From 3a5137956b1a37068d4b235a0bbb12fd3c21c1d2 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 15 Oct 2008 18:59:34 +0000 Subject: [PATCH] Rename trunk from gaworkflow to htsworkflow (and update all of the imports) Fix the queuecommands test script to deal with the 1 sec delay hack --- gaworkflow/frontend/eland_config/urls.py | 10 ---------- {gaworkflow => htsworkflow}/__init__.py | 0 .../automation/__init__.py | 0 {gaworkflow => htsworkflow}/automation/copier.py | 2 +- {gaworkflow => htsworkflow}/automation/runner.py | 4 ++-- .../automation/spoolwatcher.py | 6 +++--- {gaworkflow => htsworkflow}/frontend/__init__.py | 0 .../frontend/eland_config/__init__.py | 0 .../frontend/eland_config/forms.py | 0 .../frontend/eland_config/models.py | 0 htsworkflow/frontend/eland_config/urls.py | 10 ++++++++++ .../frontend/eland_config/views.py | 6 +++--- .../frontend/fctracker/__init__.py | 0 .../frontend/fctracker/models.py | 2 +- .../frontend/fctracker/views.py | 0 {gaworkflow => htsworkflow}/frontend/manage.py | 0 {gaworkflow => htsworkflow}/frontend/settings.py | 6 +++--- {gaworkflow => htsworkflow}/frontend/urls.py | 2 +- {gaworkflow => htsworkflow}/pipeline/__init__.py | 0 {gaworkflow => htsworkflow}/pipeline/bustard.py | 2 +- .../pipeline/configure_run.py | 8 ++++---- .../pipeline/firecrest.py | 2 +- .../pipeline/genome_mapper.py | 2 +- {gaworkflow => htsworkflow}/pipeline/gerald.py | 6 +++--- .../pipeline/recipe_parser.py | 0 .../pipeline/retrieve_config.py | 0 .../pipeline/run_status.py | 0 .../pipeline/runfolder.py | 16 ++++++++-------- .../pipeline/test/test_genome_mapper.py | 2 +- .../pipeline/test/test_runfolder026.py | 10 +++++----- .../pipeline/test/test_runfolder030.py | 10 +++++----- {gaworkflow => htsworkflow}/util/__init__.py | 0 {gaworkflow => htsworkflow}/util/alphanum.py | 0 {gaworkflow => htsworkflow}/util/ethelp.py | 0 {gaworkflow => htsworkflow}/util/fctracker.py | 0 {gaworkflow => htsworkflow}/util/makebed.py | 2 +- {gaworkflow => htsworkflow}/util/mount.py | 0 {gaworkflow => htsworkflow}/util/opener.py | 0 .../util/queuecommands.py | 0 .../util/test/test_ethelp.py | 2 +- .../util/test/test_makebed.py | 2 +- .../util/test/test_queuecommands.py | 10 ++++++---- scripts/configure_pipeline | 6 +++--- scripts/copier | 2 +- scripts/elandseq | 2 +- scripts/gerald2bed.py | 2 +- scripts/library.py | 2 +- scripts/makebed | 2 +- scripts/rerun_eland.py | 4 ++-- scripts/retrieve_config | 8 ++++---- scripts/runfolder | 4 ++-- scripts/runner | 2 +- scripts/spoolwatcher | 2 +- scripts/srf | 2 +- setup.py | 12 ++++++------ test/test_copier.py | 2 +- 56 files changed, 88 insertions(+), 86 deletions(-) delete mode 100644 gaworkflow/frontend/eland_config/urls.py rename {gaworkflow => htsworkflow}/__init__.py (100%) rename {gaworkflow => htsworkflow}/automation/__init__.py (100%) rename {gaworkflow => htsworkflow}/automation/copier.py (99%) rename {gaworkflow => htsworkflow}/automation/runner.py (98%) rename {gaworkflow => htsworkflow}/automation/spoolwatcher.py (98%) rename {gaworkflow => htsworkflow}/frontend/__init__.py (100%) rename {gaworkflow => htsworkflow}/frontend/eland_config/__init__.py (100%) rename {gaworkflow => htsworkflow}/frontend/eland_config/forms.py (100%) rename {gaworkflow => htsworkflow}/frontend/eland_config/models.py (100%) create mode 100644 htsworkflow/frontend/eland_config/urls.py rename {gaworkflow => htsworkflow}/frontend/eland_config/views.py (98%) rename {gaworkflow => htsworkflow}/frontend/fctracker/__init__.py (100%) rename {gaworkflow => htsworkflow}/frontend/fctracker/models.py (99%) rename {gaworkflow => htsworkflow}/frontend/fctracker/views.py (100%) rename {gaworkflow => htsworkflow}/frontend/manage.py (100%) rename {gaworkflow => htsworkflow}/frontend/settings.py (96%) rename {gaworkflow => htsworkflow}/frontend/urls.py (83%) rename {gaworkflow => htsworkflow}/pipeline/__init__.py (100%) rename {gaworkflow => htsworkflow}/pipeline/bustard.py (99%) rename {gaworkflow => htsworkflow}/pipeline/configure_run.py (98%) rename {gaworkflow => htsworkflow}/pipeline/firecrest.py (98%) rename {gaworkflow => htsworkflow}/pipeline/genome_mapper.py (98%) rename {gaworkflow => htsworkflow}/pipeline/gerald.py (99%) rename {gaworkflow => htsworkflow}/pipeline/recipe_parser.py (100%) rename {gaworkflow => htsworkflow}/pipeline/retrieve_config.py (100%) rename {gaworkflow => htsworkflow}/pipeline/run_status.py (100%) rename {gaworkflow => htsworkflow}/pipeline/runfolder.py (96%) rename {gaworkflow => htsworkflow}/pipeline/test/test_genome_mapper.py (96%) rename {gaworkflow => htsworkflow}/pipeline/test/test_runfolder026.py (98%) rename {gaworkflow => htsworkflow}/pipeline/test/test_runfolder030.py (99%) rename {gaworkflow => htsworkflow}/util/__init__.py (100%) rename {gaworkflow => htsworkflow}/util/alphanum.py (100%) rename {gaworkflow => htsworkflow}/util/ethelp.py (100%) rename {gaworkflow => htsworkflow}/util/fctracker.py (100%) rename {gaworkflow => htsworkflow}/util/makebed.py (98%) rename {gaworkflow => htsworkflow}/util/mount.py (100%) rename {gaworkflow => htsworkflow}/util/opener.py (100%) rename {gaworkflow => htsworkflow}/util/queuecommands.py (100%) rename {gaworkflow => htsworkflow}/util/test/test_ethelp.py (93%) rename {gaworkflow => htsworkflow}/util/test/test_makebed.py (98%) rename {gaworkflow => htsworkflow}/util/test/test_queuecommands.py (78%) diff --git a/gaworkflow/frontend/eland_config/urls.py b/gaworkflow/frontend/eland_config/urls.py deleted file mode 100644 index 2eeee70..0000000 --- a/gaworkflow/frontend/eland_config/urls.py +++ /dev/null @@ -1,10 +0,0 @@ -from django.conf.urls.defaults import * - -urlpatterns = patterns('', - # Example: - - (r'^(?P\w+)/$', 'gaworkflow.frontend.eland_config.views.config'), - (r'^$', 'gaworkflow.frontend.eland_config.views.config'), - #(r'^$', 'gaworkflow.frontend.eland_config.views.index') - -) diff --git a/gaworkflow/__init__.py b/htsworkflow/__init__.py similarity index 100% rename from gaworkflow/__init__.py rename to htsworkflow/__init__.py diff --git a/gaworkflow/automation/__init__.py b/htsworkflow/automation/__init__.py similarity index 100% rename from gaworkflow/automation/__init__.py rename to htsworkflow/automation/__init__.py diff --git a/gaworkflow/automation/copier.py b/htsworkflow/automation/copier.py similarity index 99% rename from gaworkflow/automation/copier.py rename to htsworkflow/automation/copier.py index 2e0d3ae..572cfb3 100644 --- a/gaworkflow/automation/copier.py +++ b/htsworkflow/automation/copier.py @@ -123,7 +123,7 @@ class rsync(object): class CopierBot(rpc.XmlRpcBot): def __init__(self, section=None, configfile=None): #if configfile is None: - # configfile = '~/.gaworkflow' + # configfile = '~/.htsworkflow' super(CopierBot, self).__init__(section, configfile) diff --git a/gaworkflow/automation/runner.py b/htsworkflow/automation/runner.py similarity index 98% rename from gaworkflow/automation/runner.py rename to htsworkflow/automation/runner.py index a5f6843..9c26940 100644 --- a/gaworkflow/automation/runner.py +++ b/htsworkflow/automation/runner.py @@ -9,7 +9,7 @@ import threading from benderjab import rpc -from gaworkflow.pipeline.configure_run import * +from htsworkflow.pipeline.configure_run import * #s_fc = re.compile('FC[0-9]+') s_fc = re.compile('_[0-9a-zA-Z]*$') @@ -36,7 +36,7 @@ class Runner(rpc.XmlRpcBot): """ def __init__(self, section=None, configfile=None): #if configfile is None: - # self.configfile = "~/.gaworkflow" + # self.configfile = "~/.htsworkflow" super(Runner, self).