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-rwxr-xr-xwqflask/base/data_set.py3
-rw-r--r--wqflask/utility/tools.py82
-rwxr-xr-xwqflask/wqflask/database.py5
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py6
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py10
5 files changed, 49 insertions, 57 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e37a838f..0e5a3ac1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -405,10 +405,11 @@ class DatasetGroup(object):
#print("Cache not hit")
from utility.tools import plink_command
- PLINK_PATH,PLINK_COMMAND = plink_command()
+ PLINK_RUN = plink_command()
geno_file_path = webqtlConfig.GENODIR+self.name+".geno"
plink_file_path = PLINK_PATH+"/"+self.name+".fam"
+ # @FIXME PJOTR/ZACH: .fam files should go into FLATFILES
if os.path.isfile(plink_file_path):
self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 0db195df..c3c9b292 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -9,22 +9,22 @@ import os
import sys
from wqflask import app
-def get_setting(id,default,guess,find_path):
+def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with get_valid_path is a function checking whether the
- path points to an expected directory an returns the full path e.g.
+ path points to an expected directory and returns the full path to
+ the binary command
guess = os.environ.get('HOME')+'/pylmm'
- get_setting('PYLMM_PATH',default,guess,get_valid_path)
+ get_setting('PYLMM_PATH',guess)
first tries the environment variable in +id+, next gets the Flask
- app setting for the same +id+, next tries the path passed in with
- +default+ and finally does an educated +guess+.
+ app setting for the same +id+ and finally does an educated
+ +guess+.
In all, the environment overrides the others, next is the flask
- setting, then the default and finally the guess (which is
- $HOME/repo). A valid path is returned. If none is resolved an
- exception is thrown.
+ setting, then the guess. A valid path to the binary command is
+ returned. If none is resolved an exception is thrown.
Note that we do not use the system path. This is on purpose
because it will mess up controlled (reproducible) deployment. The
@@ -33,46 +33,36 @@ def get_setting(id,default,guess,find_path):
different settings.py file (or setting the environment).
"""
- # ---- Check whether environment exists
- path = find_path(os.environ.get(id))
- # ---- Check whether setting exists
- setting = app.config.get(id)
- if not path:
- path = find_path(setting)
- # ---- Check whether default exists
- if not path:
- path = find_path(default)
- # ---- Guess directory
- if not path:
- guess = os.environ.get('HOME')+guess
- if not setting:
- setting = guess
- path = find_path(guess)
- if not path:
- raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the path')
- return path
-
-def find_command(command,id1,default,guess):
- def find_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying "+id1+" in "+path+"\n")
- binary = str.split(command)[0]
- if path and os.path.isfile(path+'/'+binary):
- return path
+ def valid(command):
+ if command:
+ sys.stderr.write("Found value "+command+"\n")
+ return command
else:
- None
+ return None
+
+ # ---- Check whether environment exists
+ sys.stderr.write("Looking for "+command_id+"\n")
+ command = valid(os.environ.get(command_id))
+ if not command:
+ # ---- Check whether setting exists in app
+ command = valid(app.config.get(command_id))
+ if not command:
+ command = valid(guess)
+ if not command:
+ raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
+ return command
- path = get_setting(id1,default,guess,find_path)
- binary = path+'/'+command
- sys.stderr.write("Found "+binary+"\n")
- return path,binary
+def pylmm_command(guess=None):
+ return get_setting("PYLMM_RUN",guess)
-def pylmm_command(default=None):
- return find_command('pylmm_gn2/lmm.py',"PYLMM_PATH",default,'/pylmm2')
+def gemma_command(guess=None):
+ return get_setting("GEMMA_RUN",guess)
-def gemma_command(default=None):
- return find_command('gemma',"GEMMA_PATH",default,'/gemma')
+def plink_command(guess=None):
+ return get_setting("PLINK_RUN",guess)
-def plink_command(default=None):
- return find_command('plink2',"PLINK_PATH",default,'/plink')
+def flat_files(subdir=None):
+ base = get_setting("GENENETWORK_FILES")
+ if subdir:
+ return base+"/"+subdir
+ return base
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 159c5d6c..2f544d44 100755
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -24,8 +24,9 @@ def init_db():
# you will have to import them first before calling init_db()
#import yourapplication.models
import wqflask.model
- print("Creating all..")
+ print("database.py: Creating all model metadata..")
Base.metadata.create_all(bind=engine)
- print("Done creating all...")
+ print("database.py: Done creating all model metadata...")
+ print("Point your browser at http://localhost:5003/")
init_db()
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a657510d..b0f5ed69 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -46,9 +46,9 @@ from wqflask.marker_regression import gemma_mapping
# runs at startup, so a missing binary will balk before running the
# service
-GEMMA_PATH,GEMMA_COMMAND = gemma_command()
-PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
-PLINK_PATH,PLINK_COMMAND = plink_command()
+GEMMA_RUN = gemma_command()
+PYLMM_RUN = pylmm_command()
+PLINK_RUN = plink_command()
# RQTL_PATH,RQTL_COMMAND = rqtl_command()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 2d4c952a..458e48da 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -16,7 +16,8 @@ from base import webqtlConfig
from base import webqtlCaseData
from wqflask.show_trait.SampleList import SampleList
from utility import webqtlUtil, Plot, Bunch, helper_functions
-from utility.tools import pylmm_command, plink_command
+# from utility.tools import plink_command
+from utility.tools import flat_files
from base.trait import GeneralTrait
from base import data_set
from dbFunction import webqtlDatabaseFunction
@@ -24,8 +25,7 @@ from basicStatistics import BasicStatisticsFunctions
from pprint import pformat as pf
-PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
-PLINK_PATH,PLINK_COMMAND = plink_command()
+MAPPING_FILES = flat_files("mapping")
###############################################
#
@@ -162,8 +162,8 @@ class ShowTrait(object):
def get_mapping_methods(self):
'''Only display mapping methods when the dataset group's genotype file exists'''
def check_plink_gemma():
- if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and
- os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")):
+ if (os.path.isfile(MAPPYING_FILES+"/"+self.dataset.group.name+".bed") and
+ os.path.isfile(MAPPING_FILES+"/"+self.dataset.group.name+".map")):
return True
else:
return False