forked from enviPath/enviPy
[Fix] Adjust Rules according to manual QA, Add missing Rule (#452)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#452
This commit is contained in:
113
epdb/migrations/0028_auto_20260812_0902.py
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113
epdb/migrations/0028_auto_20260812_0902.py
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# Generated by Django 6.0.3 on 2026-08-12 09:02
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from django.conf import settings as s
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from django.db import migrations
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from envipy_additional_information import Likelihood, RuleLikelihood
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NEW_RULE = {
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"parent": "bt0005",
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"name": "bt0005-3667",
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"description": "vic-unsubstituted Aromatic > vic-Dihydroxyaromatic",
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"smirks": "[#8:7]([H])-[#6:1]([H])-1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]([H])-1-[#8:8]([H])>>[#8:7]([H])-[#6:1]=1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]=1-[#8:8]([H])",
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"scenario_name": "bt0005-3667 aerobic likelihood",
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"scenario_aerobic_likelihood": RuleLikelihood(likelihood=Likelihood.LIKELY),
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}
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RULE_FIXES = {
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"bt0005-4282": "[c:1]([H])1:[c:2]([H]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1>>[c:1]([#8])1:[c:2]([#8]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1",
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"bt0014-4215": "[c:1]([H])1[c:8][#6,#7;a:7][c:6][c:5][c:4]1[#8;!$([OH]c:[#6,#7;a:7]([OH])):9]([H])>>[#8:9]([H])[c:4]1:[c:5]:[c:6]:[#6,#7;a:7]:[c:8]:[c:1]1[#8]([H])",
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# "bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([H:3])(=[#1,#6:7]).[#6;A:2]=O",
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# CN1C=NC2=C1C(=O)N(C)C(=O)N2 not working anymore with bt0063-3938 if change above is applied
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"bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O",
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"bt0068-3564": "[#7:4]!@-[#6:2](!@-[#7:1])=[O:5]>>[#7:4]-[#6:2](-[O+0H1])=[O:5].[#7H1:1]",
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"bt0180-2844": "[H][C:2]([#6:5]([H])([H])([H]))([#1,#6:4])!@-[#6:1]([H])([H])-[#6:3](-[#8-:8])=[O:6]>>[#6:5]([H])([H])([H])\\[#6:2](-[#1,#6:4])=[#6H:1]\\[#6:3](-[#8-:8])=[O:6]",
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"bt0181-1278": "[#8-:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-[#6:3](-[H])=[#6:5](-Cl)-[#6:6](-[#8-:10])=[O:9]>>[O+0H1:10]-[#6:6](=[O:9])-[#6:5]=[#6:3]-1-[O+0:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-1",
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"bt0298-3335": "[#6:1][N+:2]#[C:3]>>[#6:1]-[#7H2:2]-[#6:3]=O",
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"bt0322-3393": "[H:10]\\[#6:6](=[#6:9](/[#6:1]([H])([H])([H]))-[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:5](-[#16:7])=[O:8]>>[H:10]\\[#6:6](-[#6:5](-[#16:7])=[O:8])=[#6:9](\\[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:1]-[#6](-[#8-])=O",
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"bt0343-2675": "[#8-]-[#6](=O)-[c:1]1[c:6][cH:7][c:8](-[#7H2,#8H1:9])[cH:10][c:11]1>>[#8H][c:1]1[c:6][c:7][c:8]([*:9])[c:10][c:11]1",
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"bt0350-3319": "[#6:6][#7:3][#6;!R:2]=[#7;!R:1][#6:5]>>[#6:5][#7:1][#6:2]=O.[#6:6][#7:3]", # Trig before 5 -> all of them shouldn't
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"bt0374-4081": "[cH:4]1[c:16][c:15][c:14][c:13][c:3]1[#7,#8:2][c:1]1[c:8][c:9][c:10][c:11][c:12]1>>[#7,#8:2]-[c:1]1[c:12][c:11][c:10][c:9][c:8]1[c:13]1[c:14][c:15][c:16][c:4](-[#8])[c:3]1-[#8]",
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"bt0378-3188": "[#8-:7][c:1]1[c:6]([#7+]([#8-])=O)[c:5][c:4]([#7+:9]([#8-])=O)[c:3][c:2]1([#7+:8]([#8-])=O)>>[#8+0:7]=[#6:1]1-[#6:6]-[#6:5]-[#6:4]([#7+:9]([#8-])=O)-[#6:3]-[#6:2]1([#7+:8]([#8-])=O)",
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"bt0379-3190": "[#9,#17,#35,#53]-[#6:1](-[H])-1-[#6:5]-,=[#6:6]-[#6:7]-,=[#6:8]-[#6:2](-[H])-1-[#9,#17,#35,#53]>>[#6:6]~1-[#6:7]~[#6:8]-[#6:2]=[#6:1]-[#6:5]~1",
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"bt0393-3367": "[#6:5]-[#6:1](-[#7:2](-[H])(-[H]))=[S+:3]-[#8-:6]>>[#6:5]-[#6:1](=[#7H1:2])-[S+0:3](=[O])-[#8+0H1:6]",
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}
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def forward_func(apps, schema_editor):
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ContentType = apps.get_model("contenttypes", "ContentType")
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pkg_class = s.EPDB_PACKAGE_MODEL
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if len(pkg_class.split(".")) != 2:
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raise ValueError(
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f"EPDB_PACKAGE_MODEL must be of the form 'app_label.model_name', got {pkg_class}"
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)
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app_label, model_name = pkg_class.split(".")
