From e2f5c415b7132ca9d16aafe828e99dd6758021bb Mon Sep 17 00:00:00 2001
From: fmareuil <fabien.mareuil@pasteur.fr>
Date: Fri, 29 Sep 2023 19:07:13 +0200
Subject: [PATCH] add API update method
---
docker-compose.yaml | 16 +
.../management/commands/build_distances.py | 532 ++++++++++++++++++
...ty_options_alter_chain_options_and_more.py | 269 +++++++++
ippisite/ippidb/models/targetcentric.py | 26 +-
ippisite/ippidb/serializer.py | 14 +-
ippisite/ippidb/views/__init__.py | 4 +-
ippisite/ippidb/views/targetcentric.py | 44 +-
ippisite/ippisite/authentication.py | 45 ++
8 files changed, 929 insertions(+), 21 deletions(-)
create mode 100644 ippisite/ippidb/management/commands/build_distances.py
create mode 100644 ippisite/ippidb/migrations/0069_contributor_alter_cavity_options_alter_chain_options_and_more.py
create mode 100644 ippisite/ippisite/authentication.py
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 47f7a43c..efaaf0e8 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -22,6 +22,8 @@ services:
# command: python manage.py runserver 0.0.0.0:8000 # only if you have issues with gunicorn
volumes:
- ./ippisite:/code # for dev purpose only !!!
+ #- mediafiles:/code/persistent/media
+ - staticfiles:/static_root
ports:
- "8000:8000"
depends_on:
@@ -43,11 +45,25 @@ services:
- DJANGO_DEBUG=False
volumes:
- ./ippisite:/code # for dev purpose only !!!
+ #- mediafiles:/code/persistent/media
depends_on:
- db-local
- redis-local
- django # in order to have the migration applied in the db
+ nginx:
+ image: nginx:1.19-alpine
+ volumes:
+ - ./nginx/nginx.conf:/etc/nginx/conf.d/default.conf:ro
+ - staticfiles:/static
+ - ./ippisite/persistent/media:/media
+ ports:
+ - "8080:8080"
+ # - "8090:8090"
+ depends_on:
+ - django
volumes:
ippidb-dev-db-data:
+ #mediafiles:
+ staticfiles:
diff --git a/ippisite/ippidb/management/commands/build_distances.py b/ippisite/ippidb/management/commands/build_distances.py
new file mode 100644
index 00000000..c16b8a4b
--- /dev/null
+++ b/ippisite/ippidb/management/commands/build_distances.py
@@ -0,0 +1,532 @@
+"""
+Command to build matrix distances
+"""
+
+import os
+import sys
+import json
+from xml.etree.ElementTree import ParseError
+import datetime
+import numpy as np
+import pandas as pd
+from celery import states
+from django.core.management.base import AppCommand
+from django.db.utils import IntegrityError
+# from django.db import transaction
+from django.db.models import Q
+from sklearn.neighbors import NearestNeighbors
+from django.db.models.aggregates import Avg, StdDev, Max, Min
+from ippidb.models.targetcentric import (
+ Cavity,
+ Partner,
+ Chain,
+ PDB,
+ Ligand,
+ Distance,
+ MetaInformation,
+)
+from ippidb.models.ippidb import Protein
+from ippidb.ws import (
+ # convert_iupac_to_smiles,
+ convert_pdb_ligand_id_to_iupacandsmiles,
+ EntryNotFoundError,
+)
+from ippidb.management.commands import TaskOutWrapper
+
+
+def normalize_data(indata):
+ std = indata.std(axis=0)
+ std[std == 0] = 1.0
+ mu = indata.mean(axis=0)
+ return (indata - mu) / std
+
+
+def load_data(ppc):
+ """
+ >>> data, name = load_data("PPC-HD-PL_dataset_07-01-2019PDBe_matrix.csv")
