diff options
| -rw-r--r-- | wqflask/utility/temp_data.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 8 |
2 files changed, 13 insertions, 9 deletions
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index ddf2653c..60f01167 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -1,14 +1,15 @@ from __future__ import print_function, division, absolute_import from redis import Redis +import redis import simplejson as json class TempData(object): - - def __init__(self, temp_uuid, part=None): + + def __init__(self, temp_uuid, preface="tempdata", part=None): self.temp_uuid = temp_uuid self.redis = Redis() - self.key = "tempdata:{}".format(self.temp_uuid) + self.key = "{}:{}".format(preface, self.temp_uuid) if part: self.key += ":{}".format(part) @@ -19,9 +20,12 @@ class TempData(object): def get_all(self): return self.redis.hgetall(self.key) - if __name__ == "__main__": redis = Redis() for key in redis.keys(): + print("key is:", key) + if "plink" not in key: + print(" Skipping...\n") + continue for field in redis.hkeys(key): - print("{}.{}={}".format(key, field, redis.hget(key, field))) + print(" {}.{}={}\n".format(key, field, len(redis.hget(key, field)))) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 8c0e0282..a6134fdd 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -89,13 +89,13 @@ def run_human(pheno_vector, with Bench("Divide into chunks"): results = chunks.divide_into_chunks(inputs, 64) - + result_store = [] identifier = uuid.uuid4() for part, result in enumerate(results): - data_store = temp_data.TempData(identifier, part) + data_store = temp_data.TempData(identifier, "plink", part) - data_store.store(data=pickle.dumps(result)) + data_store.store("data", pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) result_store.append(data_store) for snp, this_id in plink_input: @@ -103,7 +103,7 @@ def run_human(pheno_vector, if count > 2000: break count += 1 - + percent_complete = (float(count) / total_snps) * 100 #print("percent_complete: ", percent_complete) loading_progress.store("percent_complete", percent_complete) |