def remove_pipeline_copies(self):
pipelines = self._config.get("Pipelines", {}).keys()
pipelines_to_remove = []
pipeline_renamings = {}
for index1, pipeline1 in enumerate(pipelines):
if pipeline1 in pipelines_to_remove:
continue
for pipeline2 in pipelines[index1+1:]:
if pipeline2 in pipelines_to_remove:
continue
difference = jsonTools.JsonDict.deepdiff(self._config["Pipelines"][pipeline1],
self._config["Pipelines"][pipeline2])
if len(difference[0]) == 0 and len(difference[1]) == 0:
pipelines_to_remove.append(pipeline2)
new_name = tools.find_common_string(pipeline_renamings.get(pipeline1, pipeline1),
pipeline_renamings.get(pipeline2, pipeline2))
pipeline_renamings[pipeline1] = new_name.strip("_").replace("__", "_")
for pipeline in pipelines_to_remove:
self._config["Pipelines"].pop(pipeline)
for old_name, new_name in pipeline_renamings.iteritems():
self._config["Pipelines"][new_name] = self._config["Pipelines"].pop(old_name)
def remove_pipeline_copies(self):
pipelines = self._config.get("Pipelines", {}).keys()
pipelines_to_remove = []
pipeline_renamings = {}
for index1, pipeline1 in enumerate(pipelines):
if pipeline1 in pipelines_to_remove:
continue
for pipeline2 in pipelines[index1+1:]:
if pipeline2 in pipelines_to_remove:
continue
difference = jsonTools.JsonDict.deepdiff(self._config["Pipelines"][pipeline1],
self._config["Pipelines"][pipeline2])
if len(difference[0]) == 0 and len(difference[1]) == 0:
pipelines_to_remove.append(pipeline2)
new_name = tools.find_common_string(pipeline_renamings.get(pipeline1, pipeline1),
pipeline_renamings.get(pipeline2, pipeline2))
# Needed for systematic shifts that are only applied to certain samples.
# In that case we do not want an extra pipeline with the same configuration
# as the nominal one.
if "Down" not in new_name or "Up" not in new_name:
new_name = new_name.replace(new_name.split("_")[-1], "")
# Add "nominal" to pipelines without systematic shifts
if new_name.endswith("_"):
new_name += "nominal"
elif "_" not in new_name:
new_name += "_nominal"
pipeline_renamings[pipeline1] = new_name.strip("_").replace("__", "_")
for pipeline in pipelines_to_remove:
self._config["Pipelines"].pop(pipeline)
for old_name, new_name in pipeline_renamings.iteritems():
self._config["Pipelines"][new_name] = self._config["Pipelines"].pop(old_name)
def remove_pipeline_copies(self):
pipelines = self._config.get("Pipelines", {}).keys()
pipelines_to_remove = []
pipeline_renamings = {}
for index1, pipeline1 in enumerate(pipelines):
if pipeline1 in pipelines_to_remove:
continue
for pipeline2 in pipelines[index1+1:]:
if pipeline2 in pipelines_to_remove:
continue
difference = jsonTools.JsonDict.deepdiff(self._config["Pipelines"][pipeline1],
self._config["Pipelines"][pipeline2])
if len(difference[0]) == 0 and len(difference[1]) == 0:
pipelines_to_remove.append(pipeline2)
new_name = tools.find_common_string(pipeline_renamings.get(pipeline1, pipeline1),
pipeline_renamings.get(pipeline2, pipeline2))
if new_name.endswith("_"):
new_name += "nominal"
elif "_" not in new_name:
new_name += "_nominal"
pipeline_renamings[pipeline1] = new_name.strip("_").replace("__", "_")
for pipeline in pipelines_to_remove:
self._config["Pipelines"].pop(pipeline)
for old_name, new_name in pipeline_renamings.iteritems():
self._config["Pipelines"][new_name] = self._config["Pipelines"].pop(old_name)
def remove_pipeline_copies(self):
pipelines = self._config.get("Pipelines", {}).keys()
pipelines_to_remove = []
pipeline_renamings = {}
for index1, pipeline1 in enumerate(pipelines):
if pipeline1 in pipelines_to_remove:
continue
for pipeline2 in pipelines[index1+1:]:
if pipeline2 in pipelines_to_remove:
continue
difference = jsonTools.JsonDict.deepdiff(self._config["Pipelines"][pipeline1],
self._config["Pipelines"][pipeline2])
if len(difference[0]) == 0 and len(difference[1]) == 0:
pipelines_to_remove.append(pipeline2)
new_name = tools.find_common_string(pipeline_renamings.get(pipeline1, pipeline1),
pipeline_renamings.get(pipeline2, pipeline2))
# Needed for systematic shifts that are only applied to certain samples.
# In that case we do not want an extra pipeline with the same configuration
# as the nominal one.
if "Down" not in new_name or "Up" not in new_name:
new_name = new_name.replace(new_name.split("_")[-1], "")
# Add "nominal" to pipelines without systematic shifts
if new_name.endswith("_"):
new_name += "nominal"
elif "_" not in new_name:
new_name += "_nominal"
pipeline_renamings[pipeline1] = new_name.strip("_").replace("__", "_")
for pipeline in pipelines_to_remove:
self._config["Pipelines"].pop(pipeline)
for old_name, new_name in pipeline_renamings.iteritems():
self._config["Pipelines"][new_name] = self._config["Pipelines"].pop(old_name)