From fecaccc112d39cd8e7c1e6fad2593179a52cdac4 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 15 Oct 2008 19:49:34 +0000 Subject: [PATCH] rename pipeline to pipelines to imply that we can process more than just illumina. --- htsworkflow/pipeline/__init__.py | 0 htsworkflow/pipelines/__init__.py | 6 ++++++ htsworkflow/{pipeline => pipelines}/bustard.py | 2 +- htsworkflow/{pipeline => pipelines}/configure_run.py | 8 ++++---- htsworkflow/{pipeline => pipelines}/firecrest.py | 2 +- htsworkflow/{pipeline => pipelines}/genome_mapper.py | 0 htsworkflow/{pipeline => pipelines}/gerald.py | 2 +- htsworkflow/{pipeline => pipelines}/recipe_parser.py | 0 .../{pipeline => pipelines}/retrieve_config.py | 6 +++--- htsworkflow/{pipeline => pipelines}/run_status.py | 0 htsworkflow/{pipeline => pipelines}/runfolder.py | 12 ++++++------ .../test/test_genome_mapper.py | 2 +- .../test/test_runfolder026.py | 10 +++++----- .../test/test_runfolder030.py | 10 +++++----- 14 files changed, 33 insertions(+), 27 deletions(-) delete mode 100644 htsworkflow/pipeline/__init__.py create mode 100644 htsworkflow/pipelines/__init__.py rename htsworkflow/{pipeline => pipelines}/bustard.py (99%) rename htsworkflow/{pipeline => pipelines}/configure_run.py (98%) rename htsworkflow/{pipeline => pipelines}/firecrest.py (98%) rename htsworkflow/{pipeline => pipelines}/genome_mapper.py (100%) rename htsworkflow/{pipeline => pipelines}/gerald.py (99%) rename htsworkflow/{pipeline => pipelines}/recipe_parser.py (100%) rename htsworkflow/{pipeline => pipelines}/retrieve_config.py (95%) rename htsworkflow/{pipeline => pipelines}/run_status.py (100%) rename htsworkflow/{pipeline => pipelines}/runfolder.py (97%) rename htsworkflow/{pipeline => pipelines}/test/test_genome_mapper.py (96%) rename htsworkflow/{pipeline => pipelines}/test/test_runfolder026.py (98%) rename htsworkflow/{pipeline => pipelines}/test/test_runfolder030.py (99%) diff --git a/htsworkflow/pipeline/__init__.py b/htsworkflow/pipeline/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/htsworkflow/pipelines/__init__.py b/htsworkflow/pipelines/__init__.py new file mode 100644 index 0000000..beabfd1 --- /dev/null +++ b/htsworkflow/pipelines/__init__.py @@ -0,0 +1,6 @@ +""" +Provide code to interact with the vendor tools to produce useable "raw" data. + +the illumina sub-package contains components to interact with the Illumina provided +GAPipeline +""" diff --git a/htsworkflow/pipeline/bustard.py b/htsworkflow/pipelines/bustard.py similarity index 99% rename from htsworkflow/pipeline/bustard.py rename to htsworkflow/pipelines/bustard.py index 4e268f2..1658b17 100644 --- a/htsworkflow/pipeline/bustard.py +++ b/htsworkflow/pipelines/bustard.py @@ -6,7 +6,7 @@ import os import time import re -from htsworkflow.pipeline.runfolder import \ +from htsworkflow.pipelines.runfolder import \ ElementTree, \ VERSION_RE, \ EUROPEAN_STRPTIME diff --git a/htsworkflow/pipeline/configure_run.py b/htsworkflow/pipelines/configure_run.py similarity index 98% rename from htsworkflow/pipeline/configure_run.py rename to htsworkflow/pipelines/configure_run.py index d541de3..0c1dc8b 100644 --- a/htsworkflow/pipeline/configure_run.py +++ b/htsworkflow/pipelines/configure_run.py @@ -5,10 +5,10 @@ import time import re import os -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 htsworkflow.pipelines.retrieve_config import getCombinedOptions, saveConfigFile +from htsworkflow.pipelines.retrieve_config import FlowCellNotFound, WebError404 +from htsworkflow.pipelines.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict +from htsworkflow.pipelines.run_status import GARunStatus from pyinotify import WatchManager, ThreadedNotifier from pyinotify import EventsCodes, ProcessEvent diff --git a/htsworkflow/pipeline/firecrest.py b/htsworkflow/pipelines/firecrest.py similarity index 98% rename from htsworkflow/pipeline/firecrest.py rename to htsworkflow/pipelines/firecrest.py index 89ea598..ee6fded 100644 --- a/htsworkflow/pipeline/firecrest.py +++ b/htsworkflow/pipelines/firecrest.py @@ -12,7 +12,7 @@ import os import re import time -from htsworkflow.pipeline.runfolder import \ +from htsworkflow.pipelines.runfolder import \ ElementTree, \ VERSION_RE, \ EUROPEAN_STRPTIME diff --git a/htsworkflow/pipeline/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py similarity index 100% rename from htsworkflow/pipeline/genome_mapper.py rename to htsworkflow/pipelines/genome_mapper.py diff --git a/htsworkflow/pipeline/gerald.py b/htsworkflow/pipelines/gerald.py similarity index 99% rename from htsworkflow/pipeline/gerald.py rename to htsworkflow/pipelines/gerald.py index 07ca009..109c6a8 100644 --- a/htsworkflow/pipeline/gerald.py +++ b/htsworkflow/pipelines/gerald.py @@ -9,7 +9,7 @@ import stat