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Check annotation to be of type dict while reading it from the json #930

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merged 5 commits into from
Mar 23, 2020
Merged

Check annotation to be of type dict while reading it from the json #930

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7642a1c
Annotation setter added to check for dict annotation
Hemant27031999 Feb 1, 2020
d67a8bd
Added test for annotation check
Hemant27031999 Feb 1, 2020
7e2d1d5
updated pickles and other data resources with modified Object class
Hemant27031999 Feb 2, 2020
fb156f2
added getter and setter for annotation and done small updates
Hemant27031999 Mar 21, 2020
d1270e2
modified imports
Hemant27031999 Mar 23, 2020
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13 changes: 12 additions & 1 deletion cobra/core/object.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def __init__(self, id=None, name=""):
self.name = name

self.notes = {}
self.annotation = {}
self._annotation = {}

@property
def id(self):
Expand All @@ -40,6 +40,17 @@ def id(self, value):
def _set_id_with_model(self, value):
self._id = value

@property
def annotation(self):
return self._annotation

@annotation.setter
def annotation(self, annotation):
if not isinstance(annotation, dict):
raise TypeError("Annotation must be a dict")
else:
self._annotation = annotation

def __getstate__(self):
"""To prevent excessive replication during deepcopy."""
state = self.__dict__.copy()
Expand Down
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24 changes: 24 additions & 0 deletions cobra/test/data/invalid_annotation_format.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
{
"metabolites":[
{
"id":"4crsol_c",
"name":"",
"compartment":"c",
"annotation":[
[
"KEGG Compound",
"http://identifiers.org/kegg.compound/C01468"
],
[
"CHEBI",
"http://identifiers.org/chebi/CHEBI:11981"
]
]
}
],
"reactions":[],
"genes":[],
"id":"tesut",
"compartments":{},
"version": 1
}
95 changes: 61 additions & 34 deletions cobra/test/data/mini.json
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Original file line number Diff line number Diff line change
Expand Up @@ -100,10 +100,6 @@
"id": "b2926",
"name": "pgk"
},
{
"id": "b2975",
"name": "glcA"
},
{
"id": "b2987",
"name": "pitB"
Expand All @@ -112,10 +108,6 @@
"id": "b3493",
"name": "pitA"
},
{
"id": "b3603",
"name": "lldP"
},
{
"id": "b3612",
"name": "gpmM"
Expand Down Expand Up @@ -252,7 +244,6 @@
"ADP-GROUP"
],
"cas": [
"58-64-0",
"58-64-0"
],
"chebi": [
Expand Down Expand Up @@ -294,7 +285,6 @@
"bigg.metabolite": "atp",
"biocyc": "ATP",
"cas": [
"56-65-5",
"56-65-5"
],
"chebi": [
Expand Down Expand Up @@ -336,7 +326,6 @@
"bigg.metabolite": "dhap",
"biocyc": "DIHYDROXY-ACETONE-PHOSPHATE",
"cas": [
"57-04-5",
"57-04-5"
],
"chebi": [
Expand Down Expand Up @@ -373,7 +362,6 @@
"bigg.metabolite": "f6p",
"biocyc": "FRUCTOSE-6P",
"cas": [
"643-13-0",
"643-13-0"
],
"chebi": [
Expand Down Expand Up @@ -410,7 +398,6 @@
"bigg.metabolite": "fdp",
"biocyc": "FRUCTOSE-16-DIPHOSPHATE",
"cas": [
"488-69-7",
"488-69-7"
],
"chebi": [
Expand Down Expand Up @@ -445,7 +432,6 @@
"annotation": {
"bigg.metabolite": "g3p",
"cas": [
"142-10-9",
"142-10-9"
],
"chebi": [
Expand Down Expand Up @@ -480,7 +466,6 @@
"GLC-6-P"
],
"cas": [
"56-73-5",
"56-73-5"
],
"chebi": [
Expand Down Expand Up @@ -518,7 +503,6 @@
"annotation": {
"bigg.metabolite": "glc__D",
"cas": [
"50-99-7",
"50-99-7"
],
"kegg.compound": "C00031",