+ >>> data.shape
+ (57, 109)
+ """
+ colnames = set(ppc.columns) - set(["Cavity"])
+ sel_log = set(["PMI1", "PMI2", "PMI3", "Rgyr", "Volume"])
+ sel_atanh = set(
+ [
+ "NPR1",
+ "NPR2",
+ "Asphericity",
+ "Eccentricity",
+ "InertialShapeFactor",
+ "SpherocityIndex",
+ ]
+ )
+ sel_atanh_100 = colnames - sel_log - sel_atanh
+ ppc[list(sel_log)] = np.log10(ppc[list(sel_log)])
+ ppc[list(sel_atanh)] = np.arctanh(ppc[list(sel_atanh)])
+ ppc[list(sel_atanh_100)] = np.arctanh(ppc[list(sel_atanh_100)] / 100.0)
+
+ names = ppc.Cavity
+ data = ppc[list(colnames)].values
+ error_indices = []
+ for cav in range(len(data)):
+ if np.isinf(data[cav]).sum():
+ error_indices.append(cav)
+ if np.isnan(data[cav]).sum():
+ error_indices.append(cav)
+ # Clean error entry data
+ new_data = [i for j, i in enumerate(data) if j not in error_indices]
+ new_names = [i for j, i in enumerate(names) if j not in error_indices]
+ cavitynames_error = []
+ for ind in error_indices:
+ cavitynames_error.append(names[ind])
+
+ data = np.array(new_data)
+ names = new_names
+ data = normalize_data(data)
+ return data, names, cavitynames_error
+
+
+def normalize_cavity_table():
+ cavities = Cavity.objects.all().values_list()
+ df = pd.DataFrame(list(cavities))
+
+
+def knn(data, nb_neighbors):
+ nbrs = NearestNeighbors(n_neighbors=nb_neighbors, algorithm="ball_tree").fit(data)
+ distances, indices = nbrs.kneighbors(data)
+ return distances, indices
+
+
+def dir_path(string):
+ """
+ Test if a path is a directory
+ """
+ if os.path.isdir(string):
+ return string
+ else:
+ raise NotADirectoryError(string)
+
+
+def file_exist(string):
+ """
+ Test if a file exist
+ """
+ if os.path.exists(string):
+ return string
+ else:
+ raise FileNotFoundError(string)
+
+
+class Command(AppCommand):
+ """
+ Command to import cavity descriptors,
+ we use TaskOutWrapper to manage update std_out and std_err
+ """
+
+ help = """Load Cavity descriptors from global csv file and complet directory tree.
+ Please before import cavity descriptors clean the old data with the command python manage.py clean_targetcentric"""
+
+ def __init__(
+ self, stdout=None, stderr=None, no_color=False, force_color=False, task=None,
+ ):
+ super(Command, self).__init__(
+ stdout=stdout, stderr=stderr, no_color=no_color, force_color=force_color
+ )
+ if task:
+ task.update_state(state=states.STARTED)
+ self.stdout = TaskOutWrapper(stdout or sys.stdout, task=task, std_out=True)
+ self.stderr = TaskOutWrapper(stderr or sys.stderr, task=task, std_err=True)
+
+ def add_arguments(self, parser):
+ parser.add_argument(
+ "-n",
+ "--nb_neighbors",
+ type=int,
+ help="Number of nearest neighbors to use for saved distances between cavities",
+ )
+
+ def get_iupac_from_pdb(self, content_file, code_ligand):
+ """
+ Parse Hetnam from pdb by using this record forma:
+ COLUMNS DATA TYPE FIELD DEFINITION
+ ----------------------------------------------------------------------------
+ 1 - 6 Record name "HETNAM"
+ 9 - 10 Continuation continuation Allows concatenation of multiple records.
+ 12 - 14 LString(3) hetID Het identifier, right-justified.
+ 16 - 70 String text Chemical name.
