diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000000000000000000000000000000000000..4ac0bda5ff3d4a248ed3af1303d093938fdc49e7
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,7 @@
+{
+ "python.pythonPath": "venv/bin/python",
+ "git.ignoreLimitWarning": true,
+ "python.linting.flake8Enabled": true,
+ "python.linting.pylintEnabled": false,
+ "python.linting.flake8Args": ["--max-line-length=88"]
+}
\ No newline at end of file
diff --git a/ippisite/.flake8 b/ippisite/.flake8
new file mode 100644
index 0000000000000000000000000000000000000000..dbff3b4c38c6e454b894283a282b68e5ab220c09
--- /dev/null
+++ b/ippisite/.flake8
@@ -0,0 +1,3 @@
+[flake8]
+exclude = .git,*migrations*
+max-line-length = 88
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index b167850e99938ccd10e0395cb5f5109d31003a24..499347e97ab477a2daead49ef21a0b257aaefafe 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -18,16 +18,16 @@ from django.urls import reverse
from django.utils.translation import ugettext_lazy as _
from .utils import FingerPrinter, smi2inchi, smi2inchikey
-from .ws import get_pubmed_info, get_google_patent_info, get_uniprot_info, get_taxonomy_info, get_go_info, \
- get_pfam_info, get_doi_info
+from .ws import get_pubmed_info, get_google_patent_info, get_uniprot_info, \
+ get_taxonomy_info, get_go_info, get_pfam_info, get_doi_info
class AutoFillableModel(models.Model):
"""
AutoFillableModel makes it possible to automatically fill model fields from
external sources in the autofill() method
- The save method allows to either include autofill or not. in autofill kwarg is
- set to True, save() will first call autofill(), otherwise it won't
+ The save method allows to either include autofill or not. in autofill kwarg
+ is set to True, save() will first call autofill(), otherwise it won't
"""
class Meta:
@@ -49,7 +49,8 @@ class AutoFillableModel(models.Model):
def autofill_post_save(self):
"""
- method called after the save is done, usefull for settings m2m relations
+ method called after the save is done, usefull for setting m2m
+ relations
:return:
"""
pass
@@ -74,7 +75,8 @@ class Bibliography(AutoFillableModel):
DO=re.compile("^10.\d{4,9}/.+$"),
)
source = models.CharField(
- 'Bibliographic type', max_length=2, choices=SOURCES, default=SOURCES[0][0])
+ 'Bibliographic type', max_length=2, choices=SOURCES,
+ default=SOURCES[0][0])
id_source = models.CharField('Bibliographic ID', max_length=25)
title = models.TextField('Title')
journal_name = models.TextField('Journal name', null=True, blank=True)
@@ -129,7 +131,9 @@ class Bibliography(AutoFillableModel):
if not id_source_validator.match(id_source):
raise ValidationError(
dict(
- id_source=_("Must match pattern %s for this selected source" % id_source_validator.pattern)
+ id_source=_(
+ f"Must match pattern {id_source_validator.pattern}"
+ " for this selected source")
)
)
return True
@@ -259,7 +263,8 @@ class Protein(AutoFillableModel):
def autofill_post_save(self):
info = self.__info
for go_id in info['molecular_functions']:
- mol_function, created = MolecularFunction.objects.get_or_create(go_id=go_id)
+ mol_function, created = MolecularFunction.objects.get_or_create(
+ go_id=go_id)
self.molecular_functions.add(mol_function)
for domain_id in info['domains']:
@@ -280,7 +285,8 @@ class Domain(AutoFillableModel):
pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
pfam_description = models.CharField('Pfam Description', max_length=100)
- domain_family = models.CharField('Domain family', max_length=25, blank=True, default="")
+ domain_family = models.CharField('Domain family', max_length=25,
+ blank=True, default="")
# TODO: what is this field? check database
# contents
@@ -302,7 +308,7 @@ class Domain(AutoFillableModel):
return self.pfam_id
def __str__(self):
- return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
