convert to unicode_literals

convert all the string handling to unicode.
to make the RDF stuff work I needed to mark those strings
as byte arrays

diff --git a/bcmagic/admin.py b/bcmagic/admin.py
index bb1d1d0381e80c718d57f9acecb2ec6562c5f057..a70dad82fe862e7bd80e8199259a8486cca613ea 100644 (file)
--- a/bcmagic/admin.py
+++ b/bcmagic/admin.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.contrib import admin
 from .models import KeywordMap, Printer
 

diff --git a/bcmagic/forms.py b/bcmagic/forms.py
index 000acd955651d084c0a22da05d5f1eb092072160..c80a44f49e3e0c59a04422ae380ad44a265b6e1a 100644 (file)
--- a/bcmagic/forms.py
+++ b/bcmagic/forms.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django import forms
 
 class BarcodeMagicForm(forms.Form):

diff --git a/bcmagic/models.py b/bcmagic/models.py
index 4db58a3ddd8e5b27bfcc539cae7fd12fa92a4f74..c91905b7259277d2728e61eb6cb010d2fbc070ee 100644 (file)
--- a/bcmagic/models.py
+++ b/bcmagic/models.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.db import models
 
 #FIXME: Should be made more generic and probably pre-populated supported list
@@ -27,5 +29,5 @@ class Printer(models.Model):
     label_height = models.FloatField(help_text='height in inches')
     notes = models.TextField()
 
-    def __unicode__(self):
-        return u'%s, %s, %s, %s, %sx%s' % (self.name, self.model, self.ip_address, self.label_shape, self.label_width, self.label_width)
\ No newline at end of file
+    def __str__(self):
+        return '%s, %s, %s, %s, %sx%s' % (self.name, self.model, self.ip_address, self.label_shape, self.label_width, self.label_width)

diff --git a/bcmagic/plugin.py b/bcmagic/plugin.py
index 12de8d23d575f1d7721b369ba03cc819764bcb75..09a1f8ad022e70c53b734d3f32e305a9d6cd3e66 100644 (file)
--- a/bcmagic/plugin.py
+++ b/bcmagic/plugin.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 BCM_PLUGINS = {
     #'cmd_move_sample': bcm_cmds.cmd_move_sample
 }

diff --git a/bcmagic/urls.py b/bcmagic/urls.py
index 9133391538c3521a44e9ccbdd4ae820d4e3294ee..478e3c848db721014a2fde2b85d9e239abc7066c 100644 (file)
--- a/bcmagic/urls.py
+++ b/bcmagic/urls.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf.urls import patterns
 
 urlpatterns = patterns('',

diff --git a/bcmagic/utils.py b/bcmagic/utils.py
index 9374e4ae4dfa69940065ed8ac20d37fa3c098a1e..a7982003d44477aba87a3ef961331ef0af5e3d1c 100644 (file)
--- a/bcmagic/utils.py
+++ b/bcmagic/utils.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf import settings
 
 import ftplib

diff --git a/bcmagic/views.py b/bcmagic/views.py
index 3d9206fec91e52321043f649cfb9937481f0a07e..4efbcaa7503460420b742396fcaa31922f6fed12 100644 (file)
--- a/bcmagic/views.py
+++ b/bcmagic/views.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.http import HttpResponse
 from django.template import RequestContext, Template, Context
 from django.shortcuts import render_to_response

diff --git a/eland_config/admin.py b/eland_config/admin.py
index 56107ffcca778463f0d86da98acc48d8aa5470a8..895ecb1431a0eae202a0506b49ae5b58247c3284 100644 (file)
--- a/eland_config/admin.py
+++ b/eland_config/admin.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.contrib import admin
 from django.utils.translation import ugettext_lazy as _
 

diff --git a/eland_config/forms.py b/eland_config/forms.py
index a2245f9f35548fe8f231f30cfd7505e18230ea9f..c24bb624d1ca4b335c3781db37051113066ff4d3 100644 (file)
--- a/eland_config/forms.py
+++ b/eland_config/forms.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django import forms
 from django.forms.util import ErrorList
 

diff --git a/eland_config/models.py b/eland_config/models.py
index 71a836239075aa6e6e4ecb700e9c42c95c022d91..bd4b2abe9e8520ac85fee31e2fd7ed02997b4eaa 100644 (file)
--- a/eland_config/models.py
+++ b/eland_config/models.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.db import models
 
 # Create your models here.

diff --git a/eland_config/urls.py b/eland_config/urls.py
index eff1477fa2c1eb308bd4a12ba3ab00c6875653f7..38a2cc39574fb4e4514b826dddf463cdd2572fbd 100644 (file)
--- a/eland_config/urls.py
+++ b/eland_config/urls.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf.urls import patterns, url
 
 urlpatterns = patterns('',

diff --git a/eland_config/views.py b/eland_config/views.py
index f4d765e807fad5166b9822d464313376c0c2d7ef..db307411e7141eadd740894ae437738671e4745e 100644 (file)
--- a/eland_config/views.py
+++ b/eland_config/views.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.conf import settings
 from django.http import HttpResponse

diff --git a/experiments/admin.py b/experiments/admin.py
index 4ae00607a4d742720682abbb3f24f71cf62ac2e1..b8fff8ac8cd62979d13a1df08d96bc2a589176e9 100644 (file)
--- a/experiments/admin.py
+++ b/experiments/admin.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from itertools import chain
 