__init__(section, configfile) self.cfg['notify_users'] = None diff --git a/gaworkflow/automation/spoolwatcher.py b/htsworkflow/automation/spoolwatcher.py similarity index 98% rename from gaworkflow/automation/spoolwatcher.py rename to htsworkflow/automation/spoolwatcher.py index 56ad42f..2a57535 100644 --- a/gaworkflow/automation/spoolwatcher.py +++ b/htsworkflow/automation/spoolwatcher.py @@ -6,7 +6,7 @@ import sys import time #import glob -from gaworkflow.util import mount +from htsworkflow.util import mount # this uses pyinotify import pyinotify @@ -67,14 +67,14 @@ class SpoolWatcher(rpc.XmlRpcBot): # I wonder where I should put the documentation #:Parameters: # `watchdir` - which directory tree to monitor for modifications - # `profile` - specify which .gaworkflow profile to use + # `profile` - specify which .htsworkflow profile to use # `write_timeout` - how many seconds to wait for writes to finish to # the spool # `notify_timeout` - how often to timeout from notify def __init__(self, section=None, configfile=None): #if configfile is None: - # self.configfile = "~/.gaworkflow" + # self.configfile = "~/.htsworkflow" super(SpoolWatcher, self).__init__(section, configfile) self.cfg['watchdir'] = None diff --git a/gaworkflow/frontend/__init__.py b/htsworkflow/frontend/__init__.py similarity index 100% rename from gaworkflow/frontend/__init__.py rename to htsworkflow/frontend/__init__.py diff --git a/gaworkflow/frontend/eland_config/__init__.py b/htsworkflow/frontend/eland_config/__init__.py similarity index 100% rename from gaworkflow/frontend/eland_config/__init__.py rename to htsworkflow/frontend/eland_config/__init__.py diff --git a/gaworkflow/frontend/eland_config/forms.py b/htsworkflow/frontend/eland_config/forms.py similarity index 100% rename from gaworkflow/frontend/eland_config/forms.py rename to htsworkflow/frontend/eland_config/forms.py diff --git a/gaworkflow/frontend/eland_config/models.py b/htsworkflow/frontend/eland_config/models.py similarity index 100% rename from gaworkflow/frontend/eland_config/models.py rename to htsworkflow/frontend/eland_config/models.py diff --git a/htsworkflow/frontend/eland_config/urls.py b/htsworkflow/frontend/eland_config/urls.py new file mode 100644 index 0000000..129f57c --- /dev/null +++ b/htsworkflow/frontend/eland_config/urls.py @@ -0,0 +1,10 @@ +from django.conf.urls.defaults import * + +urlpatterns = patterns('', + # Example: + + (r'^(?P\w+)/$', 'htsworkflow.frontend.eland_config.views.config'), + (r'^$', 'htsworkflow.frontend.eland_config.views.config'), + #(r'^$', 'htsworkflow.frontend.eland_config.views.index') + +) diff --git a/gaworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py similarity index 98% rename from gaworkflow/frontend/eland_config/views.py rename to htsworkflow/frontend/eland_config/views.py index f23f7ae..25edea9 100644 --- a/gaworkflow/frontend/eland_config/views.py +++ b/htsworkflow/frontend/eland_config/views.py @@ -2,9 +2,9 @@ from django.http import HttpResponse from django.shortcuts import render_to_response from django.core.exceptions import ObjectDoesNotExist -from gaworkflow.frontend.eland_config import forms -from gaworkflow.frontend import settings -from gaworkflow.frontend.fctracker import models +from htsworkflow.frontend.eland_config import forms +from htsworkflow.frontend import settings +from htsworkflow.frontend.fctracker import models import os import glob diff --git a/gaworkflow/frontend/fctracker/__init__.py b/htsworkflow/frontend/fctracker/__init__.py similarity index 100% rename from gaworkflow/frontend/fctracker/__init__.py rename to htsworkflow/frontend/fctracker/__init__.py diff --git a/gaworkflow/frontend/fctracker/models.py b/htsworkflow/frontend/fctracker/models.py similarity index 99% rename from gaworkflow/frontend/fctracker/models.py rename to htsworkflow/frontend/fctracker/models.py index 231afec..e12f0fe 100644 --- a/gaworkflow/frontend/fctracker/models.py +++ b/htsworkflow/frontend/fctracker/models.py @@ -1,6 +1,6 @@ from django.db import models from django.contrib.auth.models import User -from gaworkflow.frontend import settings +from htsworkflow.frontend import settings # Create your models here. diff --git a/gaworkflow/frontend/fctracker/views.py b/htsworkflow/frontend/fctracker/views.py similarity index 100% rename from gaworkflow/frontend/fctracker/views.py rename to htsworkflow/frontend/fctracker/views.py diff --git a/gaworkflow/frontend/manage.py b/htsworkflow/frontend/manage.py similarity index 100% rename from