+ return f'{self.pfam_acc} ({self.pfam_id}-{self.pfam_description})'
class ProteinDomainComplex(models.Model):
@@ -390,7 +396,8 @@ class Ppi(AutoFillableModel):
'Total number of pockets in the complex', default=1)
symmetry = models.ForeignKey(Symmetry, models.CASCADE)
diseases = models.ManyToManyField(Disease, blank=True)
- family = models.ForeignKey(PpiFamily, models.CASCADE, null=True, blank=True)
+ family = models.ForeignKey(PpiFamily, models.CASCADE, null=True,
+ blank=True)
name = models.TextField('PPI name', null=True, blank=True)
def __str__(self):
@@ -410,13 +417,20 @@ class Ppi(AutoFillableModel):
"""
return bound ppi complexes belonging to this ppi
"""
- return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
+ return PpiComplex.objects.filter(
+ ppi=self,
+ complex__in=ProteinDomainBoundComplex.objects.all()
+ )
def compute_name_from_protein_names(self):
all_protein_names = set(
- [ppi_complex.complex.protein.short_name for ppi_complex in self.ppicomplex_set.all()])
+ [
+ ppi_complex.complex.protein.short_name
+ for ppi_complex in self.ppicomplex_set.all()])
bound_protein_names = set(
- [ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_bound_complexes()])
+ [
+ ppi_complex.complex.protein.short_name
+ for ppi_complex in self.get_ppi_bound_complexes()])
partner_protein_names = all_protein_names - bound_protein_names
bound_str = ','.join(bound_protein_names)
partner_str = ','.join(partner_protein_names)
@@ -854,7 +868,6 @@ class Compound(AutoFillableModel):
insilico_av = models.BooleanField('In silico tests performed', null=True, blank=True)
tests_av = models.IntegerField(verbose_name='Number of tests available', null=True, blank=True)
-
class Meta:
ordering = ['id']
indexes = [
diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index ea26a69d260f2bf50664f5eb1efe1a5ad42ad574..7c5112b423ccd607d12de2e6a7af5388c3f5cadf 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -3,12 +3,10 @@ iPPI-DB unit tests
"""
import re
-from tempfile import NamedTemporaryFile
from django.core.management import call_command
from django.test import TestCase
from django.urls import reverse
-from django.contrib.auth import get_user_model
from openbabel import vectorUnsignedInt, OBFingerprint
from ippidb import ws, models
@@ -17,8 +15,7 @@ from .models import (
Compound,
CompoundTanimoto,
create_tanimoto,
- update_compound_cached_properties,
- Symmetry,
+ update_compound_cached_properties
)
from .models import DrugBankCompound
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey
@@ -337,8 +334,8 @@ class CompoundAnnotationsTestCase(TestCase):
class QueryCompoundViewsTestCase(TestCase):
@classmethod
def setUpTestData(cls):
- c = create_dummy_compound(1, "CC")
- c = create_dummy_compound(2, "CCC")
+ create_dummy_compound(1, "CC")
+ create_dummy_compound(2, "CCC")
call_command("lle_le")
call_command("pca")
diff --git a/ippisite/ippidb/tests_contribute.py b/ippisite/ippidb/tests_contribute.py
index cab5e273c6fb3cfcc2750e6f03ca61fbcccecac8..047ccfea4768b06b0c3ad6396dbcb184b489663a 100644
--- a/ippisite/ippidb/tests_contribute.py
+++ b/ippisite/ippidb/tests_contribute.py
@@ -2,7 +2,6 @@
iPPI-DB contribution module tests
"""
-import re
from tempfile import NamedTemporaryFile
from django.test import TestCase
@@ -10,7 +9,6 @@ from django.urls import reverse
from django.contrib.auth import get_user_model
from ippidb import models
-from ippidb import forms
class ContributionViewsTestCase(TestCase):
diff --git a/ippisite/ippidb/utils.py b/ippisite/ippidb/utils.py
index 41bf2a723a1d510ca42c1fefbc1b5595b8f570fa..d22aa6c5e7c676b1abe26962affdf15aa8925053 100644
--- a/ippisite/ippidb/utils.py
+++ b/ippisite/ippidb/utils.py
@@ -2,35 +2,43 @@
iPPI-DB chemoinformatics utility functions
"""
-#FIXME: to work, this currently needs awkward PYTHONPATH tweaks, like:
-#$export PYTHONPATH=/home/hmenager/openbabellocal/lib/python3.6/site-packages/:$PYTHONPATH