+ """
+ lines = content_file.split("\n")
+ iupac = []
+ for line in lines:
+ if line[0:6] == "HETNAM" and line[11:14] == code_ligand:
+ index = line[8:10].strip()
+ if index:
+ iupac.insert(int(index) - 1, line[15:70].strip())
+ else:
+ iupac.append(line[15:70].strip())
+ return "".join(iupac)
+
+ def init_cavity(self, verbose_name, uniprot_lig, dir_pdbs):
+ """
+ Initialize a Cavity object with the cavity verbose_name before save
+ all the descriptor a verbose_name can be '3spf-A-B50-501_CAVITY_N1'
+ or '1bxl-AB-Q07817-Q16611-withinA_CAVITY_N1'
+ """
+
+ splitted = verbose_name.split("-")
+ pdb_code = splitted[0]
+ chains = splitted[1]
+ cavity_number = splitted[-1].split("_")[-1].strip("N")
+ results_path = "{}/{}/results".format(dir_pdbs, pdb_code)
+ if len(splitted) == 4:
+ # Protein Ligand
+ self.stdout.write(
+ self.style.WARNING(
+ "Start import protein ligand cavity {}".format(verbose_name)
+ )
+ )
+ code_partner = splitted[2]
+ chain_uniprot = []
+ for unipdb in uniprot_lig[pdb_code]:
+ if unipdb["chain"] == chains:
+ chain_uniprot.append(unipdb["uniprot"])
+ if len(set(chain_uniprot)) > 1:
+ self.stdout.write(
+ self.style.WARNING(
+ "WARNING more than one uniprot code for pdb {}, chain {}".format(
+ pdb_code, chains
+ )
+ )
+ )
+ chain_uniprot = chain_uniprot[0]
+ chain_pdb_id = chains
+ partner_pdb_id = splitted[-1].split("_")[0]
+ base_name_file = "-".join(splitted[0:2])
+ pdb_path = "{}/{}-{}.pdb".format(
+ results_path, base_name_file, chain_uniprot
+ )
+ pdb_path_chain = "{}/{}-{}.pdb".format(
+ results_path, base_name_file, chain_uniprot
+ )
+ pdb_path_partner = "{}/{}/{}-{}-{}.pdb".format(
+ dir_pdbs, pdb_code, base_name_file, code_partner, partner_pdb_id
+ )
+ with open(pdb_path, "r") as pdbfile:
+ file_content = pdbfile.read()
+ self.stdout.write(self.style.WARNING("PDB creation {}".format(pdb_code)))
+ pdb, created = PDB.objects.get_or_create(code=pdb_code,)
+ pdb.file_content = file_content
+ pdb.save()
+ # iupac = self.get_iupac_from_pdb(file_content, code_partner)
+ # try:
+ # smiles = convert_iupac_to_smiles(iupac)
+ # except EntryNotFoundError:
+ # smiles = ""
+ iupac, smiles = convert_pdb_ligand_id_to_iupacandsmiles(code_partner)
+ with open(pdb_path_partner, "r") as compoundfile:
+ file_content_compound = compoundfile.read()
+ self.stdout.write(
+ self.style.WARNING(
+ "Ligand partner creation ligand:{} {}, pdb: {}, smile: {}".format(
+ code_partner, partner_pdb_id, pdb.code, smiles
+ )
+ )
+ )
+ partner_ligand, created = Ligand.objects.get_or_create(
+ supplementary_id=partner_pdb_id, pdb_ligand_id=code_partner, pdb=pdb,
+ )
+ partner_ligand.iupac_name = iupac
+ partner_ligand.canonical_smile = smiles
+ partner_ligand.file_content = file_content_compound
+ partner_ligand.save()
+ self.stdout.write(
+ self.style.WARNING(
+ "Partner creation, ligand: {}".format(partner_ligand.pdb_ligand_id)
+ )
+ )
+ partner, created = Partner.objects.get_or_create(ligand=partner_ligand)
+ elif len(splitted) == 5:
+ # Heterodimer
+ self.stdout.write(
+ self.style.WARNING(
+ "Start import heterodimer cavity {}".format(verbose_name)
+ )
+ )
+ within = splitted[-1].split("_")[0].strip("within")
+ chain_index = chains.index(within)
+ chain_uniprot = splitted[chain_index + 2]
+ chain_pdb_id = chains[chain_index]
+ if chain_index == 0:
+ code_index = 1
+ else:
+ code_index = 0
+ code_partner = splitted[code_index + 2]
+ partner_pdb_id = chains[code_index]
+ base_name_file = "-".join(splitted[0:4])
+ pdb_path = "{}/{}.pdb".format(results_path, base_name_file)
+ pdb_path_chain = "{}/{}-{}.pdb".format(
+ results_path, base_name_file, chain_pdb_id
+ )
+ pdb_path_partner = "{}/{}-{}.pdb".format(
+ results_path, base_name_file, partner_pdb_id
+ )
+ with open(pdb_path, "r") as pdbfile:
+ file_content = pdbfile.read()
+ self.stdout.write(self.style.WARNING("PDB creation {}".format(pdb_code)))
+ pdb, created = PDB.objects.get_or_create(code=pdb_code,)
+ pdb.file_content = file_content
+ pdb.save()
+ try:
+ self.stdout.write(
+ self.style.WARNING(