Expand All @@ -539,7 +523,6 @@
"OXONIUM"
],
"cas": [
"7732-18-5",
"7732-18-5"
],
"chebi": [
Expand Down Expand Up @@ -625,7 +608,6 @@
"OXONIUM"
],
"cas": [
"7732-18-5",
"7732-18-5"
],
"chebi": [
Expand Down Expand Up @@ -707,7 +689,6 @@
"bigg.metabolite": "h",
"biocyc": "PROTON",
"cas": [
"12408-02-5",
"12408-02-5"
],
"chebi": [
Expand Down Expand Up @@ -754,7 +735,6 @@
"bigg.metabolite": "h",
"biocyc": "PROTON",
"cas": [
"12408-02-5",
"12408-02-5"
],
"chebi": [
Expand Down Expand Up @@ -797,13 +777,53 @@
"name": "H+"
},
{
"annotation": {
"bigg.metabolite": "lac__D",
"biocyc": "META:D-LACTATE",
"chebi": [
"CHEBI:11001",
"CHEBI:16004",
"CHEBI:18684",
"CHEBI:341",
"CHEBI:42105",
"CHEBI:42111",
"CHEBI:43701"
],
"hmdb": [
"HMDB00171",
"HMDB01311"
],
"kegg.compound": "C00256",
"metanetx.chemical": "MNXM285",
"seed.compound": "cpd00221"
},
"charge": -1,
"compartment": "c",
"formula": "C3H5O3",
"id": "lac__D_c",
"name": "D-Lactate"
},
{
"annotation": {
"bigg.metabolite": "lac__D",
"biocyc": "META:D-LACTATE",
"chebi": [
"CHEBI:11001",
"CHEBI:16004",
"CHEBI:18684",
"CHEBI:341",
"CHEBI:42105",
"CHEBI:42111",
"CHEBI:43701"
],
"hmdb": [
"HMDB00171",
"HMDB01311"
],
"kegg.compound": "C00256",
"metanetx.chemical": "MNXM285",
"seed.compound": "cpd00221"
},
"charge": -1,
"compartment": "e",
"formula": "C3H5O3",
Expand All @@ -815,7 +835,6 @@
"bigg.metabolite": "nad",
"biocyc": "NAD",
"cas": [
"53-84-9",
"53-84-9"
],
"chebi": [
Expand Down Expand Up @@ -855,7 +874,6 @@
"bigg.metabolite": "nadh",
"biocyc": "NADH",
"cas": [
"58-68-4",
"58-68-4"
],
"chebi": [
Expand Down Expand Up @@ -890,7 +908,6 @@
"bigg.metabolite": "pep",
"biocyc": "PHOSPHO-ENOL-PYRUVATE",
"cas": [
"138-08-9",
"138-08-9"
],
"chebi": [
Expand Down Expand Up @@ -928,7 +945,6 @@
"CPD0-1421"
],
"cas": [
"14265-44-2",
"14265-44-2"
],
"chebi": [
Expand Down Expand Up @@ -996,7 +1012,6 @@
"CPD0-1421"
],
"cas": [
"14265-44-2",
"14265-44-2"
],
"chebi": [
Expand Down Expand Up @@ -1060,7 +1075,6 @@
"bigg.metabolite": "pyr",
"biocyc": "PYRUVATE",
"cas": [
"127-17-3",
"127-17-3"
],
"chebi": [
Expand Down Expand Up @@ -1111,15 +1125,10 @@
"upper_bound": 1000.0
},
{
"gene_reaction_rule": "b3603 or b2975",
"gene_reaction_rule": "",
"id": "D_LACt2",
"lower_bound": -1000.0,
"metabolites": {
"h_c": 1,
"h_e": -1,
"lac__D_c": 1,
"lac__D_e": -1
},
"metabolites": {},
"name": "",
"upper_bound": 1000.0
},
Expand Down Expand Up @@ -1167,6 +1176,10 @@
"upper_bound": 1000.0
},
{
"annotation": {
"bigg.reaction": "lac__D",
"sbo": "SBO:0000627"
},
"gene_reaction_rule": "",
"id": "EX_lac__D_e",
"lower_bound": 0.0,
Expand Down Expand Up @@ -1213,7 +1226,7 @@
"annotation": {
"bigg.reaction": "GLCpts"
},
"gene_reaction_rule": "( b2417 and b1621 and b2415 and b2416 ) or ( b2417 and b1101 and b2415 and b2416 ) or ( b1817 and b1818 and b1819 and b2415 and b2416 )",
"gene_reaction_rule": "( b2415 and b2417 and b1101 and b2416 ) or ( b2415 and b2417 and b1621 and b2416 ) or ( b2415 and b1818 and b1817 and b1819 and b2416 )",
"id": "GLCpts",
"lower_bound": 0.0,
"metabolites": {
Expand All @@ -1240,6 +1253,20 @@
"upper_bound": 1000.0
},
{
"annotation": {
"bigg.reaction": "LDH_D",
"biocyc": "META:DLACTDEHYDROGNAD-RXN",
"ec-code": "1.1.1.28",
"kegg.reaction": "R00704",
"metanetx.reaction": "MNXR101037",
"rhea": [
"16369",
"16370",
"16371",
"16372"
],
"sbo": "SBO:0000375"
},
"gene_reaction_rule": "b2133 or b1380",
"id": "LDH_D",
"lower_bound": -1000.0,
Expand Down
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