+# FIXME: to work, this currently needs awkward PYTHONPATH tweaks, like:
+# $export PYTHONPATH=/home/hmenager/openbabellocal/lib/python3.6/
+# site-packages/:$PYTHONPATH
import pybel
import openbabel as ob
+
def mol2smi(mol_string):
- m = pybel.readstring('mol', mol_string)
- return m.write(format='smi').strip()
+ m = pybel.readstring("mol", mol_string)
+ return m.write(format="smi").strip()
+
def smi2mol(smi_string):
- m = pybel.readstring('smi', smi_string)
+ m = pybel.readstring("smi", smi_string)
# generate 2D coordinates for MarvinJS layout
- #NB: the line below should be replaced as soon as the new version of openbabel
+ # NB: the line below should be replaced as soon as the new version of openbabel
# is out (>2.4.1), by a call to m.make2D()
- # (see https://github.com/openbabel/openbabel/blob/06e233e2ca0c6d9f86f74bafe74ffcb75e9d76cd/scripts/python/pybel.py#L577)
- pybel._operations['gen2D'].Do(m.OBMol)
- return m.write(format='mol')
+ # (see https://github.com/openbabel/openbabel/blob/
+ # 06e233e2ca0c6d9f86f74bafe74ffcb75e9d76cd/scripts/python/pybel.py#L577)
+ pybel._operations["gen2D"].Do(m.OBMol)
+ return m.write(format="mol")
+
smi2inchi_conv = ob.OBConversion()
smi2inchi_conv.SetInAndOutFormats("smi", "inchi")
+
def smi2inchi(smi_string):
mol = ob.OBMol()
smi2inchi_conv.ReadString(mol, smi_string)
return smi2inchi_conv.WriteString(mol).strip()
+
smi2inchikey_conv = ob.OBConversion()
smi2inchikey_conv.SetInAndOutFormats("smi", "inchi")
-smi2inchikey_conv.SetOptions("K",smi2inchikey_conv.OUTOPTIONS)
+smi2inchikey_conv.SetOptions("K", smi2inchikey_conv.OUTOPTIONS)
+
def smi2inchikey(smi_string):
mol = ob.OBMol()
@@ -39,7 +47,6 @@ def smi2inchikey(smi_string):
class FingerPrinter(object):
-
def __init__(self, name="FP4"):
self.fingerprinter = ob.OBFingerprint.FindFingerprint(name)
self._smiles_parser = ob.OBConversion()
@@ -58,15 +65,30 @@ class FingerPrinter(object):
return fp
def fp_dict(self, smiles_dict):
- "generate a dict of {compound id: fingerprint} from a dict of {compound id: fingerprint}"
- return {compound_id: self.fp(smiles_entry) for compound_id, smiles_entry in smiles_dict.items()}
+ """
+ generate a dict of {compound id: fingerprint} from a dict of
+ {compound id: fingerprint}
+ """
+ return {
+ compound_id: self.fp(smiles_entry)
+ for compound_id, smiles_entry in smiles_dict.items()
+ }
def tanimoto_fps(self, smiles_query, fp_dict):
- "perform a tanimoto similarity search using a smiles query string on a dict of {compound id: fingerprint}"
+ """
+ perform a tanimoto similarity search using a smiles query string
+ on a dict of {compound id: fingerprint}
+ """
fp_query = self.fp(smiles_query)
- return {compound_id: self.fingerprinter.Tanimoto(fp_query, fp_entry) for compound_id, fp_entry in fp_dict.items()}
+ return {
+ compound_id: self.fingerprinter.Tanimoto(fp_query, fp_entry)
+ for compound_id, fp_entry in fp_dict.items()
+ }
def tanimoto_smiles(self, query_smiles, smiles_dict):
- "perform a tanimoto similarity search using a smiles query on a dict of {compound id: SMILES}"
+ """
+ perform a tanimoto similarity search using a smiles query on a
+ dict of {compound id: SMILES}
+ """
fp_dict = self.fp_dict(smiles_dict)
return self.tanimoto_fps(query_smiles, fp_dict)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 0095060c4a16714cad89ef60ffad82d59d5db528..ccd86c1a82359ffc96b1b11cec1b8fe61588d1f8 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -12,13 +12,12 @@ from bs4 import BeautifulSoup
class EntryNotFoundError(Exception):
-
def __init__(self, entry_id, status_code=None):
self.entry_id = entry_id
if status_code:
- msg = '%s not found.' % entry_id
+ msg = "%s not found." % entry_id
else:
- msg = '%s not found (error_code %i).' % (entry_id, status_code)
+ msg = "%s not found (error_code %i)." % (entry_id, status_code)