@@ -185,8 +185,8 @@ class SequencerSelect(Select):
 
 
     def render_option(self, selected_choices, option_value, option_label):
-        disabled_sequencers = [ unicode(s.id) for s in self.queryset.filter(active=False) ]
-        option_value = unicode(option_value)
+        disabled_sequencers = [ str(s.id) for s in self.queryset.filter(active=False) ]
+        option_value = str(option_value)
         selected_html = (option_value in selected_choices) and u' selected="selected"' or ''
         cssclass = "strikeout" if option_value in disabled_sequencers else ''
         return u'<option class="%s" value="%s"%s>%s</option>' % (

diff --git a/experiments/experiments.py b/experiments/experiments.py
index 8738224d547ea47693902a2f48bf25c7affd526f..e9d12dee03bfc00aff72566b8ba6794ca433f54d 100644 (file)
--- a/experiments/experiments.py
+++ b/experiments/experiments.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 # some core functions of the exp tracker module
 from datetime import datetime, timedelta
@@ -43,7 +43,7 @@ def flowcell_information(flowcell_id):
             'library_name': lane.library.library_name,
             'library_id': lane.library.id,
             'library_species': lane.library.library_species.scientific_name,
-            'pM': unicode(lane.pM),
+            'pM': str(lane.pM),
             'read_length': lane.flowcell.read_length,
             'status_code': lane.status,
             'status': LANE_STATUS_MAP[lane.status]

diff --git a/experiments/experiments_factory.py b/experiments/experiments_factory.py
index 1e344b3b86293d52d16fca625fad6f0402e69a31..34e9d5f1d90de80042056c7bd22854cbf3524d13 100644 (file)
--- a/experiments/experiments_factory.py
+++ b/experiments/experiments_factory.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 import datetime
 
 import factory

diff --git a/experiments/models.py b/experiments/models.py
index 3377e28c38c95354d0e7aa972456fbb1070dd135..6e1fe27678ebee218a7bfda5b7f29e54c28c937c 100644 (file)
--- a/experiments/models.py
+++ b/experiments/models.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import datetime
 import glob
@@ -58,8 +58,8 @@ class ClusterStation(models.Model):
     class Meta:
         ordering = ["-isdefault", "name"]
 
-    def __unicode__(self):
-        return unicode(self.name)
+    def __str__(self):
+        return str(self.name)
 
     @staticmethod
     def update_isdefault(sender, instance, **kwargs):
@@ -96,10 +96,10 @@ class Sequencer(models.Model):
     class Meta:
         ordering = ["-isdefault", "-active", "name"]
 
-    def __unicode__(self):
-        name = [unicode(self.name)]
+    def __str__(self):
+        name = [str(self.name)]
         if self.instrument_name is not None:
-            name.append("(%s)" % (unicode(self.instrument_name),))
+            name.append("(%s)" % (str(self.instrument_name),))
         return " ".join(name)
 
     @models.permalink
@@ -152,8 +152,8 @@ class FlowCell(models.Model):
 
     notes = models.TextField(blank=True)
 
-    def __unicode__(self):
-        return unicode(self.flowcell_id)
+    def __str__(self):
+        return str(self.flowcell_id)
 
     def Lanes(self):
         html = ['<table>']
@@ -187,9 +187,9 @@ class FlowCell(models.Model):
         """Convert our boolean 'is paired' flag to a name
         """
         if self.paired_end:
-            return u"Paired"
+            return "Paired"
         else:
-            return u"Single"
+            return "Single"
 
     @models.permalink
     def get_absolute_url(self):
@@ -309,8 +309,8 @@ class Lane(models.Model):
         return ('experiments.views.flowcell_lane_detail',
                 [str(self.id)])
 
-    def __unicode__(self):
-        return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
+    def __str__(self):
+        return self.flowcell.flowcell_id + ':' + str(self.lane_number)
 
 
 class DataRun(models.Model):
@@ -423,8 +423,8 @@ class FileType(models.Model):
         return self.name.replace(' ', '_').lower()
     normalized_name = property(_get_normalized_name)
 
-    def __unicode__(self):
-        #return u"<FileType: %s>" % (self.name,)
+    def __str__(self):
+        #return "<FileType: %s>" % (self.name,)
         return self.name
 
 

diff --git a/experiments/test/test_cluster_station.py b/experiments/test/test_cluster_station.py
index 965faa92765f04f89c75614b6cf040a206a6347b..9bd53197f74225083de54236dad8d2bd3406ad00 100644 (file)
--- a/experiments/test/test_cluster_station.py
+++ b/experiments/test/test_cluster_station.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.test import TestCase
 from ..models import ClusterStation, cluster_station_default

diff --git a/experiments/test/test_filetype.py b/experiments/test/test_filetype.py
index fdef8bfffc0cba0d82dc7859a4fe849d6d0290a5..cb89087a797b7ef87fe9ddb8ba71cb471de5ce65 100644 (file)
--- a/experiments/test/test_filetype.py
+++ b/experiments/test/test_filetype.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.test import TestCase
 
