From 7957580488b8c73307e007beea96d8485eb11283 Mon Sep 17 00:00:00 2001
From: Isaac Hodes <isaachodes@gmail.com>
Date: Fri, 18 Dec 2015 11:29:20 -0500
Subject: [PATCH] Delete obsolete BAM indexer worker

---
 cycledash/api/bams.py |  1 -
 workers/indexer.py    | 40 ----------------------------------------
 2 files changed, 41 deletions(-)
 delete mode 100644 workers/indexer.py

diff --git a/cycledash/api/bams.py b/cycledash/api/bams.py
index febb9ec..1009643 100644
--- a/cycledash/api/bams.py
+++ b/cycledash/api/bams.py
@@ -10,7 +10,6 @@
 from cycledash import db
 from cycledash.helpers import abort_if_none_for
 from cycledash.validations import Doc
-import workers.indexer
 
 import projects
 from . import Resource, marshal_with, validate_with
diff --git a/workers/indexer.py b/workers/indexer.py
deleted file mode 100644
index 81468c2..0000000
--- a/workers/indexer.py
+++ /dev/null
@@ -1,40 +0,0 @@
-"""Index BAM Index (BAI) files
-
-This accepts a BAM HDFS path. If there's no BAM Index Index (.bam.bai.json)
-file already available, it will generate one and put it on HDFS.
-"""
-
-import json
-
-import bai_indexer
-from StringIO import StringIO
-
-from workers.shared import (get_contents_from_hdfs, worker,
-                            put_new_file_to_hdfs, does_hdfs_file_exist,
-                            HdfsFileAlreadyExistsError, register_running_task,
-                            DATABASE_URI, initialize_database)
-
-@worker.task(bind=True)
-def index(self, bam_id):
-    engine, connection, metadata = initialize_database(DATABASE_URI)
-    bams_table = metadata.tables.get('bams')
-    bam = bams_table.select().where(bams_table.c.id == bam_id).execute().fetchone()
-    bam_path = bam['uri']
-
-    if '.bam' not in bam_path:
-        raise ValueError('Expected path to BAM file, got %s' % bam_path)
-
-    bai_path = bam_path.replace('.bam', '.bam.bai')
-    bai_json_path = bam_path.replace('.bam', '.bam.bai.json')
-
-    if does_hdfs_file_exist(bai_json_path):
-        return  # nothing to do -- it's already been created
-
-    contents = get_contents_from_hdfs(bai_path)
-    index_json = bai_indexer.index_stream(StringIO(contents))
-    index_json_str = json.dumps(index_json)
-
-    try:
-        put_new_file_to_hdfs(bai_json_path, index_json_str)
-    except HdfsFileAlreadyExistsError:
-        pass  # we lost the race! (e.g. two runs were submitted simultaneously)