super().__init__(msg)
@@ -48,34 +47,37 @@ def get_pubmed_info(pmid):
:rtype: dict
"""
eu = EUtils()
- r = eu.EFetch('pubmed', pmid, retmode='dict', rettype='abstract')
+ r = eu.EFetch("pubmed", pmid, retmode="dict", rettype="abstract")
if isinstance(r, int):
raise PubMedEntryNotFound(pmid, r)
- if r['PubmedArticleSet'] is None:
+ if r["PubmedArticleSet"] is None:
raise PubMedEntryNotFound(pmid)
- article = r['PubmedArticleSet'][
- 'PubmedArticle']['MedlineCitation']['Article']
- title = article['ArticleTitle']
- authors_list = [a['LastName'] + ' ' + a['Initials']
- for a in article['AuthorList']['Author']]
- authors = ', '.join(authors_list)
- journal_name = article['Journal']['Title']
- biblio_date = article['Journal']['JournalIssue']['PubDate']
- if 'Year' in biblio_date:
- biblio_year = biblio_date['Year']
+ article = r["PubmedArticleSet"]["PubmedArticle"]["MedlineCitation"]["Article"]
+ title = article["ArticleTitle"]
+ authors_list = [
+ a["LastName"] + " " + a["Initials"] for a in article["AuthorList"]["Author"]
+ ]
+ authors = ", ".join(authors_list)
+ journal_name = article["Journal"]["Title"]
+ biblio_date = article["Journal"]["JournalIssue"]["PubDate"]
+ if "Year" in biblio_date:
+ biblio_year = biblio_date["Year"]
else:
- biblio_year = biblio_date['MedlineDate'][0:3]
- return {'title': title,
- 'journal_name': journal_name,
- 'biblio_year': biblio_year,
- 'authors_list': authors}
+ biblio_year = biblio_date["MedlineDate"][0:3]
+ return {
+ "title": title,
+ "journal_name": journal_name,
+ "biblio_year": biblio_year,
+ "authors_list": authors,
+ }
def get_epo_info(patent_number):
"""
Retrieve information about a patent using the EPO website
- WARNING: this is not to be used anymore, the 3.1 version of the EPO service is now offline
+ WARNING: this is not to be used anymore, the 3.1 version of the EPO service is now
+ offline
:param patent_number: patent number
:type patent_number: str
@@ -83,24 +85,38 @@ def get_epo_info(patent_number):
:rtype: dict
"""
resp = requests.get(
- 'http://ops.epo.org/3.1/rest-services/published-data/publication/docdb/{}/biblio.json'.format(patent_number))
+ f"http://ops.epo.org/3.1/rest-services/published-data/publication/docdb/"
+ f"{patent_number}/biblio.json"
+ )
data = resp.json()
- exchange_doc = data['ops:world-patent-data'][
- 'exchange-documents']['exchange-document']
+ exchange_doc = data["ops:world-patent-data"]["exchange-documents"][
+ "exchange-document"
+ ]
if isinstance(exchange_doc, list):
exchange_doc = exchange_doc[0]
- title = [el['$']
- for el in exchange_doc['bibliographic-data']['invention-title'] if el['@lang'] == 'en'][0]
- authors = [i['inventor-name']['name']['$']
- for i in exchange_doc['bibliographic-data']['parties']['inventors']['inventor'] if
- i['@data-format'] == 'original'][0]
- biblio_year = [el['date']['$'][:4]
- for el in exchange_doc['bibliographic-data']['publication-reference']['document-id'] if
- el['@document-id-type'] == 'epodoc'][0]
- return {'title': title,
- 'journal_name': None,
- 'biblio_year': biblio_year,
- 'authors_list': authors}
+ title = [
+ el["$"]
+ for el in exchange_doc["bibliographic-data"]["invention-title"]
+ if el["@lang"] == "en"
+ ][0]
+ authors = [
+ i["inventor-name"]["name"]["$"]
+ for i in exchange_doc["bibliographic-data"]["parties"]["inventors"]["inventor"]
+ if i["@data-format"] == "original"
+ ][0]
+ biblio_year = [
+ el["date"]["$"][:4]
+ for el in exchange_doc["bibliographic-data"]["publication-reference"][
+ "document-id"
+ ]
+ if el["@document-id-type"] == "epodoc"
+ ][0]
+ return {
+ "title": title,
+ "journal_name": None,
+ "biblio_year": biblio_year,
+ "authors_list": authors,
+ }
def get_google_patent_info_ris(patent_number):
@@ -114,7 +130,7 @@ def get_google_patent_info_ris(patent_number):
:return: patent metadata (title, journal name, publication year, authors list).