@@ -9,8 +9,8 @@ class TestFileType(TestCase):
         file_type_objects = FileType.objects
         name = 'QSEQ tarfile'
         file_type_object = file_type_objects.get(name=name)
-        self.assertEqual(u"QSEQ tarfile",
-                             unicode(file_type_object))
+        self.assertEqual("QSEQ tarfile",
+                         str(file_type_object))
 
     def test_find_file_type(self):
         file_type_objects = FileType.objects

diff --git a/experiments/test/test_sequencer.py b/experiments/test/test_sequencer.py
index 0de4f5a4cdf8858e1bb05b163bff14f35f9cf1b8..c3d4a32fd396c4b65e082d657d28950c8a4f2856 100644 (file)
--- a/experiments/test/test_sequencer.py
+++ b/experiments/test/test_sequencer.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.test import TestCase
 from ..models import Sequencer, sequencer_default

diff --git a/experiments/test_experiments.py b/experiments/test_experiments.py
index 7c5d20127243c8aa79e8232a949aa7279cbfa7d7..99079f3cce9edd776d417489a192369a826a34d2 100644 (file)
--- a/experiments/test_experiments.py
+++ b/experiments/test_experiments.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import re
 from lxml.html import fromstring

diff --git a/experiments/urls.py b/experiments/urls.py
index 8330d91f12c6b5fdf3f8394b1ef6e8be1deac940..0b1722ec1a43df24d2b1626885867b161ab508a6 100644 (file)
--- a/experiments/urls.py
+++ b/experiments/urls.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf.urls import patterns
 
 urlpatterns = patterns('',

diff --git a/experiments/views.py b/experiments/views.py
index 294aff27a7ee41e664d4d6a86be047761606a38b..e5f675da42454868a24197a5f9109a6c4e1ede77 100644 (file)
--- a/experiments/views.py
+++ b/experiments/views.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 # Create your views here.
 from datetime import datetime

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 68ecc75c1fcbc9c6c969032cdef3995c1a99a3f0..e56659f6c39975e011695d92813ec468dad5c36a 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -4,7 +4,7 @@ Extract configuration from Illumina Bustard Directory.
 This includes the version number, run date, bustard executable parameters, and
 phasing estimates.
 """
-from __future__ import print_function
+from __future__ import print_function, unicode_literals
 
 from copy import copy
 from datetime import date
@@ -113,7 +113,7 @@ class CrosstalkMatrix(object):
         for b in base_order:
             for value in self.base[b]:
                 crosstalk_value = ElementTree.SubElement(root, CrosstalkMatrix.ELEMENT)
-                crosstalk_value.text = unicode(value)
+                crosstalk_value.text = str(value)
                 crosstalk_value.tail = os.linesep
 
         return root
@@ -458,7 +458,7 @@ def main(cmdline):
     opts, args = parser.parse_args(cmdline)
 
     for bustard_dir in args:
-        print(u'analyzing bustard directory: ' + unicode(bustard_dir))
+        print(u'analyzing bustard directory: ' + str(bustard_dir))
         bustard_object = bustard(bustard_dir)
         bustard_object.dump()
 

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index b795b141ca736fa40ee815f4eb9cff1744f70d4f..e69a330248ab16b445140c7c920ff1e5f9b7821e 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -1,6 +1,6 @@
 """Provide access to information stored in the GERALD directory.
 """
-from __future__ import print_function
+from __future__ import print_function, unicode_literals
 
 import collections
 from datetime import datetime, date
@@ -72,7 +72,7 @@ class Alignment(object):
             return None
 
         gerald = ElementTree.Element(root_tag,
-                                     {'version': unicode(Gerald.XML_VERSION)})
+                                     {'version': str(Gerald.XML_VERSION)})
         gerald.append(self.tree)
         gerald.append(self.summary.get_elements())
         if self.eland_results:

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 8f454e6dbee1c8a804d7950c4c337a437dca3deb..d7081ecce3d1d039ef62459fc773b6bff0823f61 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -1,7 +1,7 @@
 """
 Analyze the Summary.htm file produced by GERALD
 """
-from __future__ import print_function
+from __future__ import print_function, unicode_literals
 
 import os
 import logging
@@ -42,7 +42,7 @@ class Summary(object):
 
     def get_elements(self):
         summary = etree.Element(Summary.SUMMARY,
-                                      {'version': unicode(Summary.XML_VERSION)})
+                                      {'version': str(Summary.XML_VERSION)})
         for end in self.lane_results:
             for lane in end.values():
                 summary.append(lane.get_elements())
@@ -282,7 +282,7 @@ class LaneResultSummary(object):
     def get_elements(self):
         lane_result = etree.Element(
                         LaneResultSummary.LANE_RESULT_SUMMARY,
-                        {'lane': unicode(self.lane), 'end': unicode(self.end)})
+                        {'lane': str(self.lane), 'end': str(self.end)})
         for tag, variable_name in LaneResultSummary.TAGS.items():
             value = getattr(self, variable_name)
             if value is None:
@@ -296,7 +296,7 @@ class LaneResultSummary(object):
                 )
             else:
                 element = etree.SubElement(lane_result, tag)
-                element.text = unicode(value)
+                element.text = str(value)
         return lane_result
 
     def set_elements(self, tree):

diff --git a/htsworkflow/util/conversion.py b/htsworkflow/util/conversion.py
index d3eb4f6cc5dad43f619ca8db662ed6abbcc402a2..f294e6ff2533c404887de3d66644bd024c64e8b2 100644 (file)
--- a/htsworkflow/util/conversion.py
+++ b/htsworkflow/util/conversion.py
@@ -1,15 +1,16 @@
 """
 Miscellaneous, more refined type casting functions
 """
+from __future__ import unicode_literals
 
