Skip test requiring network access when it is not available.

[charles-plessy]

Dear Andreas,

for the Debian package of Pysam, we need to skip tests requiring network, since it is unavailable by design in some of our build farm. Would you like to provide such an offline facility in Pysam ?

Here is how I would do on one file (inspired by bits and pieces saw on StackOverflow).

--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -7,6 +7,7 @@ and data files located there.

 import pysam
 import unittest
+import urllib2
 import os
 import shutil
 import sys
@@ -21,6 +22,12 @@ SAMTOOLS = "samtools"
 WORKDIR = "pysam_test_work"
 DATADIR = "pysam_data"

+def internet_on():
+    try:
+        response=urllib2.urlopen('http://ftp.1000genomes.ebi.ac.uk',timeout=1)
+        return True
+    except urllib2.URLError as err: pass
+    return False

 class BasicTestBAMFetch(unittest.TestCase):

@@ -973,6 +980,8 @@ class TestHeaderFromRefs(unittest.TestCase):

 class TestHeader1000Genomes(unittest.TestCase):
     '''see issue 110'''
+    if internet_on() == False:
+        self.skipTest('Internet access required for this test')
     # bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
     bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase3_EX_or_LC_only_alignment/data/HG00104/alignment/HG00104.chrom11.ILLUMINA.bwa.GBR.low_coverage.20130415.bam"

However, multiple files have tests requiring the network. Is there a better solution than cut-and-paste?

Have a nice day,

Charles

[AndreasHeger]

Hi Charles,

I have added this - will be part of the next release.

Best wishes,
Andreas

[AndreasHeger]

Need to redo, lost changes in bricked laptop.

[AndreasHeger]

see SHA:ff2b0a96974847a5a16d24628941a1c69084e9a6