:rtype: dict
"""
- url = 'https://encrypted.google.com/patents/{}.ris'.format(patent_number)
+ url = "https://encrypted.google.com/patents/{}.ris".format(patent_number)
resp = requests.get(url)
title = None
authors = []
@@ -127,10 +143,12 @@ def get_google_patent_info_ris(patent_number):
title = line[1]
elif line[0] == "Y1":
biblio_year = line[1].split("/")[0]
- return {'title': title,
- 'journal_name': None,
- 'biblio_year': biblio_year,
- 'authors_list': authors}
+ return {
+ "title": title,
+ "journal_name": None,
+ "biblio_year": biblio_year,
+ "authors_list": authors,
+ }
def get_google_patent_info(patent_number):
@@ -142,22 +160,25 @@ def get_google_patent_info(patent_number):
:return: patent metadata (title, journal name, publication year, authors list).
:rtype: dict
"""
- url = 'https://patents.google.com/patent/{}'.format(patent_number)
+ url = "https://patents.google.com/patent/{}".format(patent_number)
resp = requests.get(url)
if resp.status_code != 200:
raise PatentNotFound(patent_number, resp.status_code)
- soup = BeautifulSoup(resp.text, 'html.parser')
- title = soup.find_all('meta', attrs={'name': 'DC.title'})[0]['content'].strip()
+ soup = BeautifulSoup(resp.text, "html.parser")
+ title = soup.find_all("meta", attrs={"name": "DC.title"})[0]["content"].strip()
authors_list = []
- for author_meta in soup.find_all('meta', attrs={'name': 'DC.contributor'}):
- authors_list.append(author_meta['content'].strip())
- authors = ', '.join(authors_list)
- biblio_year = soup.find_all('meta', attrs={'name': 'DC.date'})[0]['content'].strip()[0:4]
- return {'title': title,
- 'journal_name': None,
- 'biblio_year': biblio_year,
- 'authors_list': authors}
-
+ for author_meta in soup.find_all("meta", attrs={"name": "DC.contributor"}):
+ authors_list.append(author_meta["content"].strip())
+ authors = ", ".join(authors_list)
+ biblio_year = soup.find_all("meta", attrs={"name": "DC.date"})[0][
+ "content"
+ ].strip()[0:4]
+ return {
+ "title": title,
+ "journal_name": None,
+ "biblio_year": biblio_year,
+ "authors_list": authors,
+ }
def get_doi_info(doi):
@@ -169,41 +190,55 @@ def get_doi_info(doi):
:return: publication metadata (title, journal name, publication year, authors list).
