmYTUFtmV-Btw8-O7C7VeRO',
+        'map00010': '1mTMwrnNd1n4j7SHAwJ86EtOtIt9NOqp6',
+        'map00020': '1J7bHRZv1OU6E8JkpW6JxThWp-p0sqS-N',
+        'map00030': '121nngh-p29TQrvlDeVOREhVaOZ0Qe94H',
+        'map00040': '17e-e4z5pYrLG0sJRhY1lll183MAUmfeC',
+        'map00051': '1A6lpAuilGP7VvfLh_9PsqcE23YM0_RZA',
+        'map00052': '1ZDrLZIsCxK2-2rDuYbZck_ls5g-VTYAS',
+        'map00053': '1eluZkBAA3_SSP625refRJQLAp0lSGJSq',
+        'map00061': '1RDgv4yLkpYh9p2Zy_OPDc7kmJNATHpJY',
+        'map00071': '1ieltgCeNZT11cTHQ_uvWJVtfrjZ8O-yB',
+        'map00100': '1a7WAA3y9J8gQmwuM7nDfmPABxi5M3IGU',
+        'map00130': '1OXvBIbZzz4vSgrVpfXeQsxg74N5tqSNE',
+        'map00190': '1j0SQYt5fNMCvKI3GFc1cOU0YGDyWidS5',
+        'map00195': '1ceRpKB3JuxqHVrAVRVADX9sjcLPrwsoa',
+        'map00220': '1ntN8R9NiG8kNjUntPqziIblhxoZgSR7N',
+        'map00230': '1MVWZQs4V6jBk6kYv4kPait5SoBT7ZRmA',
+        'map00240': '1-n8jzvfapLDGEvCF_jmVMhbBVy7UHf-z',
+        'map00250': '1qh0dk4-bvml3FVLb5Qbw--GM0t4r-NwX',
+        'map00260': '18l-dMc2a_uEgeSY3RcTQdScAIkvstpQo',
+        'map00270': '1TGKhD3rnPgbPzL_NPR0NpO8CkWU4mTFE',
+        'map00280': '1HSP6UibDxw5KaE0Q7LZR09OYvt8ie50R',
+        'map00290': '1eObr-DGu1FSUZC0wh18UmDfgKbdpc4ez',
+        'map00300': '1fgK9prq7Z-xskFtKSsp_nBW_avBTeKe3',
+        'map00310': '1lKxkgnzXHdPZhT7QJN7Ohf7UMJix74Sl',
+        'map00330': '1R-4vMiHQNyyZkpID0DgfunPCuVGhTz5g',
+        'map00340': '16g1_a5aDs04ZrMNrEJCc5CdpgFcJGiDZ',
+        'map00350': '1kkbmpmQY3f9zqy2GNdZKPd9HOz6MrnGc',
+        'map00360': '1BC4IeVM6Px2bWleGmcX-h109RI-9KvhC',
+        'map00380': '1ZfEK2U87gW77y1sosDTHlavJ66PLRgRY',
+        'map00400': '1PKmNTpnfUaydtLQvGrJtP8LH7tj1Ka-Z',
+        'map00450': '106flHuSeJID56rhYeJ5zJgDh8owfxW2K',
+        'map00460': '1QBPL7deHN998Maj25LpVrrEB0l6_y4Q9',
+        'map00470': '1u67PtRrS2xy8clSLt2daxiwO1j0wScRL',
+        'map00480': '12p9hrG_xw-XigK4euy4-EDH8JH1t8U4c',
+        'map00500': '1erMsLa2zcZUxizPiALZN4GmuaZSpmElF', 
+        'map00520': '1K9mU6M99_hFeOc8x_rYDpWPpVO-6NCN3',
+        'map00541': '1CDSQ8jqaSgdxAqMUIU6DsZnZXjXj7fe9', 
+        'map00543': '1MkO45ap63_7ViJ-i8KtoEDl9q5ueXfJM', 