+ "Protein partner creation {}".format(code_partner)
+ )
+ )
+ partner_protein, created = Protein.objects.get_or_create(
+ uniprot_id=code_partner
+ )
+ except (
+ IndexError,
+ TypeError,
+ IntegrityError,
+ EntryNotFoundError,
+ ParseError,
+ json.decoder.JSONDecodeError,
+ ) as err:
+ self.stdout.write(
+ self.style.WARNING(
+ "WARNING impossible to create Protein {}, error {}".format(
+ chain_uniprot, err
+ )
+ )
+ )
+ return None
+ with open(pdb_path_partner, "r") as partnerfile:
+ file_content_partner = partnerfile.read()
+ self.stdout.write(
+ self.style.WARNING(
+ "Chain partner creation, pdb: {}, chain: {}, uniprot: {}".format(
+ pdb.code, partner_pdb_id, partner_protein.uniprot_id
+ )
+ )
+ )
+ partner_chain, created = Chain.objects.get_or_create(
+ pdb_chain_id=partner_pdb_id, pdb=pdb,
+ )
+ partner_chain.protein = partner_protein
+ partner_chain.file_content = file_content_partner
+ partner_chain.save()
+ self.stdout.write(
+ self.style.WARNING(
+ "Partner creation, chain: {}".format(partner_chain.pdb_chain_id)
+ )
+ )
+ partner, created = Partner.objects.get_or_create(chain=partner_chain)
+ else:
+ raise NameError("Cavity full name is not conform")
+ try:
+ self.stdout.write(
+ self.style.WARNING("Protein creation {}".format(chain_uniprot))
+ )
+ protein, created = Protein.objects.get_or_create(uniprot_id=chain_uniprot)
+ except (
+ IndexError,
+ TypeError,
+ IntegrityError,
+ EntryNotFoundError,
+ ParseError,
+ json.decoder.JSONDecodeError,
+ ) as err:
+ self.stdout.write(
+ self.style.WARNING(
+ "WARNING impossible to create Protein {}, error {}".format(
+ chain_uniprot, err
+ )
+ )
+ )
+ return None
+ with open(pdb_path_chain, "r") as f:
+ file_content_chain = f.read()
+ self.stdout.write(
+ self.style.WARNING(
+ "Chain creation, pdb: {}, chain: {}, uniprot: {}".format(
+ pdb.code, chain_pdb_id, protein.uniprot_id
+ )
+ )
+ )
+ chain, created = Chain.objects.get_or_create(
+ pdb_chain_id=chain_pdb_id, pdb=pdb,
+ )
+ chain.protein = protein
+ chain.file_content = file_content_chain
+ chain.save()
+ mol2_path = "{}/{}-{}/CAVITY_N{}_ALL_orthosteric.mol2".format(
+ results_path,
+ "-".join(splitted[0:-1]),
+ splitted[-1].split("_")[0],
+ cavity_number,
+ )
+ with open(mol2_path, "r") as mol2file:
+ mol2_content = mol2file.read()
+ try:
+ cavity = Cavity.objects.get(
+ full_name=verbose_name,
+ chain=chain,
+ cavity_number=cavity_number,
+ partner=partner,
+ )
+ self.stdout.write(
+ self.style.WARNING(
+ "WARNING Cavity {}, already exist".format(verbose_name)
+ )
+ )
+ return None
+ except Cavity.DoesNotExist:
+ self.stdout.write(
+ self.style.SUCCESS(
+ "Info Cavity {}, doesn't already exist".format(verbose_name)
+ )
+ )
+ cavity = Cavity(
+ full_name=verbose_name,
+ mol2=mol2_content,
+ chain=chain,
+ cavity_number=cavity_number,
+ partner=partner,
+ )
+ return cavity
+
+ def handle(self, *args, **options):
+ """
+ Perform the command's actions
+ """
+ update_aggregate_only = False
+ if not update_aggregate_only:
+ csv = pd.read_csv(options["csv"], sep=",")
+ dirpath = options["path"]
+ uniprot_json_file = options["ligand_uniprot"]
+ with open("{}".format(uniprot_json_file), "r") as jsonfile:
+ data = json.load(jsonfile)
+ # with transaction.atomic():
+ for index, row in csv.iterrows():
+ try:
+ new_cavity = self.init_cavity(row["Cavity"], data, dirpath)
+ except FileNotFoundError as err:
+ self.stdout.write(
+ self.style.WARNING("File Not Found: {}".format(err))
+ )
+ new_cavity = None
+ if new_cavity:
+ for name, attr in row.items():
+ if name != "Cavity":
+ setattr(
+ new_cavity, name.lower().replace("-", "_"), attr
+ )
+ new_cavity.save()
+ self.stdout.write(
+ self.style.SUCCESS(
+ "Cavity {} successfully imported".format(
+ row["Cavity"]
+ )
+ )
+ )
+ if not update_aggregate_only:
+ self.stdout.write(self.style.SUCCESS("Matrix preparation"))
+ data, names, cavities_error = normalize_cavity_table()
+ for cavity_error in cavities_error:
+ self.stdout.write(
+ self.style.WARNING(
+ """WARNING Cavity {}: an error appeared during the normalization matrix.
