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Implement writing to compressed files for qseq2fastq
[htsworkflow.git]
/
htsworkflow
/
2016-06-21
Diane Trout
Implement writing to compressed files for qseq2fastq
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commitdiff
2016-04-20
Diane Trout
Extract part of get_json into get_response
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commitdiff
2015-12-03
Diane Trout
report run_type
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commitdiff
2015-12-03
Diane Trout
report if a flowcell was single or paired ended as...
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commitdiff
2015-12-03
Diane Trout
remove unused imports and variables
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commitdiff
2015-11-30
Diane Trout
make a more informative log message
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commitdiff
2015-11-30
Diane Trout
Read the first sequence out of the fastq to find the...
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commitdiff
2015-11-30
Diane Trout
refactor encode3 spreadsheet based object creation...
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commitdiff
2015-10-27
Diane Trout
update dotted path for python3
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commitdiff
2015-10-27
Diane Trout
update url to new standard url
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commitdiff
2015-10-27
Diane Trout
Update schema tests for upstreams release 33
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commitdiff
2015-10-27
Diane Trout
make exception dotted name python3 compliant
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commitdiff
2015-10-20
Diane Trout
this works better with python 3...
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commitdiff
2015-10-20
Diane Trout
apparently json.dump can write to a stream
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commitdiff
2015-10-20
Diane Trout
Add mode to connect to the DCC and make sure the files...
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commitdiff
2015-10-20
Diane Trout
add knowledge about file links
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commitdiff
2015-10-20
Diane Trout
updates to deal with encoded 33 path changes
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commitdiff
2015-10-20
Diane Trout
Merge branch 'django1.7' of mus.cacr.caltech.edu:htswor...
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commitdiff
2015-10-20
Diane Trout
move run_aws_cp command out of class to make it easier...
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commitdiff
2015-09-24
Diane Trout
Return read_length for file properties
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commitdiff
2015-09-23
Diane Trout
Use a re.split so we can accept both ', ' and ',' betwe...
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commitdiff
2015-09-08
Diane Trout
indicate we want text not bytes
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commitdiff
2015-09-08
Diane Trout
covert to using python3 config.get fallback=
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commitdiff
2015-07-20
Diane Trout
python3 byte vs str compatibility for constructing...
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commitdiff
2015-05-21
Diane Trout
Add AccessionAgency and LibraryAccession
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commitdiff
2015-05-12
Diane Trout
remove unused import
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commitdiff
2015-05-12
Diane Trout
move experiment templates into the experiments app
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commitdiff
2015-05-05
Diane Trout
simplify library report
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commitdiff
2015-05-05
Diane Trout
Move lanes_for from samples to experiments
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commitdiff
2015-04-06
Diane Trout
Oops I had a test function name collision. Rename one...
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commitdiff
2015-04-06
Diane Trout
Drop support for simplejson
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commitdiff
2015-04-06
Diane Trout
Update test to be more robust to changing dictionary...
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commitdiff
2015-04-06
Diane Trout
fix a white space issue
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commitdiff
2015-04-06
Diane Trout
convert non-unit-tested module to use newer raise Excep...
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commitdiff
2015-04-06
Diane Trout
convert several not covered by unit-test modules to...
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commitdiff
2015-04-06
Diane Trout
Be more careful looking up keys when the fastqname...
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commitdiff
2015-03-31
Diane Trout
add post_spreadsheet to create encoded objects from...
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commitdiff
2015-03-31
Diane Trout
also validate documents before creating them
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commitdiff
2015-03-31
Diane Trout
actually complain if we get the wrong type
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commitdiff
2015-03-31
Diane Trout
add a docstring to validate
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commitdiff
2015-03-31
Diane Trout
Add get_accession_name to use collection name to find...
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commitdiff
2015-03-31
Diane Trout
support trying to figure out object type based on what...
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commitdiff
2015-03-27
Diane Trout
Merge branch 'django1.7' of mus.cacr.caltech.edu:htswor...
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commitdiff
2015-03-27
Diane Trout
Switch encode3 submitter to use aws.
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commitdiff
2015-03-27
Diane Trout
Import flowcell details into the triple store from...
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commitdiff
2015-03-27
Diane Trout
store flowcell name in the triple store if its known
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commitdiff
2015-03-27
Diane Trout
record file size information for a file in the triple...
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commitdiff
2015-03-27
Diane Trout
getitem should only return the key
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commitdiff
2015-03-27
Diane Trout
clean up a bit of whitespace
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commitdiff
2015-03-20
Diane Trout
configure using a local postgres install
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commitdiff
2015-03-20
Diane Trout
Convert reads to an integer, if if it was a float in...
