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Filipe cobra model #23

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Merged
Fxe merged 4 commits into from
Mar 7, 2025
Merged

Filipe cobra model #23

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bf016bf
Adding support for reference chains to KBase API
Nov 5, 2024
f0b3aa3
Fixing defaults when data is missing
Nov 20, 2024
f463d0d
Enabling listing of hidden objects and adding pigment and carbohydrat…
Mar 7, 2025
ad33063
Merge branch 'cobra-model' into filipe-cobra-model
Fxe Mar 7, 2025
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18 changes: 9 additions & 9 deletions cobrakbase/core/kbasefba/newmodeltemplate_metabolite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,15 +50,15 @@ def __init__(
def from_dict(d):
return NewModelTemplateCompound(
d["id"],
d["formula"],
d["name"],
d["defaultCharge"],
d["mass"],
d["deltaG"],
d["deltaGErr"],
d["isCofactor"] == 1,
d["abbreviation"],
d["aliases"],
d.get("formula",None),
d.get("name",d["id"]),
d.get("defaultCharge",None),
d.get("mass",None),
d.get("deltaG",None),
d.get("deltaGErr",None),
d.get("isCofactor",0) == 1,
d.get("abbreviation",d["id"]),
d.get("aliases",[]),
)

def __repr__(self):
Expand Down
8 changes: 4 additions & 4 deletions cobrakbase/core/kbasegenome/genome.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,14 +191,14 @@ def from_kbase_data(kbase_data: dict, info=None, args=None):
kbase_data["id"],
kbase_data["scientific_name"],
kbase_data["domain"],
kbase_data["genome_tiers"],
kbase_data["feature_counts"],
kbase_data.get("genome_tiers",None),
kbase_data.get("feature_counts",None),
kbase_data["genetic_code"],
kbase_data["dna_size"],
kbase_data["num_contigs"],
kbase_data["molecule_type"],
kbase_data.get("molecule_type",None),
kbase_data["source"],
kbase_data["md5"],
kbase_data.get("md5",None),
kbase_data["gc_content"],
kbase_data.get("taxonomy", None),
kbase_data.get("assembly_ref", None),
Expand Down
4 changes: 2 additions & 2 deletions cobrakbase/core/kbasegenome/genome_cds_feature.py
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Original file line number Diff line number Diff line change
Expand Up @@ -294,7 +294,7 @@ def _repr_html_(self):
def from_kbase_data(kbase_data):
functions = KBaseGenomeFeature.extract_functions(kbase_data)
functions_split = KBaseGenomeFeature.split_annotation(functions)
protein_translation = kbase_data["protein_translation"]
protein_translation = kbase_data.get("protein_translation",None)
dna_sequence = kbase_data["dna_sequence"]
if protein_translation:
protein_translation = protein_translation.upper()
Expand All @@ -305,7 +305,7 @@ def from_kbase_data(kbase_data):
protein_translation,
dna_sequence,
kbase_data["location"],
kbase_data["cdss"],
kbase_data.get("cdss",None),
functions,
kbase_data.get("aliases")
)
Expand Down
10 changes: 8 additions & 2 deletions cobrakbase/kbaseapi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,10 @@ def process_workspace_identifiers(id_or_ref, workspace=None):
refs, IDs, and names for workspaces and objects
"""
objspec = {}
if len(id_or_ref.split(";")) > 1:
objspec["to_obj_ref_path"] = id_or_ref.split(";")[0:-1]
print(objspec["to_obj_ref_path"])
id_or_ref = id_or_ref.split(";")[-1]
if workspace is None:
objspec["ref"] = id_or_ref
else:
Expand Down Expand Up @@ -286,7 +290,7 @@ def save_object(self, object_id, ws, object_type, data, meta=None):
params["workspace"] = ws
return KBaseObjectInfo(self.ws_client.save_objects(params)[0])

def list_objects(self, ws, object_type=None, include_metadata=False):
def list_objects(self, ws, object_type=None, include_metadata=False,showHidden=False):
"""
List objects of a workspace (i.e., narrative) with either numerical id (e.g., 12345)
or string id (e.g., user:narrative_1111111111111)
Expand All @@ -296,7 +300,7 @@ def list_objects(self, ws, object_type=None, include_metadata=False):
:param include_metadata:
:return:
"""
params = {"includeMetadata": 0}
params = {"includeMetadata": 0, "showHidden": 0}
if type(ws) == int:
params["ids"] = [ws]
else:
Expand All @@ -305,6 +309,8 @@ def list_objects(self, ws, object_type=None, include_metadata=False):
params["type"] = object_type
if include_metadata:
params["includeMetadata"] = 1
if showHidden:
params["showHidden"] = 1
return self.ws_client.list_objects(params)

def list_workspace(self, ws, object_type=None, include_metadata=False):
Expand Down
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