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Package = apps.get_model(app_label, model_name)
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SimpleAmbitRule = apps.get_model("epdb", "SimpleAmbitRule")
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ParallelRule = apps.get_model("epdb", "ParallelRule")
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Scenario = apps.get_model("epdb", "Scenario")
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AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
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simple_ambit_rule_ct = ContentType.objects.get_for_model(SimpleAmbitRule)
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if Package.objects.filter(name="EAWAG-BBD").exists():
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p = Package.objects.get(name="EAWAG-BBD")
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if not SimpleAmbitRule.objects.filter(package=p, name=NEW_RULE["name"]).exists():
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# Create Missing Rule
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new_sr = SimpleAmbitRule()
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new_sr.polymorphic_ctype = simple_ambit_rule_ct
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new_sr.package = p
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new_sr.name = NEW_RULE["name"]
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new_sr.description = NEW_RULE["description"]
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new_sr.smirks = NEW_RULE["smirks"]
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new_sr.save()
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new_sr.url = "{}/simple-ambit-rule/{}".format(new_sr.package.url, new_sr.uuid)
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new_sr.save()
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# Add likelihood
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new_scen = Scenario()
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new_scen.package = p
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new_scen.name = NEW_RULE["scenario_name"]
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new_scen.save()
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new_scen.url = "{}/scenario/{}".format(new_scen.package.url, new_scen.uuid)
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new_scen.save()
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ai = NEW_RULE["scenario_aerobic_likelihood"]
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new_add_inf = AdditionalInformation()
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new_add_inf.package = p
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new_add_inf.type = ai.__class__.__name__
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new_add_inf.data = ai.model_dump(mode="json")
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new_add_inf.scenario = new_scen
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new_add_inf.save()
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new_add_inf.url = "{}/additional-information/{}".format(
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new_add_inf.scenario.url, new_add_inf.uuid
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)
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new_add_inf.save()
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# Link Scenario
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new_sr.scenarios.add(new_scen)
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# Link to bt0005
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pr = ParallelRule.objects.get(package=p, name="bt0005")
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pr.simple_rules.add(new_sr)
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# Update others
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for rule_name, smirks in RULE_FIXES.items():
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sr = SimpleAmbitRule.objects.get(package=p, name=rule_name)
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sr.smirks = smirks
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sr.save()
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class Migration(migrations.Migration):
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dependencies = [
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("epdb", "0027_alter_compound_aliases_and_more"),
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]
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operations = [
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migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
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]
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@ -854,9 +854,15 @@ class Compound(
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@property
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@property
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def related_reactions(self):
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def related_reactions(self):
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return (
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return (
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(
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Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
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Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
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| Reaction.objects.filter(package=self.package, products__in=[self.default_structure])
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| Reaction.objects.filter(
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).order_by("name")
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package=self.package, products__in=[self.default_structure]
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)
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)
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.distinct()
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.order_by("name")
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)
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@property
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@property
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def related_nodes(self):
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def related_nodes(self):
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@ -1080,13 +1080,17 @@ def package_model(request, package_uuid, model_uuid):
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for pr in pred_res:
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for pr in pred_res:
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if len(pr) > 0:
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if len(pr) > 0:
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products = []
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products = []
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for prod_set in pr.product_sets:
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for prod_set in pr.product_sets:
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logger.debug(f"Checking {prod_set}")
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logger.debug(f"Checking {prod_set}")
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products.append(tuple([x for x in prod_set]))
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products.append(tuple([x for x in prod_set]))
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products = list(set(products))
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for prod in products:
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res["pred"].append(
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res["pred"].append(
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{
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{
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"products": list(set(products)),
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"products": list(prod),
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"probability": pr.probability,
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"probability": pr.probability,
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"btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
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"btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
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if pr.rule is not None
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if pr.rule is not None
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@ -109,12 +109,12 @@
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res += "<th scope='row'>" + cnt + "</th>";
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res += "<th scope='row'>" + cnt + "</th>";
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res +=
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res +=
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"<th scope='row'>" +
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"<th scope='row'>" +
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data[transformation]["products"][0].join(", ") +
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data[transformation]["products"].join(", ") +
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"</th>";
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"</th>";
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res +=
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res +=
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"<th scope='row'>" +
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"<th scope='row'>" +
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"<img width='400' src='{% url 'depict' %}?smiles=" +
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"<img width='400' src='{% url 'depict' %}?smiles=" +
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encodeURIComponent(data[transformation]["products"][0].join(".")) +
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encodeURIComponent(data[transformation]["products"].join(".")) +
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"'></th>";
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"'></th>";
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res +=
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res +=
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"<th scope='row'>" +
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"<th scope='row'>" +
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@ -47,7 +47,7 @@ class ModelViewTest(TestCase):
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expected = [
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expected = [
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{
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{
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"products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
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"products": ["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"],
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"probability": 0.75,
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"probability": 0.75,
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"btrule": {
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"btrule": {
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
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@ -55,7 +55,7 @@ class ModelViewTest(TestCase):
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},
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},
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},
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},
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{
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{
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"products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
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"products": ["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"],
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"probability": 0.25,
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"probability": 0.25,
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"btrule": {
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"btrule": {
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/0e6e9290-b658-4450-b291-3ec19fa19206",
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/0e6e9290-b658-4450-b291-3ec19fa19206",
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@ -63,7 +63,7 @@ class ModelViewTest(TestCase):
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},
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},
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},
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},
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{
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{
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"products": [["CCNC(=O)C1=CC(CO)=CC=C1", "CC=O"]],
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"products": ["CCNC(=O)C1=CC(CO)=CC=C1", "CC=O"],
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"probability": 0.0,
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"probability": 0.0,
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"btrule": {
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"btrule": {
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/27a3a353-0b66-4228-bd16-e407949e90df",
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"url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/27a3a353-0b66-4228-bd16-e407949e90df",
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Reference in New Issue
Block a user