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commitdiff
2015-03-20
Diane Trout
Actually comare an integer (length of list) to an integ...
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commitdiff
2015-03-20
Diane Trout
Drop library id encoding
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commitdiff
2015-03-20
Diane Trout
Use regex to make sure scripts end with the right command
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commitdiff
2015-03-20
Diane Trout
Use six.moves to find urlencode and urlopen
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commitdiff
2015-03-20
Diane Trout
filter out None c.times in list of potential times
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commitdiff
2015-03-20
Diane Trout
use relative import for submission_test_common
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commitdiff
2015-03-20
Diane Trout
Try to detect if an object is a file type on python...
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commitdiff
2015-03-20
Diane Trout
replace xrange with enumerate
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commitdiff
2015-03-20
Diane Trout
Use ''.splitlines() instead of split('\n')
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commitdiff
2015-03-20
Diane Trout
adapt to python2 returning lists and python3 iterators
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commitdiff
2015-03-20
Diane Trout
use sorted on the iterator instead of an in-place sort
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commitdiff
2015-03-20
Diane Trout
Use max on the iterator to find the last key
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commitdiff
2015-03-20
Diane Trout
add more from __future__ import print_function, unicode...
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commitdiff
2015-03-20
Diane Trout
Call print(msg) instead of print msg
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commitdiff
2015-03-20
Diane Trout
special case unicode handling that differs between...
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commitdiff
2015-03-20
Diane Trout
Replace some unicode() with str()
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commitdiff
2015-03-20
Diane Trout
Use isinstance(object, (types)) pattern instead of...
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commitdiff
2015-03-20
Diane Trout
Specify text vs binary mode for opening files.
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commitdiff
2015-03-20
Diane Trout
prefer native string types.
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commitdiff
2015-03-20
Diane Trout
update more raise exceptions to Exception(message)...
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commitdiff
2015-03-19
Diane Trout
Use django.utils.encode smart_text or smart_str for...
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commitdiff
2015-03-18
Diane Trout
import ConfigParser classes from six.moves.configparser
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commitdiff
2015-02-03
Diane Trout
convert to unicode_literals
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commitdiff
2015-02-02
Diane Trout
take advantage of absolute_import to simplify import...
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commitdiff
2015-02-02
Diane Trout
base64.encodestring needs a bytearray in python3
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commitdiff
2015-02-02
Diane Trout
Replace elif list() > int() with else
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commitdiff
2015-01-30
Diane Trout
properly call usrlib.parse instead of urlparse
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commitdiff
2015-01-30
Diane Trout
Convert alphanum sort from comparitor to key operator
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commitdiff
2015-01-29
Diane Trout
update srf2fastq detection code to work with byte arrays
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commitdiff
2015-01-29
Diane Trout
assume we are writing text with gzip
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commitdiff
2015-01-29
Diane Trout
replace iterkeys with python 3 equivalents
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commitdiff
2015-01-29
Diane Trout
convert has_key to X in dictionary
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commitdiff
2015-01-29
Diane Trout
use six.moves to work around urllib / urllib2 / urlpars...
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commitdiff
2015-01-29
Diane Trout
remove unicode_literals from things going to redland RDF
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commitdiff
2015-01-29
Diane Trout
remove some commented out code
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commitdiff
2015-01-29
Diane Trout
convert some print statements to logger messages
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commitdiff
2015-01-29
Diane Trout
convert to print_function, and start adding unicode_lit...
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commitdiff
2015-01-29
Diane Trout
remove ,'s from more except blocks, and now a raise too
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commitdiff
2015-01-29
Diane Trout
more use six.moves to import StringIO
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commitdiff
2015-01-29
Diane Trout
use six.moves to get to python3-style urllib
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commitdiff
2015-01-29
Diane Trout
whitespace-cleanup
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commitdiff
2015-01-29
Diane Trout
remove some commented out code
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commitdiff
2015-01-29
Diane Trout
convert to print_function
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commitdiff
2015-01-29
Diane Trout
use six to work around rename of configparser
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commitdiff
2015-01-29
Diane Trout
Convert old style except blocks to except Exception...
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commitdiff
2015-01-28
Diane Trout
make the search tool more flexible
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commitdiff
2015-01-21
Diane Trout
Update test_retrieve_config to work with factories
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commitdiff
2015-01-14
Diane Trout
fix spelling error in module name
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commitdiff
2015-01-13
Diane Trout
Don't pass null authentication information to ENCODED.
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