# HG changeset patch
# User peterjc
# Date 1390329200 18000
# Node ID de11e1a921c4ba077ed57ae456369d99d49ad4fa
# Parent 5ec5dece43cb17a4f41870e636f110063aa08cc5
Uploaded v0.0.18, tweak display_data for running tests
diff -r 5ec5dece43cb -r de11e1a921c4 README.rst
--- a/README.rst Tue Jan 21 13:32:49 2014 -0500
+++ b/README.rst Tue Jan 21 13:33:20 2014 -0500
@@ -39,6 +39,8 @@
- Development moved to GitHub, https://github.com/peterjc/galaxy_blast
- Nucleotide database definition aware of MegaBLAST index superheader
v0.0.17 - Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
+v0.0.18 - Add retries to BLAST XML merge code.
+ - Modify display_data method to allow unit tests to function.
======= ======================================================================
diff -r 5ec5dece43cb -r de11e1a921c4 blast.py
--- a/blast.py Tue Jan 21 13:32:49 2014 -0500
+++ b/blast.py Tue Jan 21 13:33:20 2014 -0500
@@ -7,6 +7,11 @@
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.metadata import MetadataElement
+from time import sleep
+import os
+import logging
+
+log = logging.getLogger(__name__)
class BlastXml( GenericXml ):
"""NCBI Blast XML Output data"""
@@ -64,13 +69,26 @@
out = open(output_file, "w")
h = None
for f in split_files:
+ if not os.path.isfile(f):
+ log.warning("BLAST XML file %s missing, retry in 1s..." % f)
+ sleep(1)
+ if not os.path.isfile(f):
+ log.error("BLAST XML file %s missing" % f)
+ raise ValueError("BLAST XML file %s missing" % f)
h = open(f)
body = False
header = h.readline()
if not header:
out.close()
h.close()
- raise ValueError("BLAST XML file %s was empty" % f)
+ #Retry, could be transient error with networked file system...
+ log.warning("BLAST XML file %s empty, retry in 1s..." % f)
+ sleep(1)
+ h = open(f)
+ header = h.readline()
+ if not header:
+ log.error("BLAST XML file %s was empty" % f)
+ raise ValueError("BLAST XML file %s was empty" % f)
if header.strip() != '':
out.write(header) #for diagnosis
out.close()
@@ -150,15 +168,34 @@
def display_data(self, trans, data, preview=False, filename=None,
to_ext=None, size=None, offset=None, **kwd):
- """Apparently an old display method, but still gets called.
+ """Documented as an old display method, but still gets called via tests etc
This allows us to format the data shown in the central pane via the "eye" icon.
"""
- return "This is a BLAST database."
-
- def get_mime(self):
- """Returns the mime type of the datatype (pretend it is text for peek)"""
- return 'text/plain'
+ if filename is not None and filename != "index":
+ #Change nothing - important for the unit tests to access child files:
+ return Data.display_data(self, trans, data, preview, filename,
+ to_ext, size, offset, **kwd)
+ if self.file_ext == "blastdbn":
+ title = "This is a nucleotide BLAST database"
+ elif self.file_ext =="blastdbp":
+ title = "This is a protein BLAST database"
+ else:
+ #Error?
+ title = "This is a BLAST database."
+ msg = ""
+ try:
+ #Try to use any text recorded in the dummy index file:
+ handle = open(data.file_name, "rU")
+ msg = handle.read().strip()
+ handle.close()
+ except Exception, err:
+ #msg = str(err)
+ pass
+ if not msg:
+ msg = title
+ #Galaxy assumes HTML for the display of composite datatypes,
+ return "%s%s
" % (title, msg)
def merge(split_files, output_file):
"""Merge BLAST databases (not implemented for now)."""
@@ -174,7 +211,8 @@
class BlastNucDb( _BlastDb, Data ):
"""Class for nucleotide BLAST database files."""
file_ext = 'blastdbn'
- composite_type ='basic'
+ allow_datatype_change = False
+ composite_type = 'basic'
def __init__(self, **kwd):
Data.__init__(self, **kwd)
@@ -197,19 +235,12 @@
# self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column
# The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc.
- def display_data(self, trans, data, preview=False, filename=None,
- to_ext=None, size=None, offset=None, **kwd):
- """Apparently an old display method, but still gets called.
-
- This allows us to format the data shown in the central pane via the "eye" icon.
- """
- return "This is a BLAST nucleotide database."
-
class BlastProtDb( _BlastDb, Data ):
"""Class for protein BLAST database files."""
file_ext = 'blastdbp'
- composite_type ='basic'
+ allow_datatype_change = False
+ composite_type = 'basic'
def __init__(self, **kwd):
Data.__init__(self, **kwd)
@@ -228,11 +259,3 @@
# self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
# self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
# The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.
-
- def display_data(self, trans, data, preview=False, filename=None,
- to_ext=None, size=None, offset=None, **kwd):
- """Apparently an old display method, but still gets called.
-
- This allows us to format the data shown in the central pane via the "eye" icon.
- """
- return "This is a BLAST protein database."