From 837ce8b9c779b1da6e4390220ccd353b289c1fca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 09:11:31 -0600
Subject: Bring in some earlier work - mostly documentation and startup
 handling

---
 wqflask/utility/tools.py | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

(limited to 'wqflask/utility/tools.py')

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c5685cdd..63b7149c 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -147,9 +147,14 @@ def assert_writable_dir(dir):
         fh.close()
         os.remove(fn)
     except IOError:
-        raise Exception('Unable to write test.txt to directory ' + dir )
+        raise Exception('Unable to write test.txt to directory ' + dir)
     return dir
 
+def assert_file(fn):
+    if not valid_file(fn):
+        raise Exception('Unable to find file '+fn)
+    return fn
+
 def mk_dir(dir):
     if not valid_path(dir):
         os.makedirs(dir)
@@ -174,6 +179,9 @@ def locate(name, subdir=None):
     if subdir: sys.stderr.write(subdir)
     raise Exception("Can not locate "+name+" in "+base)
 
+def locate_phewas(name, subdir=None):
+    return locate(name,'/phewas/'+subdir)
+
 def locate_ignore_error(name, subdir=None):
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
@@ -243,11 +251,11 @@ JS_GUIX_PATH       = get_setting('JS_GUIX_PATH')
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
-PYLMM_COMMAND         = pylmm_command()
-GEMMA_COMMAND         = gemma_command()
-GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
-PLINK_COMMAND         = plink_command()
-TEMPDIR               = tempdir() # defaults to UNIX TMPDIR
+PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
+GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
+PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
+TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
+assert_dir(TEMPDIR)
 
 # ---- Handle specific JS modules
 JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
@@ -267,3 +275,10 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             else:
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
+
+assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
+assert_dir(get_setting("JS_BIODALLIANCE"))
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
+assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
-- 
cgit v1.2.3


From 8ae775f831c278a3ad97372ad90cba5845e8e6ca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 10:02:43 -0600
Subject: tools: find path for JS and gemma_wrapper

---
 wqflask/utility/tools.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

(limited to 'wqflask/utility/tools.py')

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 63b7149c..57f97a81 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -105,7 +105,7 @@ def js_path(module=None):
     try_guix = get_setting("JS_GUIX_PATH")+"/"+module
     if valid_path(try_guix):
         return try_guix
-    raise "No JS path found for "+module+" (check JS_GN_PATH)"
+    raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
 
 def pylmm_command(guess=None):
     return assert_bin(get_setting("PYLMM_COMMAND",guess))
@@ -247,13 +247,14 @@ USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
 JS_GUIX_PATH       = get_setting('JS_GUIX_PATH')
-# assert_dir(JS_GUIX_PATH) - don't enforce right now
+assert_dir(JS_GUIX_PATH)
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
 PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
 GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
 PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
+GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 assert_dir(TEMPDIR)
 
@@ -276,9 +277,9 @@ if os.environ.get('WQFLASK_OVERRIDES'):
                 OVERRIDES[k] = cmd
             logger.debug(OVERRIDES)
 
-assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-assert_dir(get_setting("JS_BIODALLIANCE"))
-assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
-assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
-assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
+# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
+# assert_dir(get_setting("JS_BIODALLIANCE"))
+# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
+# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
+# assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
-- 
cgit v1.2.3