+ This cavity was not taken into account in order to normalize the matrix.
+ Please check the cavity before recalculating the distance matrix.
+ You can use the clean_targetcentric command to clean up the database
+ if you delete the cavity or the import_targetcentric command
+ to update the matrix if you correct the cavity""".format(
+ cavity_error
+ )
+ )
+ )
+ distances, indices = knn(data, options["nb_neighbors"])
+ for cav1_index, name in enumerate(names):
+ bulk_distance_create = []
+ bulk_distance_update = []
+ try:
+ cavity1 = Cavity.objects.get(full_name=name)
+ except Cavity.DoesNotExist:
+ cavity1 = None
+ if cavity1:
+ self.stdout.write(
+ self.style.SUCCESS(
+ "{}: Distances for cavity {}".format(
+ datetime.datetime.now(), name
+ )
+ )
+ )
+ for dist_index, cav2_index in enumerate(indices[cav1_index]):
+ try:
+ cavity2 = Cavity.objects.get(
+ full_name=names[cav2_index]
+ )
+ except Cavity.DoesNotExist:
+ cavity2 = None
+ if cavity2 and cavity1 != cavity2:
+ if distances[cav1_index][dist_index] == 0:
+ self.stdout.write(
+ self.style.WARNING(
+ "WARNING Distance between {} and {}, is null".format(
+ cavity1.full_name, cavity2.full_name
+ )
+ )
+ )
+ try:
+ dist = Distance.objects.get(
+ Q(cavity1=cavity1, cavity2=cavity2)
+ | Q(cavity1=cavity2, cavity2=cavity1)
+ )
+ if (
+ dist.distance
+ != distances[cav1_index][dist_index]
+ ):
+ dist.distance = distances[cav1_index][
+ dist_index
+ ]
+ bulk_distance_update.append(dist)
+ except Distance.DoesNotExist:
+ dist = Distance(
+ cavity1=cavity1,
+ cavity2=cavity2,
+ distance=distances[cav1_index][dist_index],
+ )
+ bulk_distance_create.append(dist)
+ except Distance.MultipleObjectsReturned as err:
+ self.stdout.write(
+ self.style.ERROR(
+ "ERROR: Multiple distances for {}, {}: {}".format(
+ name, names[cav2_index], err
+ )
+ )
+ )
+ Distance.objects.bulk_create(bulk_distance_create)
+ Distance.objects.bulk_update(bulk_distance_update, ["distance"])
+ average_std = Distance.objects.aggregate(
+ average=Avg("distance"),
+ std=StdDev("distance"),
+ maximum=Max("distance"),
+ minimum=Min("distance"),
+ )
+ metainfo = MetaInformation.objects.all()
+ if metainfo.count() > 1:
+ metainfo.delete()
+ elif metainfo.count() == 0:
+ MetaInformation.objects.create(
+ average=average_std["average"],
+ std=average_std["std"],
+ maximum=average_std["maximum"],
+ minimum=average_std["minimum"],
+ )
+ else:
+ metainfofirst = metainfo.first()
+ metainfofirst.average = average_std["average"]
+ metainfofirst.std = average_std["std"]
+ metainfofirst.maximum = average_std["maximum"]
+ metainfofirst.minimum = average_std["minimum"]
+ metainfofirst.save()
diff --git a/ippisite/ippidb/migrations/0069_contributor_alter_cavity_options_alter_chain_options_and_more.py b/ippisite/ippidb/migrations/0069_contributor_alter_cavity_options_alter_chain_options_and_more.py
new file mode 100644
index 00000000..419cf79d
--- /dev/null
+++ b/ippisite/ippidb/migrations/0069_contributor_alter_cavity_options_alter_chain_options_and_more.py
@@ -0,0 +1,269 @@
+# Generated by Django 4.2.5 on 2023-09-20 23:30
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('contenttypes', '0002_remove_content_type_name'),
+ ('auth', '0012_alter_user_first_name_max_length'),
+ ('ippidb', '0068_auto_20210310_1052'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Contributor',
+ fields=[
+ ],
+ options={
+ 'proxy': True,
+ 'indexes': [],
+ 'constraints': [],
+ },
+ bases=('auth.user',),
+ ),
+ migrations.AlterModelOptions(
+ name='cavity',
+ options={'ordering': ['chain', 'cavity_number'], 'verbose_name_plural': 'Cavities'},
+ ),
+ migrations.AlterModelOptions(
+ name='chain',
+ options={'ordering': ['pdb', 'pdb_chain_id']},
+ ),
+ migrations.AddField(
+ model_name='partner',
+ name='type_binding',
+ field=models.CharField(default='orthosteric', max_length=50, verbose_name='Type of Binding'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='cavity',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='cellline',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='chain',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundaction',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundactivityresult',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundcytotoxicityresult',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundjob',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundpkresult',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='compoundpkresult',