+        'map00550': '1HCvMcqThZqTZXa2ErL3ZpcJ86gBw2Sh3', 
+        'map00552': '1GcRd4ADgLVRg-RuI-6CklkNao4EgVL5s',
+        'map00561': '17_hAqfz89xBX3f_eUkGefEFiqZ0xS-hL',
+        'map00562': '1HxBd0LbZaqbrnjhpxxK7lEQGlW7HN3bU',
+        'map00564': '1XI3tcJgJbBDkDj6DVBAuzZ-Ok6uK_TfB', 
+        'map00620': '1e9lGVCYs3nt-LgTPY55vLeeQtWk4Zpna',
+        'map00630': '1LXW-Htoh25wAWXdrWu6wTnegxuK9BNy5', 
+        'map00640': '1kjummzfu7lgy91QVZr3IV_coLFjU9nsS',
+        'map00650': '1fBOBJzPpTmNIUnpsSeM3JxSUTqHVFJ00', 
+        'map00660': '1N9HbppTMcFTWTfBQhI1bF_SxbWhkGlKe',
+        'map00670': '12jolzJP2sOUnL1z8MPGJy4dr3Jz4K0y0',
+        'map00680': '1wopxju_tgy37Lb5uO7xkcE5hiUgppzJ2', 
+        'map00710': '1HF1-j4h76nPgq-x0foqNmPj9Icb3CJet',
+        'map00720': '1v40fQu6ByNq7g2_qiZ9qucBXYJPeKvpK',  
+        'map00730': '1Spryv2M2eiPXF55dZoNb1_nv_f0oxN1v', 
+        'map00740': '1WJ6iydXKLb2s1K8_F8OCIIurDBbGNAfM',
+        'map00750': '1Z_7Z4710P738MOQJFuExjz7Nsff0_EZk',
+        'map00760': '1PKJs7sZ2xvdHQAdz_E4faFugaownqXxw',
+        'map00770': '1nbbTwRtUF4vOxwMUSwcyU1K4ltgLNVbx',
+        'map00780': '1HUvLt4_xK_pnGbqiz8UjvZyvaGIomAxf', 
+        'map00790': '13r-w61f0zPsDnpUHqJQU_r8ZXvE-cxhx',
+        'map00791': '1SX8WSG6zUOf144RhAT9QycDrjEskZi4w',
+        'map00860': '18DqnA4rNfDp2pCNyvwRg4XoTS8KefFAc',
+        'map00900': '1Xm9g8dTDJWJmQ7AY9PPybefcE6G3smTh',
+        'map00906': '1jnMtXsHVXipy9ApialPNFQDW_GCgpKas',
+        'map00910': '196D351gJ10416ZI6y1rJGLrmxCBiHLkI',
+        'map00920': '1tnm0WGewYgINyvrj-A-iv2tO--bAKwxV',
+        'map00930': '1UycN6OXFGR3g4Vwfz5zQXHmdaAJmqpox',
+        'map00970': '1-bDiZJNxkM6JhcUpbI44O3kWvhTSYlGq',
+    }
+    
+    
+    
+    # return None if not requested
+    if map_id == None or map_id == '-': 
+        return None
+    
+    
+    # check the esistance of the map  
+    if map_id not in dict_escher_maps.keys():
+        logger.warning(f"No online folder is tracked for '{map_id}' yet. Please contact the developer to start tracking '{map_id}'.")
+        return None    
+    
+    
+    # object to be returned
     lastmap = dict()  
     