-def unicode_or_none(value):
+def str_or_none(value):
     """
-    Convert value to unicode if its not none.
+    Convert value to unicode string if its not none.
     """
     if value is None:
         return None
     else:
-        return unicode(value)
+        return str(value)
 
 def parse_flowcell_id(flowcell_id):
     """

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index 89db4832dd4d4a516d13e2fa2dc012fded964b32..33197ddb9631f4f07cfb6114bea4a3516a034ed0 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -295,7 +295,7 @@ def load_string_into_model(model, parser_name, data, ns=None):
     ns = fixup_namespace(ns)
     logger.debug("load_string_into_model parser={0}, len={1}".format(
         parser_name, len(data)))
-    rdf_parser = RDF.Parser(name=parser_name)
+    rdf_parser = RDF.Parser(name=str(parser_name))
 
     for s in rdf_parser.parse_string_as_stream(data, ns):
         conditionally_add_statement(model, s, ns)

diff --git a/inventory/admin.py b/inventory/admin.py
index b418f997ed2f00855bd2376ec2ed221c635d6e04..5c17d3d35a3d5e6d8dc92916beb72566f6022ec6 100644 (file)
--- a/inventory/admin.py
+++ b/inventory/admin.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.contrib import admin
 

diff --git a/inventory/bcmagic.py b/inventory/bcmagic.py
index a3cb409ca429ff6166a04affe0bc3b775401bc5b..703c0973b39729233e93aa6f52623f10f7319347 100644 (file)
--- a/inventory/bcmagic.py
+++ b/inventory/bcmagic.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from .models import Item
 

diff --git a/inventory/inventory_factory.py b/inventory/inventory_factory.py
index 1698f279825554dc31ff62d3661c3c9660590bf5..e75ea415ddd25a63a360381705a5ccfb91fc5712 100644 (file)
--- a/inventory/inventory_factory.py
+++ b/inventory/inventory_factory.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import datetime
 

diff --git a/inventory/models.py b/inventory/models.py
index 1e8509600336bb38a8797fbf097e431b48f13ffc..7e5c2390777565d83a9c288f3259893de7fadbb0 100644 (file)
--- a/inventory/models.py
+++ b/inventory/models.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import logging
 
@@ -48,8 +48,8 @@ class Vendor(models.Model):
     name = models.CharField(max_length=256)
     url = models.URLField(blank=True, null=True)
 
-    def __unicode__(self):
-        return u"%s" % (self.name)
+    def __str__(self):
+        return "%s" % (self.name)
 
 
 class Location(models.Model):
@@ -64,11 +64,11 @@ class Location(models.Model):
 
     notes = models.TextField(blank=True, null=True)
 
-    def __unicode__(self):
+    def __str__(self):
         if len(self.location_description) > 16:
-            return u"%s: %s" % (self.name, self.location_description[0:16]+u"...")
+            return "%s: %s" % (self.name, self.location_description[0:16]+"...")
         else:
-            return u"%s: %s" % (self.name, self.location_description)
+            return "%s: %s" % (self.name, self.location_description)
 
 post_init.connect(_assign_uuid, sender=Location)
 
@@ -88,16 +88,16 @@ class ItemInfo(models.Model):
 
     notes = models.TextField(blank=True, null=True)
 
-    def __unicode__(self):
+    def __str__(self):
         name = u''
         if self.model_id:
-            name += u"model:%s " % (self.model_id)
+            name += "model:%s " % (self.model_id)
         if self.part_number:
-            name += u"part:%s " % (self.part_number)
+            name += "part:%s " % (self.part_number)
         if self.lot_number:
-            name += u"lot:%s " % (self.lot_number)
+            name += "lot:%s " % (self.lot_number)
 
-        return u"%s: %s" % (name, self.purchase_date)
+        return "%s: %s" % (name, self.purchase_date)
 
     class Meta:
         verbose_name_plural = "Item Info"
@@ -108,15 +108,15 @@ class ItemType(models.Model):
     name = models.CharField(max_length=64, unique=True)
     description = models.TextField(blank=True, null=True)
 
-    def __unicode__(self):
-        return u"%s" % (self.name)
+    def __str__(self):
+        return "%s" % (self.name)
 
 
 class ItemStatus(models.Model):
     name = models.CharField(max_length=64, unique=True)
     notes = models.TextField(blank=True, null=True)
 
-    def __unicode__(self):
+    def __str__(self):
         return self.name
 
     class Meta:
@@ -149,11 +149,11 @@ class Item(models.Model):
 
     notes = models.TextField(blank=True, null=True)
 
-    def __unicode__(self):
+    def __str__(self):
         if self.barcode_id is None or len(self.barcode_id) == 0:
-            return u"invu|%s" % (self.uuid)
+            return "invu|%s" % (self.uuid)
         else:
-            return u"invb|%s" % (self.barcode_id)
+            return "invb|%s" % (self.barcode_id)
 
     def get_absolute_url(self):
         return '/inventory/%s/' % (self.uuid)
@@ -172,7 +172,7 @@ class PrinterTemplate(models.Model):
 
     template = models.TextField()
 