+ name='tolerated',
+ field=models.BooleanField(null=True, verbose_name='Tolerated'),
+ ),
+ migrations.AlterField(
+ model_name='compoundtanimoto',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='contribution',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='disease',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='distance',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='domain',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='drugbankcompoundtanimoto',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='interactfile',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='job',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='lellebiplotdata',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='ligand',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='average',
+ field=models.DecimalField(decimal_places=8, help_text='partial matrix mean value', max_digits=11, verbose_name='Average'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='maximum',
+ field=models.DecimalField(decimal_places=8, help_text='partial matrix maximum value', max_digits=11, verbose_name='Maximum'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='minimum',
+ field=models.DecimalField(decimal_places=8, help_text='partial matrix minimum value', max_digits=11, verbose_name='Minimum'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='normalize_factor',
+ field=models.DecimalField(blank=True, decimal_places=8, default=4.5859973, help_text='complet matrix standard deviation', max_digits=11, null=True, verbose_name='Normalize Factor'),
+ ),
+ migrations.AlterField(
+ model_name='metainformation',
+ name='std',
+ field=models.DecimalField(decimal_places=8, help_text='partial matrix standard deviation', max_digits=11, verbose_name='Standard Deviation'),
+ ),
+ migrations.AlterField(
+ model_name='molecularfunction',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='network',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='partner',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='pcabiplotdata',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='pdb',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='ppi',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='ppicomplex',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='ppifamily',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='protein',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='proteindomaincomplex',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='proteindomaincomplex',
+ name='polymorphic_ctype',
+ field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
+ ),
+ migrations.AlterField(
+ model_name='proteindomaincomplexgroup',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='refcompoundbiblio',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='symmetry',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='taxonomy',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='testactivitydescription',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='testcytotoxdescription',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterField(
+ model_name='testpkdescription',
+ name='id',
+ field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='partner',
+ unique_together={('ligand', 'chain')},
+ ),
+ ]
diff --git a/ippisite/ippidb/models/targetcentric.py b/ippisite/ippidb/models/targetcentric.py
index ccbf3660..29e42050 100644
--- a/ippisite/ippidb/models/targetcentric.py
+++ b/ippisite/ippidb/models/targetcentric.py
@@ -2,8 +2,9 @@ from django.db import models
from django.forms import ValidationError
from django.db.models import Q
from django.dispatch import receiver
-from django.db.models.signals import pre_delete, post_save
+from django.db.models.signals import pre_delete, post_save, pre_save
from .ippidb import Protein
+from ippidb.ws import convert_pdb_ligand_id_to_iupacandsmiles
import json
@@ -165,7 +166,6 @@ class Chain(models.Model):
partner_message = "with partner "
return "{}{}".format(partner_message, self.protein.recommended_name_long)
-