     
-    folder_id = "1YE4l8IFL9pRgonAmFCf2SMRnpGJCHjil"
-    folder_url = f"https://drive.google.com/drive/folders/{folder_id}?usp=sharing"
-
-    
     # the temporary folder (/tmp/on-the-fly-code) will be deleted once exiting the with statement
     with tempfile.TemporaryDirectory() as tmp_dir:
         
         
-        # get available versions without downloading: 
+        # get available versions without downloading:
+        folder_id = dict_escher_maps[map_id]
+        folder_url = f"https://drive.google.com/drive/folders/{folder_id}?usp=sharing"
         contents = gdown.download_folder(folder_url, output=tmp_dir, quiet=True, skip_download=True)
 
+        # check empty folder
         if len(contents) == 0:
-            logger.error("Online folder 'universe.escher' seems empty. Please contact the developer.")
-            return 1
+            logger.warning(f"Online folder for '{map_id}' seems empty. Please draw and upload '{map_id}-v1.json'.")
+            return None
         
+        # check crowded folder
+        if len(contents) > 40:
+            logger.warning(f"Online folder for '{map_id}' contains >40 versions. An error will be raised at 50 versions. Please free space by moving older versions into 'older/' now.")
         
-        # get the last version
+        # create dict of available files:
         files = {i.path: i.id for i in contents}
-        files = dict(sorted(files.items()))   # sort keys in alphabetical order
-        last_file_name = list(files.keys())[-1]
+        
+        # check file name consistency
+        map_ids = set([i.rsplit('-v',1)[0] for i in files.keys()])
+        if len(map_ids) != 1:
+            logger.error(f"Several different map names in online folder for '{map_id}'.")
+            return 1
+        
+        # check concordance to mother folder
+        if list(map_ids)[0] != map_id:
+            logger.error(f"Online folder for '{map_id}' contains versions for another map.")
+            return 1
+        
+        # get the last available version (natural order)
+        last_version = max([int(i.rsplit('-v',1)[-1].replace('.json', '')) for i in files.keys()])
+        last_file_name = list(files.keys())[0].rsplit('-v',1)[0] + f"-v{last_version}.json"
         last_file_id = files[last_file_name]
         lastmap['filename'] = last_file_name
         
-        
         # download last version:
         try: pathfile_tmpfolder = gdown.download(id=last_file_id, output=f"{tmp_dir}/{last_file_name}", quiet=True)
         except: 
-            logger.error("Downloading of last-version universal Escher map failed. Retry. If persists, please contact the developer.")
+            logger.error(f"Downloading of last-version for '{map_id}'. Retry. If persists, please contact the developer.")
             return 1
         
         # load json
@@ -182,34 +308,44 @@ def get_eschermap(logger):
         
     
     
-def get_databases(logger): 
-    
+def get_databases(logger, map_id): 
     
-    def run_with_result(func, logger, results_dict, key):
-        result = func(logger)
+
+    # define a function to fill the dict
+    def run_with_result(func, logger, results_dict, key, *extra_args):
+        result = func(logger, *extra_args)
         results_dict[key] = result
         
     
+    # start threads
     results_dict = dict()
-    t1 = threading.Thread(target=run_with_result, args=(get_dbuni, logger, results_dict, 'dbuni'))
-    t2 = threading.Thread(target=run_with_result, args=(get_dbexp, logger, results_dict, 'dbexp'))
-    t3 = threading.Thread(target=run_with_result, args=(get_eschermap, logger, results_dict, 'eschermap'))
+    t1 = threading.Thread(target=run_with_result, args=(
+        get_dbuni, logger, results_dict, 'dbuni'))
+    t2 = threading.Thread(target=run_with_result, args=(
+        get_dbexp, logger, results_dict, 'dbexp'))
+    t3 = threading.Thread(target=run_with_result, args=(
+        get_eschermap, logger, results_dict, 'eschermap', map_id))
 
     
-    # wait for the longest download (assess every 0.001 seconds):
+    # wait for the longest download:
     t1.start()
     t2.start()
     t3.start()
+    slw = SimpleLoadingWheel(msg="Please wait... ")
     while t1.is_alive() or t2.is_alive() or t3.is_alive():
-        time.sleep(0.001)  
-
-        
+        slw.proceed()
+    slw.clear()
+    
+    
+    # check if errors where raised:
     if type(results_dict['dbuni'])==int:
         return 1
     if type(results_dict['dbexp'])==int:
         return 1
     if type(results_dict['eschermap'])==int:
         return 1
+    
+    
     return (results_dict['dbuni'], results_dict['dbexp'], results_dict['eschermap'])
 
 
@@ -277,65 +413,4 @@ def check_taxon(logger, taxon, idcollection_dict):
         return 1
     