-    def __unicode__(self):
+    def __str__(self):
         if self.default:
             return u'%s %s' % (self.item_type.name, self.printer.name)
         else:
@@ -190,8 +190,8 @@ class LongTermStorage(models.Model):
     creation_date = models.DateTimeField(auto_now_add=True)
     modified_date = models.DateTimeField(auto_now=True)
 
-    def __unicode__(self):
-        return u"%s: %s" % (str(self.flowcell), ', '.join([str(s) for s in self.storage_devices.iterator()]))
+    def __str__(self):
+        return "%s: %s" % (str(self.flowcell), ', '.join([str(s) for s in self.storage_devices.iterator()]))
 
     class Meta:
         verbose_name_plural = "Long Term Storage"
@@ -213,8 +213,8 @@ class ReagentFlowcell(ReagentBase):
     """
     flowcell = models.ForeignKey(FlowCell)
 
-    def __unicode__(self):
-        return u"%s: %s" % (str(self.flowcell), ', '.join([str(s) for s in self.reagent.iterator()]))
+    def __str__(self):
+        return "%s: %s" % (str(self.flowcell), ', '.join([str(s) for s in self.reagent.iterator()]))
 
 
 class ReagentLibrary(ReagentBase):
@@ -223,5 +223,5 @@ class ReagentLibrary(ReagentBase):
     """
     library = models.ForeignKey(Library)
 
-    def __unicode__(self):
-        return u"%s: %s" % (str(self.library), ', '.join([str(s) for s in self.reagent.iterator()]))
+    def __str__(self):
+        return "%s: %s" % (str(self.library), ', '.join([str(s) for s in self.reagent.iterator()]))

diff --git a/inventory/test_inventory.py b/inventory/test_inventory.py
index b30da8c757ebfb5603cf442ad0ec6c0270afc4e4..6a5c59552e1c92ebcf3f833ed21e30379064d512 100644 (file)
--- a/inventory/test_inventory.py
+++ b/inventory/test_inventory.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import RDF
 
@@ -41,7 +41,7 @@ class InventoryTestCase(TestCase):
 
         itemNode = RDF.Node(RDF.Uri(url))
         item_type = fromTypedNode(
-            model.get_target(itemNode, inventoryOntology['item_type']))
+            model.get_target(itemNode, inventoryOntology[b'item_type']))
         self.failUnlessEqual(item_type, item.item_type.name)
 
     def test_itemindex(self):

diff --git a/inventory/urls.py b/inventory/urls.py
index ff71a6bc9534183edaf16ee052237e6077658031..98ece191231dd9b48d48ae0ea770c9aa34b7e614 100644 (file)
--- a/inventory/urls.py
+++ b/inventory/urls.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf.urls import patterns
 
 urlpatterns = patterns('',

diff --git a/inventory/views.py b/inventory/views.py
index 149710ff22466df20da3905a2ccb12180113f434..23b720017cf4b73b5cb60ccbc004f2ca3e784312 100644 (file)
--- a/inventory/views.py
+++ b/inventory/views.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.conf import settings
 from django.contrib.auth.decorators import login_required

diff --git a/labels/admin.py b/labels/admin.py
index 3ae391ec64e43a3a4be76810e3875064f39cd0aa..d2c7fcf07e024d18cc858669e693b62701c050c5 100644 (file)
--- a/labels/admin.py
+++ b/labels/admin.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.template import Context, Template
 from django.contrib import admin
 

diff --git a/labels/models.py b/labels/models.py
index 8794492d0e5dab2b85f92ea58d656d65474f32e7..fa5920bb5a10ebe26c12966b6c453524aff09704 100644 (file)
--- a/labels/models.py
+++ b/labels/models.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.db import models
 
 class LabelPrinter(models.Model):
@@ -10,8 +12,8 @@ class LabelPrinter(models.Model):
     labels = models.CharField(max_length=200)
     notes = models.TextField(null=True, blank=True)
 
-    def __unicode__(self):
-        return u'%s: %s' % (self.name, self.labels)
+    def __str__(self):
+        return '%s: %s' % (self.name, self.labels)
 
 class LabelTemplate(models.Model):
     """
@@ -23,7 +25,7 @@ class LabelTemplate(models.Model):
     
     ZPL_code = models.TextField('template')
     
-    def __unicode__(self):
+    def __str__(self):
             return '%s %s' % (self.name, self.printer.name)
 
 class LabelContent(models.Model):

diff --git a/labels/test_labels.py b/labels/test_labels.py
index ca3633bb6d2c73635640d8dca26ef16f3fc9999b..b09de7a301caeacc8b66aee9b01d45c4ff1b5bf0 100644 (file)
--- a/labels/test_labels.py
+++ b/labels/test_labels.py
@@ -4,6 +4,7 @@ unittest). These will both pass when you run "manage.py test".
 
