Dev umi

MONSDA/Configurator.py

@@ -28,12 +28,10 @@
         os.sep.join(["lib", pythonversion, "site-packages", "MONSDA"]), "share"
     )
 except:
-    installpath = os.path.cwd()
+    installpath = os.getcwd()
 
 configpath = os.path.join(installpath, "MONSDA", "configs")
 current_path = os.getcwd()
-dir_path = os.path.dirname(os.path.realpath(__file__))
-os.chdir(dir_path)
 
 template = load_configfile(os.sep.join([configpath, "template_base_commented.json"]))
 none_workflow_keys = ["WORKFLOWS", "BINS", "MAXTHREADS", "SETTINGS", "VERSION"]
@@ -70,6 +68,13 @@
     help="takes configuration file to modify",
 )
 
+parser.add_argument(
+    "--samplesheet",
+    type=str,
+    default=False,
+    help="CSV or TSV samplesheet to populate SETTINGS and condition tree for new configs/projects",
+)
+
 args = parser.parse_args()
 
 
@@ -315,6 +320,21 @@ def get_conditions_from_dict(root, keylist=[]):
         keylist.pop()
 
 
+def get_conditions_from_settings(root, keylist=[]):
+    """Yield condition paths from SETTINGS leaves that contain a SAMPLES key."""
+    if not isinstance(root, dict):
+        return
+    if "SAMPLES" in root and isinstance(root.get("SAMPLES"), list):
+        yield ":".join(keylist)
+        return
+    for k, v in root.items():
+        if not isinstance(v, dict):
+            continue
+        keylist.append(k)
+        yield from get_conditions_from_settings(v, keylist)
+        keylist.pop()
+
+
 def getPathesFromDict(d, value=None):
     def yield_func(d):
         q = [(d, [])]
@@ -790,6 +810,8 @@ def create_condition_tree():
 def add_sample_dirs(only_conditions=None):
     pickle_unfinished("add_sample_dirs")
     # project.current_func_arg = only_conditions
+    if args.samplesheet and only_conditions is None and project.mode in ["project", "config"]:
+        return assign_samplesheet()
     if "FETCH" in project.workflowsDict.keys():
         return assign_SRA(only_conditions)
     print("\n  FASTQ files:")
@@ -876,6 +898,58 @@ def add_sample_dirs(only_conditions=None):
     return assign_samples(only_conditions)
 
 
+def assign_samplesheet():
+    pickle_unfinished("assign_samplesheet")
+    prCyan("\n  Sample Assignment: samplesheet\n")
+
+    samplesheet = str(args.samplesheet)
+    if not os.path.isfile(samplesheet):
+        prRed(f"Could not find samplesheet file: {samplesheet}")
+        exit(1)
+
+    cwd = os.getcwd()
+    try:
+        # Params initializes logging at import time via Utils.setup_logger and expects
+        # a writable LOGS/ directory in the current working directory.
+        os.makedirs(os.path.join(current_path, "LOGS"), exist_ok=True)
+        os.chdir(current_path)
+        from .Params import samplesheet_to_settings
+
+        sheet_settings = samplesheet_to_settings(samplesheet)
+    except Exception as e:
+        prRed(f"Failed to parse samplesheet '{samplesheet}': {e}")
+        exit(1)
+    finally:
+        os.chdir(cwd)
+
+    if not sheet_settings:
+        prRed(f"Samplesheet '{samplesheet}' did not produce SETTINGS entries")
+        exit(1)
+
+    project.settingsDict = decouple(sheet_settings)
+    project.conditionsDict = NestedDefaultDict()
+    project.samplesDict = NestedDefaultDict()
+
+    condition_paths = [
+        x.split(":") for x in get_conditions_from_settings(project.settingsDict)
+    ]
+    if not condition_paths:
+        prRed(
+            "No condition leaves with SAMPLES found in parsed samplesheet SETTINGS"
+        )
+        exit(1)
+
+    for path in condition_paths:
+        setInDict(project.conditionsDict, path, {})
+
+    prGreen("Loaded condition tree and SETTINGS from samplesheet:")
+    print_dict(project.conditionsDict, gap="      ")
+    print("")
+    print_dict(project.settingsDict, gap="      ")
+    show_settings()
+    return select_conditioning()
+
+
 def assign_SRA(only_conditions=None):
     pickle_unfinished("assign_SRA")
     prCyan("\n  Sample Assignment:  SRA Accession Numbers\n")
@@ -1882,6 +1956,14 @@ def main():
     global guide
     project = PROJECT()
     guide = GUIDE()
+    if args.samplesheet:
+        if not str(args.samplesheet).lower().endswith((".csv", ".tsv", ".txt")):
+            print("Samplesheet flag requires a .csv/.tsv/.txt file")
+            exit()
+        args.samplesheet = os.path.abspath(args.samplesheet)
+        if not os.path.isfile(args.samplesheet):
+            print(f"Samplesheet file not found: {args.samplesheet}")
+            exit()
     if args.test:
         guide.testing = True
     if args.config:

MONSDA/Logger.py

@@ -1,47 +1,5 @@
 # Logger.py ---
-#
-# Filename: Logger.py
-# Description:
-# Author: Joerg Fallmann
-# Maintainer:
-# Created: Mon Aug 12 10:26:55 2019 (+0200)
-# Version:
-# Package-Requires: ()
-# Last-Updated: Wed Apr 29 16:42:40 2020 (+0200)
-#           By: Joerg Fallmann
-#     Update #: 91
-# URL:
-# Doc URL:
-# Keywords:
-# Compatibility:
-#
-#
-
-# Commentary:
-#
-#
-#
-#
-
-# Change Log:
-#
-#
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or (at
-# your option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
-#
-#
+
 
 # Code:
 import logging