     
-    """
-    sorted(list(df.query("kingdom == 'Bacteria'")['phylum'].unique()))
-    ['Acidobacteriota',
-     'Actinomycetota',
-     'Alphaproteobacteria',
-     'Aquificota',
-     'Armatimonadota',
-     'Atribacterota',
-     'Bacilli',
-     'Bacteria incertae sedis',
-     'Bacteroidota',
-     'Balneolota',
-     'Bdellovibrionota',
-     'Betaproteobacteria',
-     'Caldisericota',
-     'Calditrichota',
-     'Campylobacterota',
-     'Chlamydiota',
-     'Chlorobiota',
-     'Chloroflexota',
-     'Chrysiogenota',
-     'Cloacimonadota',
-     'Clostridia',
-     'Coprothermobacterota',
-     'Cyanobacteriota',
-     'Deferribacterota',
-     'Deinococcota',
-     'Deltaproteobacteria',
-     'Dictyoglomota',
-     'Elusimicrobiota',
-     'Enterobacteria',
-     'Fibrobacterota',
-     'Fidelibacterota',
-     'Fusobacteriota',
-     'Gemmatimonadota',
-     'Ignavibacteriota',
-     'Kiritimatiellota',
-     'Lentisphaerota',
-     'Melainabacteria',
-     'Mycoplasmatota',
-     'Myxococcota',
-     'Nitrospinota',
-     'Nitrospirota',
-     'Omnitrophota',
-     'Planctomycetota',
-     'Rhodothermota',
-     'Spirochaetota',
-     'Synergistota',
-     'Thermodesulfobacteriota',
-     'Thermodesulfobiota',
-     'Thermomicrobiota',
-     'Thermosulfidibacterota',
-     'Thermotogota',
-     'Verrucomicrobiota',
-     'Vulcanimicrobiota',
-     'other Bacillota',
-     'other Gammaproteobacteria',
-     'other Pseudomonadota',
-     'unclassified Bacteria']
-    """
-    
     return 0

gsrap-0.10.1/src/gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py

@@ -0,0 +1,112 @@
+import warnings
+import logging
+import threading
+
+import cobra
+
+from .downloads import SimpleLoadingWheel
+
+
+
+def print_json_tree(data, level=0, max_level=2):
+    # explore contents of a json object
+    
+    if level > max_level:
+        return
+    indent = '  ' * level
+    if isinstance(data, dict):
+        for key, value in data.items():
+            print(f"{indent}{key}")
+            print_tree(value, level + 1, max_level)
+    elif isinstance(data, list):
+        for i, item in enumerate(data):
+            print(f"{indent}[{i}]")
+            print_tree(item, level + 1, max_level)
+            
+            
+            
+def subset_for_focus(universe, rids_in_group, outdir, focus):
+            
+    universe_focus = universe.copy()
+    to_remove = [r for r in universe_focus.reactions if r.id not in rids_in_group]
+
+
+    # trick to avoid the WARNING "cobra/core/group.py:147: UserWarning: need to pass in a list" 
+    # triggered when trying to remove reactions that are included in groups. 
+    with warnings.catch_warnings():  # temporarily suppress warnings for this block
+        warnings.simplefilter("ignore")  # ignore all warnings
+        cobra_logger = logging.getLogger("cobra.util.solver")
+        old_level = cobra_logger.level
+        cobra_logger.setLevel(logging.ERROR)   
+
+        universe_focus.remove_reactions(to_remove, remove_orphans=True)
+
+        # restore original behaviour: 
+        cobra_logger.setLevel(old_level)  
+
+
+    # save the subset for drawing in Escher!
+    cobra.io.save_json_model(universe_focus, f'{outdir}/focus_{focus}.json')
+            
+            
+        
+def count_undrawn_rids_focus(logger, universe, lastmap, focus, outdir):
+    
+    
+    # there could be no tracked folder / no versions for this group
+    if lastmap == None:
+        return
+    
+    
+    # get modeled reads for this --focus:
+    rids_in_group = set()
+    try: gr = universe.groups.get_by_id(focus)
+    except: 
+        logger.warning(f"Group '{focus}' not found!")
+        return 
+    for r in gr.members:
+        rids_in_group.add(r.id)
+
+
+    # get rids on Escher: 
+    drawn_rids = set()
+    for key, value in lastmap['json'][1]['reactions'].items():
+        drawn_rids.add(value['bigg_id'])
+
+        
+    # get remaining rids for this map:
+    remainings = rids_in_group - drawn_rids
+    remainings_krs = set()
+    for rid in remainings: 
+        r = universe.reactions.get_by_id(rid)
+        if 'kegg.reaction' in r.annotation.keys():
+            krs = r.annotation['kegg.reaction']
+            for kr in krs: 
+                remainings_krs.add(kr)
+    
+    
+    if len(remainings) > 0:
+        if focus != 'gr_transport':
+            logger.warning(f"Current '{lastmap['filename']}' is {len(remainings)} reactions behind: {' '.join(list(remainings_krs))}.")
+        else:
+            logger.warning(f"Current '{lastmap['filename']}' is {len(remainings)} reactions behind.")  # usually no kegg codes for tranport reactions
+        
+        
+        # subset the universe to ease the drawing: 
+        next_version_filename = f"{focus}-v{(int(lastmap['filename'].rsplit('-v',1)[-1].replace('.json', ''))+1)}.json"
+        logger.warning(f"Writing model '{outdir}/focus_{focus}.json' to ease the drawing of '{next_version_filename}'...")
+        
+        
+        t1 = threading.Thread(target = subset_for_focus, args=(
+            universe, rids_in_group, outdir, focus))
+        t1.start()
+        slw = SimpleLoadingWheel(msg="Please wait... ")
+        while t1.is_alive():
+            slw.proceed()
+        slw.clear()
+        
+        
+        logger.warning(f"'{outdir}/focus_{focus}.json' created!")
+    else:
+        logger.info(f"Current '{lastmap['filename']}' is 0 reactions behind. Thank you ♥")
+        

