diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 82 | ||||
| -rwxr-xr-x | wqflask/wqflask/database.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 6 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 10 |
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 |