1 files changed, 33 insertions, 0 deletions
diff --git a/Code/publish_mapped_data.py b/Code/publish_mapped_data.py
new file mode 100644
index 0000000..2bd655c
--- /dev/null
+++ b/Code/publish_mapped_data.py
@@ -0,0 +1,33 @@
+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_files):
+    redis_host = os.getenv('REDIS_HOST', '127.0.0.1')
+    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 mapped_files:
+        print(fname)
+        try:
+            file_basename = os.path.basename(fname)
+            with open(fname, 'r') as f:
+                data = f.read()
+            r.publish(REDIS_CHANNEL, json.dumps({'filename':file_basename, 'data':data}))
+            time.sleep(3)
+        except Exception as e:
+            print(f'ERROR {e}')
+            r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_ERROR.txt', 'data':str(e)}))
+
+
+# after mapping is finished, move all resulting files to MAPPED_RDATA_DIR
+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.')