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py

@@ -171,9 +171,15 @@ def write_excel_model(model, filepath, nofigs, memote_results_dict, df_E, df_B,
     df_R = df_R[df_R_first_cols + sorted([c for c in df_R.columns if c not in df_R_first_cols])]
     df_T = df_T[df_R_first_cols + sorted([c for c in df_T.columns if c not in df_R_first_cols])]
     df_A = df_A[df_R_first_cols + sorted([c for c in df_A.columns if c not in df_R_first_cols])]
-    df_G_first_cols = ['gid', 'name', 'involved_in']
+    df_G_first_cols = ['gid', 'name', 'involved_in', 'kingdom']
     df_G = df_G[df_G_first_cols + sorted([c for c in df_G.columns if c not in df_G_first_cols])]
     
+    # drop unused columns
+    df_M = df_M.drop(columns=["curator_codes", "curator_notes"])
+    df_R = df_R.drop(columns=["curator_codes", "curator_notes"])
+    df_T = df_T.drop(columns=["curator_codes", "curator_notes"])
+    df_G = df_G.drop(columns=["phylum"])
+    
     
     
     with pnd.ExcelWriter(filepath, engine='xlsxwriter') as writer:

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py

@@ -54,30 +54,30 @@ def show_contributions(logger, db, goodbefore):
     
     
     if goodbefore != [None, None, None]:
-        logger.debug(f"Contributions  counter disabled when using --goodbefore.")
+        logger.debug(f"Contributions counter disabled when using --goodbefore.")
         return 0
     
     
     # create a counter for each author
-    cnt = {author: 0 for author in db['authors']['username']}
+    cnt = {author: 0 for author in db['curators']['username']}
     cnt_tot = 0
     
     
     for index, row in db['R'].iterrows():
-        if type(row['author']) != str: 
-            logger.error(f"Missing author in tab 'R', rid '{row['rid']}'.")
+        if type(row['curator']) != str: 
+            logger.error(f"Missing curator in tab 'R', rid '{row['rid']}'.")
             return 1
-        for author in row['author'].split(';'):
+        for author in row['curator'].split(';'):
             author = author.rstrip().strip()
             cnt[author] += 1
             cnt_tot += 1
             
             
     for index, row in db['T'].iterrows():
-        if type(row['author']) != str: 
-            logger.error(f"Missing author in tab 'T', rid '{row['rid']}'.")
+        if type(row['curator']) != str: 
+            logger.error(f"Missing curator in tab 'T', rid '{row['rid']}'.")
             return 1
-        for author in row['author'].split(';'):
+        for author in row['curator'].split(';'):
             author = author.rstrip().strip()
             cnt[author] += 1
             cnt_tot += 1

{gsrap-0.9.0 → gsrap-0.10.1}/src/gsrap/commons/biomass.py

@@ -160,6 +160,9 @@ def get_precursors_to_pathway():
 def introduce_universal_biomass(logger, dbexp, universe): 
     
     
+    logger.debug("Introducing universal biomass reaction...")
+    
+    
     biomass_dict = get_biomass_dict(logger, universe, dbexp)