 Replace these with more appropriate tests for your application.
 """
+from __future__ import unicode_literals
 
 from django.test import TestCase
 

diff --git a/labels/views.py b/labels/views.py
index 60f00ef0ef347811e7b0c0921b7fda097acd9fcc..6f984966c521f47889eb0e3c9143b3d3899906a0 100644 (file)
--- a/labels/views.py
+++ b/labels/views.py
@@ -1 +1,2 @@
+from __future__ import unicode_literals
 # Create your views here.

diff --git a/samples/admin.py b/samples/admin.py
index 5b9b858b1cb52297a9c70cdb5b6243f031516175..69fe059db1931231b7e34cf06e47385fe3caf8f4 100644 (file)
--- a/samples/admin.py
+++ b/samples/admin.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.contrib import admin
 from django.contrib.admin import widgets

diff --git a/samples/auth_backend.py b/samples/auth_backend.py
index aacf43b3d3a7b52b5af36983117a0995554ac6e1..18fbe5c61fd19c7850db91bb4f0feb1ce1c3236a 100644 (file)
--- a/samples/auth_backend.py
+++ b/samples/auth_backend.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 from django.conf import settings
 from django.contrib.auth.backends import ModelBackend

diff --git a/samples/changelist.py b/samples/changelist.py
index 716713aa0d4042961b4dc22f585000c153c35213..842eb0adc04c8cfc51ccdc020de7ded052888895 100644 (file)
--- a/samples/changelist.py
+++ b/samples/changelist.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import django
 from django.contrib.admin.views.main import ChangeList

diff --git a/samples/models.py b/samples/models.py
index 5cf2e9097ee1693ddcb15b0306b0ed33ed654bb8..94cd075bd641b2ad949b080a253289e31549236d 100644 (file)
--- a/samples/models.py
+++ b/samples/models.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 import types
 import logging
 from django.db import models
@@ -24,8 +26,8 @@ class Antibody(models.Model):
     source = models.CharField(max_length=500, blank=True, null=True, db_index=True)
     biology = models.TextField(blank=True, null=True)
     notes = models.TextField(blank=True, null=True)
-    def __unicode__(self):
-        return u'%s - %s' % (self.antigene, self.antibodies)
+    def __str__(self):
+        return '%s - %s' % (self.antigene, self.antibodies)
     class Meta:
         verbose_name_plural = "antibodies"
         ordering = ["antigene"]
@@ -38,8 +40,8 @@ class Cellline(models.Model):
         db_index=True)
 
     notes = models.TextField(blank=True)
-    def __unicode__(self):
-        return unicode(self.cellline_name)
+    def __str__(self):
+        return str(self.cellline_name)
 
     class Meta:
         ordering = ["cellline_name"]
@@ -54,8 +56,8 @@ class Condition(models.Model):
         verbose_name = 'Short Name')
     notes = models.TextField(blank=True)
 
-    def __unicode__(self):
-        return unicode(self.condition_name)
+    def __str__(self):
+        return str(self.condition_name)
 
     class Meta:
         ordering = ["condition_name"]
@@ -64,8 +66,8 @@ class Condition(models.Model):
 class ExperimentType(models.Model):
   name = models.CharField(max_length=50, unique=True)
 
-  def __unicode__(self):
-    return unicode(self.name)
+  def __str__(self):
+    return str(self.name)
 
 class Tag(models.Model):
   tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
@@ -79,8 +81,8 @@ class Tag(models.Model):
   context = models.CharField(max_length=50,
       choices=TAG_CONTEXT, default='Library')
 
-  def __unicode__(self):
-    return u'%s' % (self.tag_name)
+  def __str__(self):
+    return '%s' % (self.tag_name)
 
   class Meta:
     ordering = ["context","tag_name"]
@@ -93,8 +95,8 @@ class Species(models.Model):
   common_name = models.CharField(max_length=256, blank=True)
   #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
 
-  def __unicode__(self):
-    return u'%s (%s)' % (self.scientific_name, self.common_name)
+  def __str__(self):
+    return '%s (%s)' % (self.scientific_name, self.common_name)
 
   class Meta:
     verbose_name_plural = "species"
@@ -111,15 +113,15 @@ class Affiliation(models.Model):
   users = models.ManyToManyField('HTSUser', null=True, blank=True)
   users.admin_order_field = "username"
 
-  def __unicode__(self):
-    str = unicode(self.name)
+  def __str__(self):
+    name = str(self.name)
     if self.contact is not None and len(self.contact) > 0:
-      str += u' ('+self.contact+u')'
-    return str
+      name += ' ('+self.contact+')'
+    return name
 
   def Users(self):
       users = self.users.all().order_by('username')
-      return ", ".join([unicode(a) for a in users ])
+      return ", ".join([str(a) for a in users ])
 
   class Meta:
     ordering = ["name","contact"]
@@ -133,8 +135,8 @@ class LibraryType(models.Model):
   can_multiplex = models.BooleanField(default=True,
                     help_text="Does this adapter provide multiplexing?")
 