gaworkflow/frontend/manage.py rename to htsworkflow/frontend/manage.py diff --git a/gaworkflow/frontend/settings.py b/htsworkflow/frontend/settings.py similarity index 96% rename from gaworkflow/frontend/settings.py rename to htsworkflow/frontend/settings.py index 853cc1e..c9bee20 100644 --- a/gaworkflow/frontend/settings.py +++ b/htsworkflow/frontend/settings.py @@ -66,7 +66,7 @@ MIDDLEWARE_CLASSES = ( 'django.middleware.doc.XViewMiddleware', ) -ROOT_URLCONF = 'gaworkflow.frontend.urls' +ROOT_URLCONF = 'htsworkflow.frontend.urls' TEMPLATE_DIRS = ( # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates". @@ -81,8 +81,8 @@ INSTALLED_APPS = ( 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.sites', - 'gaworkflow.frontend.eland_config', - 'gaworkflow.frontend.fctracker', + 'htsworkflow.frontend.eland_config', + 'htsworkflow.frontend.fctracker', 'django.contrib.databrowse', ) diff --git a/gaworkflow/frontend/urls.py b/htsworkflow/frontend/urls.py similarity index 83% rename from gaworkflow/frontend/urls.py rename to htsworkflow/frontend/urls.py index 0c67015..a791b85 100644 --- a/gaworkflow/frontend/urls.py +++ b/htsworkflow/frontend/urls.py @@ -8,7 +8,7 @@ databrowse.site.register(FlowCell) urlpatterns = patterns('', # Base: - (r'^eland_config/', include('gaworkflow.frontend.eland_config.urls')), + (r'^eland_config/', include('htsworkflow.frontend.eland_config.urls')), # Admin: (r'^admin/', include('django.contrib.admin.urls')), # Databrowser: diff --git a/gaworkflow/pipeline/__init__.py b/htsworkflow/pipeline/__init__.py similarity index 100% rename from gaworkflow/pipeline/__init__.py rename to htsworkflow/pipeline/__init__.py diff --git a/gaworkflow/pipeline/bustard.py b/htsworkflow/pipeline/bustard.py similarity index 99% rename from gaworkflow/pipeline/bustard.py rename to htsworkflow/pipeline/bustard.py index 5a7a1f3..4e268f2 100644 --- a/gaworkflow/pipeline/bustard.py +++ b/htsworkflow/pipeline/bustard.py @@ -6,7 +6,7 @@ import os import time import re -from gaworkflow.pipeline.runfolder import \ +from htsworkflow.pipeline.runfolder import \ ElementTree, \ VERSION_RE, \ EUROPEAN_STRPTIME diff --git a/gaworkflow/pipeline/configure_run.py b/htsworkflow/pipeline/configure_run.py similarity index 98% rename from gaworkflow/pipeline/configure_run.py rename to htsworkflow/pipeline/configure_run.py index e75d73a..d541de3 100644 --- a/gaworkflow/pipeline/configure_run.py +++ b/htsworkflow/pipeline/configure_run.py @@ -5,10 +5,10 @@ import time import re import os -from gaworkflow.pipeline.retrieve_config import getCombinedOptions, saveConfigFile -from gaworkflow.pipeline.retrieve_config import FlowCellNotFound, WebError404 -from gaworkflow.pipeline.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict -from gaworkflow.pipeline.run_status import GARunStatus +from htsworkflow.pipeline.retrieve_config import getCombinedOptions, saveConfigFile +from htsworkflow.pipeline.retrieve_config import FlowCellNotFound, WebError404 +from htsworkflow.pipeline.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict +from htsworkflow.pipeline.run_status import GARunStatus from pyinotify import WatchManager, ThreadedNotifier from pyinotify import EventsCodes, ProcessEvent diff --git a/gaworkflow/pipeline/firecrest.py b/htsworkflow/pipeline/firecrest.py similarity index 98% rename from gaworkflow/pipeline/firecrest.py rename to htsworkflow/pipeline/firecrest.py index dd06aec..89ea598 100644 --- a/gaworkflow/pipeline/firecrest.py +++ b/htsworkflow/pipeline/firecrest.py @@ -12,7 +12,7 @@ import os import re import time -from gaworkflow.pipeline.runfolder import \ +from htsworkflow.pipeline.runfolder import \ ElementTree, \ VERSION_RE, \ EUROPEAN_STRPTIME diff --git a/gaworkflow/pipeline/genome_mapper.py b/htsworkflow/pipeline/genome_mapper.py similarity index 98% rename from gaworkflow/pipeline/genome_mapper.py rename to htsworkflow/pipeline/genome_mapper.py index 90c619b..a8ea871 100644 --- a/gaworkflow/pipeline/genome_mapper.py +++ b/htsworkflow/pipeline/genome_mapper.py @@ -6,7 +6,7 @@ import re import logging -from gaworkflow.util.alphanum import alphanum +from htsworkflow.util.alphanum import alphanum class DuplicateGenome(Exception): pass diff --git a/gaworkflow/pipeline/gerald.py b/htsworkflow/pipeline/gerald.py similarity index 99% rename from gaworkflow/pipeline/gerald.py rename to htsworkflow/pipeline/gerald.py index f268767..07ca009 100644 --- a/gaworkflow/pipeline/gerald.py +++ b/htsworkflow/pipeline/gerald.py @@ -9,13 +9,13 @@ import stat import time import types -from gaworkflow.pipeline.runfolder import \ +from htsworkflow.pipeline.runfolder import \ ElementTree, \ EUROPEAN_STRPTIME, \ LANES_PER_FLOWCELL, \ VERSION_RE -from gaworkflow.util.ethelp import indent, flatten -from gaworkflow.util.opener import autoopen +from htsworkflow.util.ethelp import indent, flatten +from htsworkflow.util.opener import autoopen class Gerald(object): """ diff --git a/gaworkflow/pipeline/recipe_parser.py b/htsworkflow/pipeline/recipe_parser.py similarity index 100% rename from gaworkflow/pipeline/recipe_parser.py rename to htsworkflow/pipeline/recipe_parser.py diff --git a/gaworkflow/pipeline/retrieve_config.py b/htsworkflow/pipeline/retrieve_config.py similarity index 100% rename from gaworkflow/pipeline/retrieve_config.py rename to htsworkflow/pipeline/retrieve_config.py diff --git a/gaworkflow/pipeline/run_status.py b/htsworkflow/pipeline/run_status.py similarity index 100% rename from gaworkflow/pipeline/run_status.py rename to htsworkflow/pipeline/run_status.py diff --git a/gaworkflow/pipeline/runfolder.py b/htsworkflow/pipeline/runfolder.py similarity index 96% rename from gaworkflow/pipeline/runfolder.py rename to htsworkflow/pipeline/runfolder.py index 65f6191..492d103 100644 --- a/gaworkflow/pipeline/runfolder.py +++ b/htsworkflow/pipeline/runfolder.py @@ -22,8 +22,8 @@ VERSION_RE = "([0-9\.]+)" USER_RE = "([a-zA-Z0-9]+)" LANES_PER_FLOWCELL = 8 -from gaworkflow.util.alphanum import alphanum -from gaworkflow.util.ethelp import indent, flatten +from htsworkflow.util.alphanum import alphanum +from htsworkflow.util.ethelp import indent, flatten class PipelineRun(object): @@ -86,9 +86,9 @@ class PipelineRun(object): def set_elements(self, tree): # this file gets imported by all the others, # so we need to hide the imports to avoid a cyclic imports - from gaworkflow.pipeline import firecrest - from gaworkflow.pipeline import bustard - from gaworkflow.pipeline import gerald + from htsworkflow.pipeline import firecrest + from htsworkflow.pipeline import bustard + from htsworkflow.pipeline import gerald tag = tree.tag.lower() if tag != PipelineRun.PIPELINE_RUN.lower(): @@ -142,9 +142,9 @@ def get_runs(runfolder): generate two different PipelineRun objects, that differ in there gerald component. """ - from gaworkflow.pipeline import firecrest - from gaworkflow.pipeline import bustard - from gaworkflow.pipeline import gerald + from htsworkflow.pipeline import firecrest + from htsworkflow.pipeline import bustard + from htsworkflow.pipeline import gerald datadir = os.path.join(runfolder, 'Data') diff --git a/gaworkflow/pipeline/test/test_genome_mapper.py b/htsworkflow/pipeline/test/test_genome_mapper.py similarity index 96% rename from gaworkflow/pipeline/test/test_genome_mapper.py rename to htsworkflow/pipeline/test/test_genome_mapper.py index c8366d1..8916965 100644 --- a/gaworkflow/pipeline/test/test_genome_mapper.py +++ b/htsworkflow/pipeline/test/test_genome_mapper.py @@ -1,7 +1,7 @@ import unittest from StringIO import StringIO -from gaworkflow.pipeline import genome_mapper +from htsworkflow.pipeline import genome_mapper class testGenomeMapper(unittest.TestCase): def test_construct_mapper(self): diff --git a/gaworkflow/pipeline/test/test_runfolder026.py b/htsworkflow/pipeline/test/test_runfolder026.py similarity index 98% rename from gaworkflow/pipeline/test/test_runfolder026.py rename to htsworkflow/pipeline/test/test_runfolder026.py index f539cfa..74247a6 100644 --- a/gaworkflow/pipeline/test/test_runfolder026.py +++ b/htsworkflow/pipeline/test/test_runfolder026.py @@ -6,11 +6,11 @@ import tempfile import shutil import unittest -from gaworkflow.pipeline import firecrest -from gaworkflow.pipeline import bustard -from gaworkflow.pipeline import gerald -from gaworkflow.pipeline import runfolder -from gaworkflow.pipeline.runfolder import ElementTree +from htsworkflow.pipeline import firecrest +from htsworkflow.pipeline import bustard +from htsworkflow.pipeline import gerald +from htsworkflow.pipeline import runfolder +from htsworkflow.pipeline.runfolder import ElementTree def make_flowcell_id(runfolder_dir, flowcell_id=None): diff --git a/gaworkflow/pipeline/test/test_runfolder030.py b/htsworkflow/pipeline/test/test_runfolder030.py similarity index 99% rename from gaworkflow/pipeline/test/test_runfolder030.py rename to htsworkflow/pipeline/test/test_runfolder030.py index 5078412..e5d1ea1 100644 --- a/gaworkflow/pipeline/test/test_runfolder030.py +++ b/htsworkflow/pipeline/test/test_runfolder030.py @@ -6,11 +6,11 @@ import tempfile import shutil import unittest -from gaworkflow.pipeline import firecrest -from gaworkflow.pipeline import bustard -from gaworkflow.pipeline import gerald -from gaworkflow.pipeline import runfolder -from gaworkflow.pipeline.runfolder import ElementTree +from htsworkflow.pipeline import firecrest +from htsworkflow.pipeline import bustard +from htsworkflow.pipeline import gerald +from htsworkflow.pipeline import runfolder +from htsworkflow.pipeline.runfolder import ElementTree def make_flowcell_id(runfolder_dir, flowcell_id=None): diff --git a/gaworkflow/util/__init__.py b/htsworkflow/util/__init__.py similarity index 100% rename from gaworkflow/util/__init__.py rename to htsworkflow/util/__init__.py diff --git a/gaworkflow/util/alphanum.py b/htsworkflow/util/alphanum.py similarity index 100% rename from gaworkflow/util/alphanum.py rename to htsworkflow/util/alphanum.py diff --git a/gaworkflow/util/ethelp.py b/htsworkflow/util/ethelp.py similarity index 100% rename from gaworkflow/util/ethelp.py rename to htsworkflow/util/ethelp.py diff --git a/gaworkflow/util/fctracker.py b/htsworkflow/util/fctracker.py similarity index 100% rename from gaworkflow/util/fctracker.py rename to htsworkflow/util/fctracker.py diff --git a/gaworkflow/util/makebed.py b/htsworkflow/util/makebed.py similarity index 98% rename from gaworkflow/util/makebed.py rename to htsworkflow/util/makebed.py index 6f1511c..4f2b17f 100755 --- a/gaworkflow/util/makebed.py +++ b/htsworkflow/util/makebed.py @@ -121,7 +121,7 @@ def make_description(database, flowcell_id, lane): """ compute a bedfile name and description from the fctracker database """ - from gaworkflow.util.fctracker import fctracker + from htsworkflow.util.fctracker import fctracker fc = fctracker(database) cells = fc._get_flowcells("where flowcell_id='%s'" % (flowcell_id)) diff --git a/gaworkflow/util/mount.py b/htsworkflow/util/mount.py similarity index 100% rename from gaworkflow/util/mount.py rename to htsworkflow/util/mount.py diff --git a/gaworkflow/util/opener.py b/htsworkflow/util/opener.py similarity index 100% rename from gaworkflow/util/opener.py rename to htsworkflow/util/opener.py diff --git a/gaworkflow/util/queuecommands.py b/htsworkflow/util/queuecommands.py similarity index 100% rename from gaworkflow/util/queuecommands.py rename to htsworkflow/util/queuecommands.py diff --git a/gaworkflow/util/test/test_ethelp.py b/htsworkflow/util/test/test_ethelp.py similarity index 93% rename from gaworkflow/util/test/test_ethelp.py rename to htsworkflow/util/test/test_ethelp.py index 98df518..63f0ac3 100644 --- a/gaworkflow/util/test/test_ethelp.py +++ b/htsworkflow/util/test/test_ethelp.py @@ -6,7 +6,7 @@ try: except ImportError, e: from elementtree import ElementTree -from gaworkflow.util.ethelp import indent, flatten +from htsworkflow.util.ethelp import indent, flatten class testETHelper(unittest.TestCase): def setUp(self): diff --git a/gaworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py