import time import types -from htsworkflow.pipeline.runfolder import \ +from htsworkflow.pipelines.runfolder import \ ElementTree, \ EUROPEAN_STRPTIME, \ LANES_PER_FLOWCELL, \ diff --git a/htsworkflow/pipeline/recipe_parser.py b/htsworkflow/pipelines/recipe_parser.py similarity index 100% rename from htsworkflow/pipeline/recipe_parser.py rename to htsworkflow/pipelines/recipe_parser.py diff --git a/htsworkflow/pipeline/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py similarity index 95% rename from htsworkflow/pipeline/retrieve_config.py rename to htsworkflow/pipelines/retrieve_config.py index 72cff17..380c0de 100644 --- a/htsworkflow/pipeline/retrieve_config.py +++ b/htsworkflow/pipelines/retrieve_config.py @@ -8,8 +8,8 @@ import os import sys import urllib2 -CONFIG_SYSTEM = '/etc/ga_frontend/ga_frontend.conf' -CONFIG_USER = os.path.expanduser('~/.ga_frontend.conf') +CONFIG_SYSTEM = '/etc/hts_frontend/hts_frontend.conf' +CONFIG_USER = os.path.expanduser('~/.hts_frontend.conf') #Disable or enable commandline arg parsing; disabled by default. DISABLE_CMDLINE = True @@ -58,7 +58,7 @@ def constructOptionParser(): parser = OptionParser(formatter=PreformattedDescriptionFormatter()) - parser.set_description('Retrieves eland config file from ga_frontend web frontend.') + parser.set_description('Retrieves eland config file from hts_frontend web frontend.') parser.epilog = """ Config File: diff --git a/htsworkflow/pipeline/run_status.py b/htsworkflow/pipelines/run_status.py similarity index 100% rename from htsworkflow/pipeline/run_status.py rename to htsworkflow/pipelines/run_status.py diff --git a/htsworkflow/pipeline/runfolder.py b/htsworkflow/pipelines/runfolder.py similarity index 97% rename from htsworkflow/pipeline/runfolder.py rename to htsworkflow/pipelines/runfolder.py index 492d103..dee3231 100644 --- a/htsworkflow/pipeline/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -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 htsworkflow.pipeline import firecrest - from htsworkflow.pipeline import bustard - from htsworkflow.pipeline import gerald + from htsworkflow.pipelines import firecrest + from htsworkflow.pipelines import bustard + from htsworkflow.pipelines 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 htsworkflow.pipeline import firecrest - from htsworkflow.pipeline import bustard - from htsworkflow.pipeline import gerald + from htsworkflow.pipelines import firecrest + from htsworkflow.pipelines import bustard + from htsworkflow.pipelines import gerald datadir = os.path.join(runfolder, 'Data') diff --git a/htsworkflow/pipeline/test/test_genome_mapper.py b/htsworkflow/pipelines/test/test_genome_mapper.py similarity index 96% rename from htsworkflow/pipeline/test/test_genome_mapper.py rename to htsworkflow/pipelines/test/test_genome_mapper.py index 8916965..8ba1ba5 100644 --- a/htsworkflow/pipeline/test/test_genome_mapper.py +++ b/htsworkflow/pipelines/test/test_genome_mapper.py @@ -1,7 +1,7 @@ import unittest from StringIO import StringIO -from htsworkflow.pipeline import genome_mapper +from htsworkflow.pipelines import genome_mapper class testGenomeMapper(unittest.TestCase): def test_construct_mapper(self): diff --git a/htsworkflow/pipeline/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py similarity index 98% rename from htsworkflow/pipeline/test/test_runfolder026.py rename to htsworkflow/pipelines/test/test_runfolder026.py index 74247a6..40d29cf 100644 --- a/htsworkflow/pipeline/test/test_runfolder026.py +++ b/htsworkflow/pipelines/test/test_runfolder026.py @@ -6,11 +6,11 @@ import tempfile import shutil import unittest -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 +from htsworkflow.pipelines import firecrest +from htsworkflow.pipelines import bustard +from htsworkflow.pipelines import gerald +from htsworkflow.pipelines import runfolder +from htsworkflow.pipelines.runfolder import ElementTree def make_flowcell_id(runfolder_dir, flowcell_id=None): diff --git a/htsworkflow/pipeline/test/test_runfolder030.py b/htsworkflow/pipelines/test/test_runfolder030.py similarity index 99% rename from htsworkflow/pipeline/test/test_runfolder030.py rename to htsworkflow/pipelines/test/test_runfolder030.py index e5d1ea1..7457b12 100644 --- a/htsworkflow/pipeline/test/test_runfolder030.py +++ b/htsworkflow/pipelines/test/test_runfolder030.py @@ -6,11 +6,11 @@ import tempfile import shutil import unittest -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 +from htsworkflow.pipelines import firecrest +from htsworkflow.pipelines import bustard +from htsworkflow.pipelines import gerald +from htsworkflow.pipelines import runfolder +from htsworkflow.pipelines.runfolder import ElementTree def make_flowcell_id(runfolder_dir, flowcell_id=None): -- 2.30.2