def fetch_reads_refs_from_sampleset(ref, ws_url, srv_wiz_url):
"""
From the given object ref, return a list of all reads objects that are a part of that
object. E.g., if ref is a ReadsSet, return a list of all PairedEndLibrary or SingleEndLibrary
refs that are a member of that ReadsSet. This is returned as a list of dictionaries as follows:
{
"ref": reads object reference,
"condition": condition string associated with that reads object,
"name": reads object name (needed for saving an AlignmentSet)
}
The only one required is "ref", all other keys may or may not be present, based on the reads
object or object type in initial ref variable. E.g. a RNASeqSampleSet might have condition info
for each reads object, but a single PairedEndLibrary may not have that info.
If ref is already a Reads library, just returns a list with ref as a single element.
"""
obj_type = get_object_type(ref, ws_url)
refs = list()
if "KBaseSets.ReadsSet" in obj_type or "KBaseRNASeq.RNASeqSampleSet" in obj_type:
print("Looking up reads references in ReadsSet object")
set_client = SetAPI(srv_wiz_url)
reads_set = set_client.get_reads_set_v1({
"ref": ref,
"include_item_info": 0,
"include_set_item_ref_paths": 1
})
print("Got results from ReadsSet object")
pprint(reads_set)
ref_list = [r["ref_path"] for r in reads_set["data"]["items"]]
reads_names = get_object_names(ref_list, ws_url)
for reads in reads_set["data"]["items"]:
ref = reads["ref_path"]
refs.append({
"ref": ref,
"condition": reads["label"],
"name": reads_names[ref]
})
elif ("KBaseAssembly.SingleEndLibrary" in obj_type or
"KBaseFile.SingleEndLibrary" in obj_type or
"KBaseAssembly.PairedEndLibrary" in obj_type or
"KBaseFile.PairedEndLibrary" in obj_type):
refs.append({
"ref": ref,
"name": get_object_names([ref], ws_url)[ref]
})
else:
raise ValueError("Unable to fetch reads reference from object {} "
"which is a {}".format(ref, obj_type))
return refs
def fetch_reads_refs_from_sampleset(ref, ws_url, callback_url, params):
"""
From the given object ref, return a list of all reads objects that are a part of that
object. E.g., if ref is a ReadsSet, return a list of all PairedEndLibrary or SingleEndLibrary
refs that are a member of that ReadsSet. This is returned as a list of dictionaries as follows:
{
"ref": reads object reference,
"condition": condition string associated with that reads object
}
The only one required is "ref", all other keys may or may not be present, based on the reads
object or object type in initial ref variable. E.g. a RNASeqSampleSet might have condition info
for each reads object, but a single PairedEndLibrary may not have that info.
If ref is already a Reads library, just returns a list with ref as a single element.
"""
obj_type = get_object_type(ref, ws_url)
ws = Workspace(ws_url)
refs = list()
refs_for_ws_info = list()
if "KBaseSets.ReadsSet" in obj_type:
print("Looking up reads references in ReadsSet object")
set_client = SetAPI(callback_url)
reads_set = set_client.get_reads_set_v1({
"ref": ref,
"include_item_info": 0
})
for reads in reads_set["data"]["items"]:
refs.append({"ref": reads["ref"], "condition": reads["label"]})
refs_for_ws_info.append({'ref': reads['ref']})
elif "KBaseRNASeq.RNASeqSampleSet" in obj_type:
print("Looking up reads references in RNASeqSampleSet object")
sample_set = ws.get_objects2({"objects": [{
"ref": ref
}]})["data"][0]["data"]
for i in range(len(sample_set["sample_ids"])):
refs.append({
"ref": sample_set["sample_ids"][i],
"condition": sample_set["condition"][i]
})
refs_for_ws_info.append({'ref': sample_set['sample_ids'][i]})
elif ("KBaseAssembly.SingleEndLibrary" in obj_type
or "KBaseFile.SingleEndLibrary" in obj_type
or "KBaseFile.SingleEndLibrary-2.0" in obj_type
or "KBaseFile.SingleEndLibrary-2.1" in obj_type
or "KBaseAssembly.PairedEndLibrary" in obj_type
or "KBaseFile.PairedEndLibrary" in obj_type
or "KBaseFile.PairedEndLibrary-2.0" in obj_type
or "KBaseFile.PairedEndLibrary-2.1" in obj_type):
refs.append({"ref": ref})
refs_for_ws_info.append({'ref': ref})
else:
raise ValueError("Unable to fetch reads reference from object {} "
"which is a {}".format(ref, obj_type))
# get object info so we can name things properly
infos = ws.get_object_info3({'objects': refs_for_ws_info})['infos']
name_ext = '_alignment'
if ('alignment_suffix' in params
and params['alignment_suffix'] is not None):
ext = params['alignment_suffix'].replace(' ', '')
if ext:
name_ext = ext
unique_names = get_unique_names(infos)
for k in range(0, len(refs)):
refs[k]['info'] = infos[k]
name = unique_names[k] + name_ext
refs[k]['alignment_output_name'] = name
return refs