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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py6
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/standalone.py5
2 files changed, 9 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 66c952aa..95272818 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -57,10 +57,11 @@ import gwas
# ---- A trick to decide on the environment:
try:
from wqflask.my_pylmm.pyLMM import chunks
- from gn2 import uses
+ from gn2 import uses, set_progress_storage
except ImportError:
has_gn2=False
- from standalone import uses
+ import standalone as handlers
+ from standalone import uses, set_progress_storage
sys.stderr.write("WARNING: LMM standalone version missing the Genenetwork2 environment\n")
pass
@@ -816,6 +817,7 @@ def gn2_redis(key,species,new_code=True):
params = json.loads(json_params)
tempdata = temp_data.TempData(params['temp_uuid'])
+ set_progress_storage(tempdata)
print('kinship', np.array(params['kinship_matrix']))
print('pheno', np.array(params['pheno_vector']))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index 538007f1..e20d4092 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -17,7 +17,12 @@ logger = logging.getLogger('lmm2')
logging.basicConfig(level=logging.DEBUG)
np.set_printoptions(precision=3,suppress=True)
+def set_progress_storage(location):
+ global storage
+ storage = location
+
def progress(location, count, total):
+ storage['percentage'] = round(count*100.0)/total)
logger.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
def mprint(msg,data):