similarity index 98% rename from gaworkflow/util/test/test_makebed.py rename to htsworkflow/util/test/test_makebed.py index e96f29b..03c7919 100644 --- a/gaworkflow/util/test/test_makebed.py +++ b/htsworkflow/util/test/test_makebed.py @@ -2,7 +2,7 @@ import os from StringIO import StringIO import unittest -from gaworkflow.util import makebed +from htsworkflow.util import makebed class testMakeBed(unittest.TestCase): def test_multi_1_0_0_limit_1(self): diff --git a/gaworkflow/util/test/test_queuecommands.py b/htsworkflow/util/test/test_queuecommands.py similarity index 78% rename from gaworkflow/util/test/test_queuecommands.py rename to htsworkflow/util/test/test_queuecommands.py index 6c54c04..424da88 100644 --- a/gaworkflow/util/test/test_queuecommands.py +++ b/htsworkflow/util/test/test_queuecommands.py @@ -4,7 +4,7 @@ import time import unittest -from gaworkflow.util.queuecommands import QueueCommands +from htsworkflow.util.queuecommands import QueueCommands class testQueueCommands(unittest.TestCase): def setUp(self): @@ -26,8 +26,9 @@ class testQueueCommands(unittest.TestCase): q.run() end = time.time()-start # we should only take the length of the longest sleep - self.failUnless( end > 1.9 and end < 2.1, - "took %s seconds, exected ~5" % (end,)) + # pity I had to add a 1 second sleep + self.failUnless( end > 2.9 and end < 3.1, + "took %s seconds, exected ~3" % (end,)) def test_limited_run(self): """ @@ -42,7 +43,8 @@ class testQueueCommands(unittest.TestCase): start = time.time() q.run() end = time.time()-start - self.failUnless( end > 3.9 and end < 4.1, + # pity I had to add a 1 second sleep + self.failUnless( end > 5.9 and end < 6.1, "took %s seconds, expected ~6" % (end,)) def suite(): diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline index 6c94b91..4b2e3a0 100644 --- a/scripts/configure_pipeline +++ b/scripts/configure_pipeline @@ -2,9 +2,9 @@ import os import sys import re -from gaworkflow.pipeline.configure_run import * -from gaworkflow.pipeline import retrieve_config as _rc -from gaworkflow.pipeline.run_status import startCmdLineStatusMonitor +from htsworkflow.pipeline.configure_run import * +from htsworkflow.pipeline import retrieve_config as _rc +from htsworkflow.pipeline.run_status import startCmdLineStatusMonitor logging.basicConfig(level=logging.DEBUG, format='%(asctime)s %(levelname)-8s %(message)s', diff --git a/scripts/copier b/scripts/copier index 7025d57..9338b07 100644 --- a/scripts/copier +++ b/scripts/copier @@ -1,6 +1,6 @@ #!/usr/bin/env python import sys -from gaworkflow.automation.copier import main +from htsworkflow.automation.copier import main if __name__ == "__main__": sys.exit(main(sys.argv[1:])) diff --git a/scripts/elandseq b/scripts/elandseq index ece4bf3..787fd98 100755 --- a/scripts/elandseq +++ b/scripts/elandseq @@ -3,7 +3,7 @@ import optparse import os import sys -from gaworkflow.pipeline.gerald import extract_eland_sequence +from htsworkflow.pipeline.gerald import extract_eland_sequence def make_parser(): usage = "usage: %prog [options] infile [outfile]" diff --git a/scripts/gerald2bed.py b/scripts/gerald2bed.py index c49cc9c..7a726e7 100644 --- a/scripts/gerald2bed.py +++ b/scripts/gerald2bed.py @@ -8,7 +8,7 @@ import optparse import sys import os -from gaworkflow.util.makebed import make_bed_from_eland_stream, make_description +from htsworkflow.util.makebed import make_bed_from_eland_stream, make_description def make_bed_for_gerald(eland_dir, output_dir, prefix, database, flowcell): """ diff --git a/scripts/library.py b/scripts/library.py index eeeed90..35532f4 100644 --- a/scripts/library.py +++ b/scripts/library.py @@ -7,7 +7,7 @@ installed, so it can run on machines other than the webserver. from optparse import OptionParser import sys -from gaworkflow.util import fctracker +from htsworkflow.util import fctracker def make_parser(): """ diff --git a/scripts/makebed b/scripts/makebed index a4a414b..4878697 100755 --- a/scripts/makebed +++ b/scripts/makebed @@ -3,7 +3,7 @@ import optparse