diff options
Diffstat (limited to 'wqflask/utility/tools.py')
| -rw-r--r-- | wqflask/utility/tools.py | 189 |
1 files changed, 121 insertions, 68 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index b8a41f60..dd8c4a1e 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,84 +1,137 @@ # Tools/paths finder resolves external paths from settings and/or environment # variables -# -# Currently supported: -# -# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool import os import sys from wqflask import app -def get_setting(id,default,guess,get_valid_path): - """ - Resolve a setting from the environment or the global settings in app.config +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 and returns the full path to + the binary command + + guess = os.environ.get('HOME')+'/pylmm' + get_setting('PYLMM_PATH',guess) + + first tries the environment variable in +id+, next gets the Flask + 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 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 + proper way is to either use the GNU Guix defaults as listed in + etc/default_settings.py or override them yourself by creating a + different settings.py file (or setting the environment). + """ + def value(command): + if command: + sys.stderr.write("Found path "+command+"\n") + return command + else: + return None + # ---- Check whether environment exists - path = get_valid_path(os.environ.get(id)) - # ---- Check whether setting exists - setting = app.config.get(id) - if not path: - path = get_valid_path(setting) - # ---- Check whether default exists - if not path: - path = get_valid_path(default) - # ---- Guess directory - if not path: - if not setting: - setting = guess - path = get_valid_path(guess) - if not path: - raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository') - - return path - -def pylmm_command(default=None): + sys.stderr.write("Looking for "+command_id+"\n") + command = value(os.environ.get(command_id)) + if not command: + # ---- Check whether setting exists in app + command = value(app.config.get(command_id)) + if not command: + command = value(guess) + if not command: + raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') + return command + +def valid_bin(bin): + if os.path.islink(bin) or valid_file(bin): + return bin + return None + +def valid_file(fn): + if os.path.isfile(fn): + return fn + return None + +def valid_path(dir): + if os.path.isdir(dir): + return dir + return None + +def pylmm_command(guess=None): + return valid_bin(get_setting("PYLMM_COMMAND",guess)) + +def gemma_command(guess=None): + return valid_bin(get_setting("GEMMA_COMMAND",guess)) + +def plink_command(guess=None): + return valid_bin(get_setting("PLINK_COMMAND",guess)) + +def flat_files(subdir=None): + base = get_setting("GENENETWORK_FILES") + if subdir: + return assert_dir(base+"/"+subdir) + return assert_dir(base) + +def assert_dir(dir): + if not valid_path(dir): + raise Exception("ERROR: can not find directory "+dir) + return dir + +def mk_dir(dir): + if not valid_path(dir): + os.makedirs(dir) + return assert_dir(dir) + +def locate(name, subdir=None): """ - Return the path to the repository and the python command to call + Locate a static flat file in the GENENETWORK_FILES environment. + + This function throws an error when the file is not found. """ - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PYLMM_PATH in "+path+"\n") - if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'): - return path + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_file(lookfor): + print("Found: file "+lookfor+"\n") + return lookfor else: - None + raise Exception("Can not locate "+lookfor) + if subdir: sys.stderr.write(subdir) + raise Exception("Can not locate "+name+" in "+base) - guess = os.environ.get('HOME')+'/pylmm_gn2' - path = get_setting('PYLMM_PATH',default,guess,get_valid_path) - pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py' - return path,pylmm_command - -def plink_command(default=None): +def locate_ignore_error(name, subdir=None): """ - Return the path to the repository and the python command to call + Locate a static flat file in the GENENETWORK_FILES environment. + + This function does not throw an error when the file is not found + but returns None. """ - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None - - guess = os.environ.get('HOME')+'/plink_gemma' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - plink_command = path+'/plink' - return path,plink_command - -def gemma_command(default=None): - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_file(lookfor): + print("Found: file "+name+"\n") + return lookfor + sys.stderr.write("WARNING: file "+name+" not found\n") + return None + +def tempdir(): + return valid_path(get_setting("TEMPDIR","/tmp")) - guess = os.environ.get('HOME')+'/plink' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - gemma_command = path+'/gemma' - return path, gemma_command
\ No newline at end of file + +# Cached values +PYLMM_COMMAND = pylmm_command() +GEMMA_COMMAND = gemma_command() +PLINK_COMMAND = plink_command() +FLAT_FILES = flat_files() +TEMPDIR = tempdir() |