-  def __unicode__(self):
-      return unicode(self.name)
+  def __str__(self):
+      return str(self.name)
 
   class Meta:
       ordering = ["-id"]
@@ -201,7 +203,7 @@ class Library(models.Model):
 
   undiluted_concentration = models.DecimalField("Concentration",
       max_digits=5, decimal_places=2, blank=True, null=True,
-      help_text=u"Undiluted concentration (ng/\u00b5l)")
+      help_text = "Undiluted concentration (ng/\u00b5l)")
       # note \u00b5 is the micro symbol in unicode
   successful_pM = models.DecimalField(max_digits=9,
                                       decimal_places=1, blank=True, null=True)
@@ -213,11 +215,11 @@ class Library(models.Model):
   bioanalyzer_summary = models.TextField(blank=True,default="")
   bioanalyzer_concentration = models.DecimalField(max_digits=5,
                                 decimal_places=2, blank=True, null=True,
-                                help_text=u"(ng/\u00b5l)")
+                                help_text="(ng/\u00b5l)")
   bioanalyzer_image_url = models.URLField(blank=True,default="")
 
-  def __unicode__(self):
-    return u'#%s: %s' % (self.id, self.library_name)
+  def __str__(self):
+    return '#%s: %s' % (self.id, self.library_name)
 
   class Meta:
       verbose_name_plural = "libraries"
@@ -292,7 +294,7 @@ class Library(models.Model):
     tstr = ''
     ar = []
     for t in affs:
-        ar.append(t.__unicode__())
+        ar.append(t.__str__())
     return '%s' % (", ".join(ar))
 
   def is_archived(self):
@@ -317,8 +319,8 @@ class Library(models.Model):
     affs = self.tags.all().order_by('tag_name')
     ar = []
     for t in affs:
-      ar.append(t.__unicode__())
-    return u'%s' % ( ", ".join(ar))
+      ar.append(t.__str__())
+    return '%s' % ( ", ".join(ar))
 
   def DataRun(self):
     str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
@@ -333,7 +335,7 @@ class Library(models.Model):
 
     # Check data sanity
     if res[2] != "OK":
-      return u'<div style="border:solid red 2px">'+res[2]+'</div>'
+      return '<div style="border:solid red 2px">'+res[2]+'</div>'
 
     rc = "%1.2f" % (res[1]/1000000.0)
     # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
@@ -352,7 +354,7 @@ class Library(models.Model):
            if res[1] > rc_thr[2]:
              bgcolor ='#ffcc33'  # Orange
       tstr = '<div style="background-color:'+bgcolor+';color:black">'
-      tstr += res[0].__unicode__()+' Lanes, '+rc+' M Reads'
+      tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
       tstr += '</div>'
     else: tstr = 'not processed yet'
     return tstr
@@ -384,9 +386,9 @@ class HTSUser(User):
     def admin_url(self):
         return '/admin/%s/%s/%d' % (self._meta.app_label, self._meta.module_name, self.id)
 
-    def __unicode__(self):
-        #return unicode(self.username) + u" (" + unicode(self.get_full_name()) + u")"
-        return unicode(self.get_full_name()) + u' (' + unicode(self.username) + ')'
+    def __str__(self):
+        #return str(self.username) + " (" + str(self.get_full_name()) + u")"
+        return str(self.get_full_name()) + ' (' + str(self.username) + ')'
 
 def HTSUserInsertID(sender, instance, **kwargs):
     """

diff --git a/samples/results.py b/samples/results.py
index 2724a378a3f6b50610a13325a92812df5252bc41..6949d4d269118c965785e87e4ee21155c9da9863 100644 (file)
--- a/samples/results.py
+++ b/samples/results.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf import settings
 
 import glob

diff --git a/samples/samples_factory.py b/samples/samples_factory.py
index 3dd35f5b13f6b9ac8b3467b9fe7b3bd9b57faad0..09b7988d90c936bf0953d2dba3a415891cd87683 100644 (file)
--- a/samples/samples_factory.py
+++ b/samples/samples_factory.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 import datetime
 
 import factory

diff --git a/samples/test_samples.py b/samples/test_samples.py
index 61fc9305cb938382b3fa2205eead9e701cc1d817..4d14538c3d1c17780d67161ab0b55aba13a2e7ad 100644 (file)
--- a/samples/test_samples.py
+++ b/samples/test_samples.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 import datetime
 import unittest
@@ -12,7 +12,7 @@ from .views import library_dict, library_json, library
 from .samples_factory import *
 
 from htsworkflow.auth import apidata
-from htsworkflow.util.conversion import unicode_or_none
+from htsworkflow.util.conversion import str_or_none
 from htsworkflow.util.ethelp import validate_xhtml
 
 class LibraryTestCase(TestCase):
@@ -52,7 +52,7 @@ class SampleWebTestCase(TestCase):
         lib_dict = library_dict(library.id)
         url = '/samples/library/%s/json' % (library.id,)
         lib_response = self.client.get(url, apidata)
-        lib_json = json.loads(lib_response.content)['result']
+        lib_json = json.loads(str(lib_response.content))['result']
 
         for d in [lib_dict, lib_json]:
             # amplified_from_sample is a link to the library table,
@@ -63,7 +63,7 @@ class SampleWebTestCase(TestCase):
             #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
             self.failUnlessEqual(d['antibody_id'], library.antibody_id)
             self.failUnlessEqual(d['cell_line_id'], library.cell_line_id)
-            self.failUnlessEqual(d['cell_line'], unicode_or_none(library.cell_line))
+            self.failUnlessEqual(d['cell_line'], str_or_none(library.cell_line))
             self.failUnlessEqual(d['experiment_type'], library.experiment_type.name)
             self.failUnlessEqual(d['experiment_type_id'], library.experiment_type_id)
             self.failUnlessEqual(d['gel_cut_size'], library.gel_cut_size)
@@ -82,7 +82,7 @@ class SampleWebTestCase(TestCase):
             self.failUnlessEqual(d['stopping_point'], library.stopping_point)
             self.failUnlessEqual(d['successful_pM'], library.successful_pM)
             self.failUnlessEqual(d['undiluted_concentration'],
-                                 unicode(library.undiluted_concentration))
+                                 str(library.undiluted_concentration))
 