import sys import os -from gaworkflow.util.makebed import make_bed_from_eland_stream, make_bed_from_multi_eland_stream, make_description +from htsworkflow.util.makebed import make_bed_from_eland_stream, make_bed_from_multi_eland_stream, make_description def make_parser(): parser = optparse.OptionParser() diff --git a/scripts/rerun_eland.py b/scripts/rerun_eland.py index c271970..7eb30bb 100644 --- a/scripts/rerun_eland.py +++ b/scripts/rerun_eland.py @@ -6,8 +6,8 @@ import os import subprocess import sys -from gaworkflow.pipeline import gerald -from gaworkflow.pipeline import runfolder +from htsworkflow.pipeline import gerald +from htsworkflow.pipeline import runfolder def make_query_filename(eland_obj, output_dir): query_name = '%s_%s_eland_query.txt' diff --git a/scripts/retrieve_config b/scripts/retrieve_config index b0ddd46..cdd2c5b 100644 --- a/scripts/retrieve_config +++ b/scripts/retrieve_config @@ -1,9 +1,9 @@ #!/usr/bin/env python import sys -from gaworkflow.pipeline.retrieve_config import * -from gaworkflow.pipeline import retrieve_config -from gaworkflow.pipeline.genome_mapper import getAvailableGenomes -from gaworkflow.pipeline.genome_mapper import constructMapperDict +from htsworkflow.pipeline.retrieve_config import * +from htsworkflow.pipeline import retrieve_config +from htsworkflow.pipeline.genome_mapper import getAvailableGenomes +from htsworkflow.pipeline.genome_mapper import constructMapperDict #Turn on built-in command-line parsing. retrieve_config.DISABLE_CMDLINE = False diff --git a/scripts/runfolder b/scripts/runfolder index d54bf60..8b4444a 100644 --- a/scripts/runfolder +++ b/scripts/runfolder @@ -31,8 +31,8 @@ import logging import optparse import sys -from gaworkflow.pipeline import runfolder -from gaworkflow.pipeline.runfolder import ElementTree +from htsworkflow.pipeline import runfolder +from htsworkflow.pipeline.runfolder import ElementTree def make_parser(): usage = 'usage: %prog [options] runfolder_root_dir' diff --git a/scripts/runner b/scripts/runner index 6b6da11..560299f 100644 --- a/scripts/runner +++ b/scripts/runner @@ -1,6 +1,6 @@ #!/usr/bin/env python import sys -from gaworkflow.automation.runner import main +from htsworkflow.automation.runner import main if __name__ == "__main__": sys.exit(main(sys.argv[1:])) diff --git a/scripts/spoolwatcher b/scripts/spoolwatcher index 269292e..b2f833e 100644 --- a/scripts/spoolwatcher +++ b/scripts/spoolwatcher @@ -1,6 +1,6 @@ #!/usr/bin/env python import sys -from gaworkflow.automation.spoolwatcher import main +from htsworkflow.automation.spoolwatcher import main if __name__ == "__main__": sys.exit(main(sys.argv[1:])) diff --git a/scripts/srf b/scripts/srf index f8617ea..0f11514 100644 --- a/scripts/srf +++ b/scripts/srf @@ -7,7 +7,7 @@ import os import subprocess import sys -from gaworkflow.util import queuecommands +from htsworkflow.util import queuecommands def make_commands(run_name, lanes, site_name, destdir): """ diff --git a/setup.py b/setup.py index 2229ed6..0cc5fb5 100644 --- a/setup.py +++ b/setup.py @@ -1,15 +1,15 @@ from setuptools import setup setup( - name="gaworkflow", + name="htsworkflow", description="some bots and other utilities to help deal with data from an illumina sequencer", author="Diane Trout & Brandon King", author_email="diane@caltech.edu", - packages=["gaworkflow", - "gaworkflow.pipeline", - "gaworkflow.frontend", - "gaworkflow.frontend.fctracker", - "gaworkflow.frontend.eland_config" + packages=["htsworkflow", + "htsworkflow.pipeline", + "htsworkflow.frontend", + "htsworkflow.frontend.fctracker", + "htsworkflow.frontend.eland_config" ], scripts=[ 'scripts/configure_pipeline', diff --git a/test/test_copier.py b/test/test_copier.py index 910f3ea..9a1b738 100644 --- a/test/test_copier.py +++ b/test/test_copier.py @@ -1,7 +1,7 @@ import unittest from StringIO import StringIO -from gaworkflow.automation import copier +from htsworkflow.automation import copier class testCopier(unittest.TestCase): def test_runfolder_validate(self): -- 2.30.2