class InteractFile(models.Model):
chain = models.ForeignKey(Chain, on_delete=models.CASCADE)
label = models.CharField(max_length=250, blank=False, null=False)
@@ -174,6 +174,9 @@ class InteractFile(models.Model):
default=0.7, verbose_name="Default isolevel value"
)
+ class Meta:
+ unique_together = [['chain', 'label']]
+
def __unicode__(self):
return "{}".format(self.interact_file)
@@ -223,6 +226,14 @@ class Ligand(models.Model):
partner_message = "with ligand "
return "%s%s_%s" % (partner_message, self.pdb_ligand_id, self.supplementary_id)
+ def save(self, *args, **kwargs):
+ super(Ligand, self).save(*args, **kwargs)
+ if not self.canonical_smile or not self.iupac_name:
+ iupac, smiles = convert_pdb_ligand_id_to_iupacandsmiles(self.pdb_ligand_id)
+ self.canonical_smile = smiles
+ self.iupac_name = iupac
+ self.save()
+
class Partner(models.Model):
"""
@@ -231,6 +242,12 @@ class Partner(models.Model):
ligand = models.ForeignKey(Ligand, on_delete=models.CASCADE, blank=True, null=True)
chain = models.ForeignKey(Chain, on_delete=models.CASCADE, blank=True, null=True)
+ type_binding = models.CharField(
+ "Type of Binding", max_length=50, default="orthosteric", blank=False, null=False
+ )
+ class Meta:
+ unique_together = [['ligand', 'chain']]
+
def save(self, *args, **kwargs):
if self.ligand and self.chain:
@@ -509,3 +526,8 @@ def interactdelete(sender, instance, **kwargs):
interactfile.interact_file.name
):
interactfile.interact_file.delete()
+
+
+@receiver(pre_save, sender=Chain)
+def updatemrcfile(sender, instance, **kwargs):
+ print(instance.mrc_file.path, kwargs)
diff --git a/ippisite/ippidb/serializer.py b/ippisite/ippidb/serializer.py
index aca1fa6b..1df73491 100644
--- a/ippisite/ippidb/serializer.py
+++ b/ippisite/ippidb/serializer.py
@@ -114,7 +114,7 @@ class CavityDistanceSerializer(serializers.ModelSerializer):
class Meta:
model = Cavity
- exclude = ("mol2",)
+ exclude = ('mol2',)
class DistanceSerializer(serializers.ModelSerializer):
@@ -130,17 +130,19 @@ class CavitySerializer(serializers.ModelSerializer):
class Meta:
model = Cavity
fields = "__all__"
+ write_only_fields = ("mol2",)
+ read_only_fields = ("t120",)
-class PartnerSerializer(serializers.ModelSerializer):
+class InteractFileSerializer(serializers.ModelSerializer):
class Meta:
- model = Partner
+ model = InteractFile
fields = "__all__"
-class InteractFileSerializer(serializers.ModelSerializer):
+class PartnerSerializer(serializers.ModelSerializer):
class Meta:
- model = InteractFile
+ model = Partner
fields = "__all__"
@@ -169,9 +171,11 @@ class ChainSerializer(serializers.ModelSerializer):
class LigandSerializer(serializers.ModelSerializer):
partner_set = PartnerSerializer(many=True, read_only=True)
+
class Meta:
model = Ligand
fields = "__all__"
+ read_only_fields = ['canonical_smile', 'iupac_name']
class PdbSerializer(serializers.ModelSerializer):
diff --git a/ippisite/ippidb/views/__init__.py b/ippisite/ippidb/views/__init__.py
index 81683b9a..a83fe149 100644
--- a/ippisite/ippidb/views/__init__.py
+++ b/ippisite/ippidb/views/__init__.py
@@ -23,7 +23,8 @@ from .targetcentric import (
PartnerViewSet,
InteractFileViewSet,
CavityViewSet,
- BuildDistancesViewSet)
+ BuildDistancesViewSet,
+ pocketome_html,)
from .contribute import ippidb_wizard_view, ContributionDetailView
from .compound_query import (
CompoundListView,
@@ -134,4 +135,5 @@ __all__ = [
get_json_network,
IppiDbCompoundSitemap,
IppiDbContributorsSitemap,
+ pocketome_html,
]
diff --git a/ippisite/ippidb/views/targetcentric.py b/ippisite/ippidb/views/targetcentric.py
index 065daced..f305a06d 100644
--- a/ippisite/ippidb/views/targetcentric.py
+++ b/ippisite/ippidb/views/targetcentric.py
@@ -36,6 +36,13 @@ from rest_framework.permissions import IsAdminUser, SAFE_METHODS
from rest_framework.authtoken.models import Token
from ippidb.tasks import launch_build_matrix_distance
from rest_framework.response import Response
+from django.views.decorators.clickjacking import xframe_options_exempt
+
+from django.shortcuts import render
+
+@xframe_options_exempt
+def pocketome_html(request):
+ return render(request, 'PocketBook_MST_Euclidean_log_trim_scratch_sec61.html')
class IsAdminUserOrReadOnly(IsAdminUser):
@@ -54,13 +61,12 @@ class PdbViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
