Merge https://github.com/genenetwork/genenetwork2

1 files changed, 84 insertions, 0 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
new file mode 100644
index 00000000..760ded7c
--- /dev/null
+++ b/wqflask/utility/tools.py
@@ -0,0 +1,84 @@
+# 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
+    """
+    # ---- 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):
+    """
+    Return the path to the repository and the python command to call
+    """
+    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
+        else:
+            None
+
+    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):
+    """
+    Return the path to the repository and the python command to call
+    """
+    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'
+    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
+
+    guess = os.environ.get('HOME')+'/plink'
+    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
+    gemma_command = path+'/gemma'
+    return path, gemma_command
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