Do not write empty per-sample fastq files

Author: Adam Robbins-Pianka

qiita_ware/commands.py

@@ -7,7 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from os.path import join, isdir
-from os import makedirs
+from os import makedirs, remove
 from functools import partial
 from tempfile import mkdtemp
 from gzip import open as gzopen
@@ -43,6 +43,11 @@ def submit_EBI(preprocessed_data_id, action, send, fastq_dir_fp=None):
         True to actually send the files
     fastq_dir_fp : str, optional
         The fastq filepath
+
+    Notes
+    -----
+    If fastq_dir_fp is passed, it must not contain any empty files, or
+    gzipped empty files
     """
     preprocessed_data = PreprocessedData(preprocessed_data_id)
     preprocessed_data_id_str = str(preprocessed_data_id)
@@ -99,9 +104,14 @@ def submit_EBI(preprocessed_data_id, action, send, fastq_dir_fp=None):
                                                       list(sample_template)):
                 demux_samples.add(samp)
                 sample_fp = join(fastq_dir_fp, "%s.fastq.gz" % samp)
+                wrote_sequences = False
                 with gzopen(sample_fp, 'w') as fh:
                     for record in iterator:
                         fh.write(record)
+                        wrote_sequences = True
+
+                if not wrote_sequences:
+                    remove(sample_fp)
 
     output_dir = fastq_dir_fp + '_submission'
 

qiita_ware/test/test_ebi.py

@@ -14,7 +14,6 @@
 from os import close, remove, path
 from os.path import join
 from tempfile import mkstemp, gettempdir
-from shutil import rmtree
 from unittest import TestCase, main
 from xml.dom import minidom
 from xml.etree import ElementTree as ET
@@ -577,10 +576,6 @@ def test_generate_curl_command(self):
         <TAG>library_construction_protocol</TAG>
         <VALUE>library protocol</VALUE>
       </EXPERIMENT_ATTRIBUTE>
-      <EXPERIMENT_ATTRIBUTE>
-        <TAG>md5</TAG>
-        <VALUE>506d31c82999a2cbcda138a369955e7d</VALUE>
-      </EXPERIMENT_ATTRIBUTE>
       <EXPERIMENT_ATTRIBUTE>
         <TAG>platform</TAG>
         <VALUE>ILLUMINA</VALUE>
@@ -594,7 +589,8 @@ def test_generate_curl_command(self):
 <?xml version="1.0" encoding="UTF-8"?>
 <RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:no\
 NamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_3/SRA.run.xsd">
-  <RUN alias="%(study_alias)s_sample1.fastq.gz_run" center_name="CCME-COLORADO">
+  <RUN alias="%(study_alias)s_sample1.fastq.gz_run" \
+center_name="CCME-COLORADO">
     <EXPERIMENT_REF refname="%(organization_prefix)s_ppdid_001:test1"/>
     <DATA_BLOCK>
       <FILES>