Running the publisher as a seperate script seems solved the problem of not being able to receive messages.

3 files changed, 25 insertions, 14 deletions

diff --git a/Code/download_and_map.py b/Code/download_and_map.py
index 0e8f160..2a0a157 100644
--- a/Code/download_and_map.py
+++ b/Code/download_and_map.py
@@ -392,6 +392,7 @@ def publish(mapped_data_directory):
     redis_password = os.getenv('REDIS_PASSWORD', '123456')
     r = redis.Redis(host=redis_host, port=6379, password=redis_password, db=0)
     r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_START.txt', 'data':str(datetime.now())}))
+    time.sleep(3)
     for fname in glob.glob('%s/*_quant.txt' % (mapped_data_directory.rstrip('/'))):
         try:
             file_basename = os.path.basename(fname)
@@ -400,7 +401,7 @@ def publish(mapped_data_directory):
             r.publish(REDIS_CHANNEL, json.dumps({'filename':file_basename, 'data':data}))
         except Exception as e:
             r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_ERROR.txt', 'data':str(e)}))
-        time.sleep(1)
+        time.sleep(3)
 
 ## main
 
@@ -421,6 +422,8 @@ if not last_session_finished(DOWNLOADED_SRA_ID_LOG_FILE): # last session not fin
     write_network_log_file(s, UPDATE_NETWORK_LOG_FILE)
     if age_of_file_in_hours(DOWNLOADED_SRA_ID_LOG_FILE) > 24: # add DONE to the log file anyway
         append_done(DOWNLOADED_SRA_ID_LOG_FILE)
+        download_log_file(DOWNLOADED_SRA_ID_LOG_FILE, 'DONE at %s\n' % (curr_time))
+        reverse_lines(DOWNLOADED_SRA_ID_LOG_FILE, os.path.splitext(DOWNLOADED_SRA_ID_LOG_FILE)[0] + '_reversed.txt')
     kill_process('wget')
     sys.exit()
 
@@ -450,14 +453,21 @@ if not os.path.isdir(MAPPED_RDATA_DIR):
 
 # after mapping is finished, move all resulting files to MAPPED_RDATA_DIR
 if glob.glob('%s/*_quant.txt' % (SALMON_MAP_RESULT_DIR.rstrip('/'))) != []:
-    publish(SALMON_MAP_RESULT_DIR)
-    cmd = 'mv %s/*_quant.txt %s' % (SALMON_MAP_RESULT_DIR.rstrip('/'), MAPPED_RDATA_DIR)
+
+    try:
+        write_log_file('[download_and_map.py] Ready to publish quant files.', UPDATE_NETWORK_LOG_FILE)
+        publish(SALMON_MAP_RESULT_DIR)
+        time.sleep(5)
+    except Exception as e:
+        write_log_file('[download_and_map.py] Publish error %s.' % (str(e)), UPDATE_NETWORK_LOG_FILE)
+
+    cmd = 'cp %s/*_quant.txt %s' % (SALMON_MAP_RESULT_DIR.rstrip('/'), MAPPED_RDATA_DIR)
     os.system(cmd)
     print('[download_and_map.py] Done. Check directory %s.' % (os.path.abspath(MAPPED_RDATA_DIR)))
 else:
     print('[download_and_map.py] No quant files to move.')
-
+    write_log_file('[download_and_map.py] No quant files to move.', UPDATE_NETWORK_LOG_FILE)
 
 write_download_log_file(DOWNLOADED_SRA_ID_LOG_FILE, '%s\n' % ('\n'.join(map_list)))
-write_download_log_file(DOWNLOADED_SRA_ID_LOG_FILE, 'DONE at %s\n' % (curr_time))
+download_log_file(DOWNLOADED_SRA_ID_LOG_FILE, 'DONE at %s\n' % (curr_time))
 reverse_lines(DOWNLOADED_SRA_ID_LOG_FILE, os.path.splitext(DOWNLOADED_SRA_ID_LOG_FILE)[0] + '_reversed.txt')
diff --git a/Code/test_redis_publish2.py b/Code/publish_mapped_data.py
index eeda27d..2bd655c 100644
--- a/Code/test_redis_publish2.py
+++ b/Code/publish_mapped_data.py
@@ -2,14 +2,13 @@ import redis
 from configure import DAILY_MAP_NUMBER, MIN_FASTQ_FILE_SIZE, RNA_SEQ_INFO_FILE, DOWNLOADED_SRA_ID_LOG_FILE, IGNORED_SRA_ID_LOG_FILE, UPDATE_NETWORK_LOG_FILE, MAPPED_RDATA_DIR, RAW_RDATA_DIR, SALMON_MAP_RESULT_DIR, REDIS_CHANNEL
 import json, glob, os, time
 from datetime import datetime
-def publish(mapped_data_directory):
+def publish(mapped_files):
     redis_host = os.getenv('REDIS_HOST', '127.0.0.1')
-    #redis_host = os.getenv('REDIS_HOST', '0.0.0.0')
     redis_password = os.getenv('REDIS_PASSWORD', '123456')
     print(redis_password)
     r = redis.Redis(host=redis_host, port=6379, password=redis_password, db=0)
     r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_START.txt', 'data':str(datetime.now())}))
-    for fname in glob.glob('%s/*_quant.txt' % (mapped_data_directory.rstrip('/'))):
+    for fname in mapped_files:
         print(fname)
         try:
             file_basename = os.path.basename(fname)
@@ -23,10 +22,12 @@ def publish(mapped_data_directory):
 
 
 # after mapping is finished, move all resulting files to MAPPED_RDATA_DIR
-if glob.glob('%s/*_quant.txt' % (SALMON_MAP_RESULT_DIR.rstrip('/'))) != []:
-    publish(SALMON_MAP_RESULT_DIR)
-    #cmd = 'mv %s/*_quant.txt %s' % (SALMON_MAP_RESULT_DIR.rstrip('/'), MAPPED_RDATA_DIR)
-    #os.system(cmd)
+mapped_files = glob.glob('%s/*_quant.txt' % (SALMON_MAP_RESULT_DIR.rstrip('/')))
+print(mapped_files)
+publish(mapped_files)
+if mapped_files != []:
+    cmd = 'mv %s/*_quant.txt %s' % (SALMON_MAP_RESULT_DIR.rstrip('/'), MAPPED_RDATA_DIR)
+    os.system(cmd)
     print('[download_and_map.py] Done. Check directory %s.' % (os.path.abspath(MAPPED_RDATA_DIR)))
 else:
     print('[download_and_map.py] No quant files to move.')
diff --git a/Code/test_redis_publish.py b/Code/test_redis_publish.py
index 937833f..722e80e 100644
--- a/Code/test_redis_publish.py
+++ b/Code/test_redis_publish.py
@@ -8,7 +8,7 @@ def publish(number):
     r.publish(REDIS_CHANNEL, json.dumps({'filename':'a.txt', 'data':str(number)}))
 
 n = 0
-while True:
+while n < 10:
     publish(n)
-    time.sleep(3)
+    time.sleep(2)
     n += 1