 
         def junk(self):
@@ -271,9 +271,9 @@ try:
     import RDF
     HAVE_RDF = True
 
-    rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
-    xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
-    libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
+    rdfNS = RDF.NS(b"http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+    xsdNS = RDF.NS(b"http://www.w3.org/2001/XMLSchema#")
+    libNS = RDF.NS(b"http://jumpgate.caltech.edu/wiki/LibraryOntology#")
 
     from htsworkflow.util.rdfhelp import dump_model
 except ImportError as e:
@@ -288,7 +288,7 @@ class TestRDFaLibrary(TestCase):
     def test_parse_rdfa(self):
 
         model = get_rdf_memory_model()
-        parser = RDF.Parser(name='rdfa')
+        parser = RDF.Parser(name=b'rdfa')
 
         bob = AffiliationFactory.create(name='Bob')
 
@@ -309,20 +309,20 @@ class TestRDFaLibrary(TestCase):
         #with open('/tmp/test.ttl', 'w') as outstream:
         #    dump_model(model, outstream)
         # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
-        self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
+        self.check_literal_object(model, ['Bob'], p=libNS[b'affiliation'])
         self.check_literal_object(model,
                                   ['experiment type name'],
-                                  p=libNS['experiment_type'])
-        self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
+                                  p=libNS[b'experiment_type'])
+        self.check_literal_object(model, ['400'], p=libNS[b'gel_cut'])
         self.check_literal_object(model,
                                   ['microfluidics bot 7321'],
-                                  p=libNS['made_by'])
+                                  p=libNS[b'made_by'])
         self.check_literal_object(model,
                                   [lib_object.library_name],
-                                  p=libNS['name'])
+                                  p=libNS[b'name'])
         self.check_literal_object(model,
                                   [lib_object.library_species.scientific_name],
-                                  p=libNS['species_name'])
+                                  p=libNS[b'species_name'])
 
 
     def check_literal_object(self, model, values, s=None, p=None, o=None):
@@ -340,7 +340,7 @@ class TestRDFaLibrary(TestCase):
         self.failUnlessEqual(len(statements), len(values),
                         "Couln't find %s %s %s" % (s,p,o))
         for s in statements:
-            self.failUnless(unicode(s.object.uri) in values)
+            self.failUnless(str(s.object.uri) in values)
 
 
 

diff --git a/samples/urls.py b/samples/urls.py
index 3d09dd4182718d97da0bbf5605639d9f8667ad3b..1bda463ed3c6a965d61ee287e464e13e984a3277 100644 (file)
--- a/samples/urls.py
+++ b/samples/urls.py
@@ -1,3 +1,5 @@
+from __future__ import unicode_literals
+
 from django.conf.urls import patterns, url
 
 urlpatterns = patterns('samples.views',

diff --git a/samples/views.py b/samples/views.py
index 0684ee7f5589cf8436a5a1e6c1fff1cb8e023150..cc94c620474ce1e8267b0e969921157141e63a3a 100644 (file)
--- a/samples/views.py
+++ b/samples/views.py
@@ -1,4 +1,4 @@
-from __future__ import absolute_import, print_function
+from __future__ import absolute_import, print_function, unicode_literals
 
 # Create your views here.
 import logging
@@ -30,7 +30,7 @@ from bcmagic.forms import BarcodeMagicForm
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.eland import ResultLane
 from htsworkflow.pipelines.samplekey import SampleKey
-from htsworkflow.util.conversion import unicode_or_none, parse_flowcell_id
+from htsworkflow.util.conversion import str_or_none, parse_flowcell_id
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
 
@@ -93,7 +93,7 @@ def create_library_context(cl):
         summary['lanes_run'] = lanes_run
         summary['is_archived'] = lib.is_archived()
         records.append(summary)
-    cl.result_count = unicode(cl.paginator._count)
+    cl.result_count = str(cl.paginator._count)
     return {'library_list': records}
 
 
@@ -492,7 +492,7 @@ def library_dict(library_id):
         #'antibody_name': lib.antibody_name(), # we have no antibodies.
         'antibody_id': lib.antibody_id,
         'cell_line_id': lib.cell_line_id,
-        'cell_line': unicode_or_none(lib.cell_line),
+        'cell_line': str_or_none(lib.cell_line),
         'experiment_type': lib.experiment_type.name,
         'experiment_type_id': lib.experiment_type_id,
         'gel_cut_size': lib.gel_cut_size,
@@ -511,8 +511,8 @@ def library_dict(library_id):
         'notes': lib.notes,
         'replicate': lib.replicate,
         'stopping_point': lib.stopping_point,
-        'successful_pM': unicode_or_none(lib.successful_pM),
-        'undiluted_concentration': unicode_or_none(lib.undiluted_concentration)
+        'successful_pM': str_or_none(lib.successful_pM),
+        'undiluted_concentration': str_or_none(lib.undiluted_concentration)
         }
     if lib.library_type_id is None:
         info['library_type'] = None