+ queryset = PDB.objects.all().values("code", "id")
code = self.request.GET.get("code")
if "pk" in self.kwargs:
queryset = PDB.objects.filter(pk=self.kwargs["pk"])
elif code:
queryset = PDB.objects.filter(code=code)
- else:
- queryset = PDB.objects.all().values("code", "id")
return queryset
@@ -70,11 +76,10 @@ class ProteinViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
+ queryset = Protein.objects.all()
uniprot_id = self.request.GET.get("uniprot_id")
if uniprot_id:
- queryset = Protein.objects.filter(uniprot_id=uniprot_id)
- else:
- queryset = Protein.objects.all()
+ queryset = queryset.filter(uniprot_id=uniprot_id)
return queryset
@@ -84,15 +89,14 @@ class ChainViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
+ queryset = Chain.objects.all()
pdb = self.request.GET.get("pdb_id")
pdb_chain_id = self.request.GET.get("pdb_chain_id")
if pdb:
if pdb_chain_id:
- queryset = Chain.objects.filter(pdb=pdb, pdb_chain_id=pdb_chain_id)
+ queryset = queryset.filter(pdb=pdb, pdb_chain_id=pdb_chain_id)
else:
- queryset = Chain.objects.filter(pdb=pdb)
- else:
- queryset = Chain.objects.all()
+ queryset = queryset.filter(pdb=pdb)
return queryset
@@ -108,13 +112,11 @@ class LigandViewSet(viewsets.ModelViewSet):
supplementary_id = self.request.GET.get("supplementary_id")
if pdb:
if pdb_ligand_id and supplementary_id:
- queryset = Ligand.objects.filter(pdb=pdb,
+ queryset = queryset.filter(pdb=pdb,
pdb_ligand_id=pdb_ligand_id,
supplementary_id=supplementary_id)
else:
- queryset = Ligand.objects.filter(pdb=pdb)
- else:
- queryset = Ligand.objects.all()
+ queryset = queryset.filter(pdb=pdb)
return queryset
@@ -125,6 +127,12 @@ class PartnerViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
queryset = Partner.objects.all()
+ chain = self.request.GET.get("chain")
+ ligand = self.request.GET.get("ligand")
+ if chain:
+ queryset = queryset.filter(chain=chain)
+ if ligand:
+ queryset = queryset.filter(ligand=ligand)
return queryset
@@ -135,6 +143,13 @@ class InteractFileViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
queryset = InteractFile.objects.all()
+ chain = self.request.GET.get("chain")
+ label = self.request.GET.get("label")
+ if chain:
+ if label:
+ queryset = queryset.filter(chain=chain, label=label)
+ else:
+ queryset = queryset.filter(chain=chain)
return queryset
@@ -145,6 +160,9 @@ class CavityViewSet(viewsets.ModelViewSet):
@action(detail=True, methods=["get", "post"])
def get_queryset(self):
queryset = Cavity.objects.all()
+ full_name = self.request.GET.get("full_name")
+ if full_name:
+ queryset = queryset.filter(full_name=full_name)
return queryset
diff --git a/ippisite/ippisite/authentication.py b/ippisite/ippisite/authentication.py
new file mode 100644
index 00000000..e49585d8
--- /dev/null
+++ b/ippisite/ippisite/authentication.py
@@ -0,0 +1,45 @@
+from rest_framework.authtoken.models import Token
+from rest_framework.authentication import TokenAuthentication
+from rest_framework.exceptions import AuthenticationFailed
+from datetime import timedelta
+from django.utils import timezone
+from django.conf import settings
+
+
+
+#this return left time
+def expires_in(token):
+ time_elapsed = timezone.now() - token.created
+ left_time = timedelta(seconds = settings.TOKEN_EXPIRED_AFTER_SECONDS) - time_elapsed
+ return left_time
+
+# token checker if token expired or not
+def is_token_expired(token):
+ return expires_in(token) < timedelta(seconds = 0)
+
+def token_expire_handler(token):
+ is_expired = is_token_expired(token)
+ if is_expired:
+ token.delete()
+ token = None
+ return is_expired, token
+
+class ExpiringTokenAuthentication(TokenAuthentication):
+ """
+ If token is expired then it will be removed
+ and new one with different key will be created
+ """
+ def authenticate_credentials(self, key):
+ try:
+ token = Token.objects.get(key = key)
+ except Token.DoesNotExist:
+ raise AuthenticationFailed("Invalid Token")
+
+ if not token.user.is_active:
+ raise AuthenticationFailed("User is not active")
+
+ is_expired, token = token_expire_handler(token)
+ if is_expired:
+ raise AuthenticationFailed("The Token is expired, return on the admin interface to generate a new token")
+
+ return (token.user, token)
\ No newline at end of file
--
GitLab