:rtype: dict
"""
- resp = requests.get('http://dx.doi.org/%s' % doi, headers={'Accept':'application/vnd.citationstyles.csl+json'})
+ resp = requests.get(
+ "http://dx.doi.org/%s" % doi,
+ headers={"Accept": "application/vnd.citationstyles.csl+json"},
+ )
resp.raise_for_status()
json_data = resp.json()
- title = json_data['title']
- journal_name = json_data.get("container-title", json_data.get("original-title", None))
- biblio_year=0
+ title = json_data["title"]
+ journal_name = json_data.get(
+ "container-title", json_data.get("original-title", None)
+ )
+ biblio_year = 0
try:
- if 'journal-issue' in json_data and 'published-print' in json_data['journal-issue']:
- biblio_year = json_data['journal-issue']['published-print']['date-parts'][0][0]
- elif 'published-print' in json_data:
- biblio_year = json_data['published-print']['date-parts'][0][0]
- elif 'issued' in json_data:
- biblio_year = json_data['issued']['date-parts'][0][0]
+ if (
+ "journal-issue" in json_data
+ and "published-print" in json_data["journal-issue"]
+ ):
+ biblio_year = json_data["journal-issue"]["published-print"]["date-parts"][
+ 0
+ ][0]
+ elif "published-print" in json_data:
+ biblio_year = json_data["published-print"]["date-parts"][0][0]
+ elif "issued" in json_data:
+ biblio_year = json_data["issued"]["date-parts"][0][0]
else:
- biblio_year = json_data['published-online']['date-parts'][0][0]
+ biblio_year = json_data["published-online"]["date-parts"][0][0]
except KeyError as e:
- print('http://dx.doi.org/%s' % doi)
+ print("http://dx.doi.org/%s" % doi)
print(json_data)
raise e
authors_list = []
- for author_data in json_data['author']:
+ for author_data in json_data["author"]:
try:
- if 'family' in author_data:
- authors_list.append('%s %s' % (author_data["family"], author_data.get("given", "")))
+ if "family" in author_data:
+ authors_list.append(
+ "%s %s" % (author_data["family"], author_data.get("given", ""))
+ )
else:
- authors_list.append(author_data['name'])
+ authors_list.append(author_data["name"])
except KeyError as e:
- print('http://dx.doi.org/%s' % doi)
+ print("http://dx.doi.org/%s" % doi)
print(json_data)
raise e
- authors = ', '.join(authors_list)
- return {'title': title,
- 'journal_name': journal_name,
- 'biblio_year': biblio_year,
- 'authors_list': authors}
+ authors = ", ".join(authors_list)
+ return {
+ "title": title,
+ "journal_name": journal_name,
+ "biblio_year": biblio_year,
+ "authors_list": authors,
+ }
def get_uniprot_info(uniprot_id):
@@ -212,66 +247,76 @@ def get_uniprot_info(uniprot_id):
:param uniprot_id: Uniprot ID
:type uniprot_id: str
- :return: protein metadata (recommended name, organism, gene, entry name, short name, molecular functions).
+ :return: protein metadata (recommended name, organism, gene, entry name,
+ short name, molecular functions).
:rtype: dict
"""
uniprot_client = UniProt()
- ns = {'u': 'http://uniprot.org/uniprot'}
+ ns = {"u": "http://uniprot.org/uniprot"}
try:
resp = uniprot_client.retrieve(uniprot_id)
except TypeError:
raise EntryNotFoundError(uniprot_id)
- if resp.root == '':
+ if resp.root == "":
raise EntryNotFoundError(uniprot_id)
try:
recommended_name = resp.root.findall(
- 'u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
+ "u:entry/u:protein/u:recommendedName/u:fullName", ns
+ )[0].text
except:
recommended_name = None
try:
recommended_short_name = resp.root.findall(
- 'u:entry/u:protein/u:recommendedName/u:shortName', ns)[0].text
+ "u:entry/u:protein/u:recommendedName/u:shortName", ns
+ )[0].text
except:
recommended_short_name = None
organism = resp.root.findall(
- 'u:entry/u:organism/u:dbReference[@type="NCBI Taxonomy"]', ns)[0].attrib['id']
+ 'u:entry/u:organism/u:dbReference[@type="NCBI Taxonomy"]', ns
+ )[0].attrib["id"]
gene_names = []
- for el in resp.root.findall('u:entry/u:gene/u:name', ns):
- gene_name = {'name': el.text, 'type': el.attrib['type']}
+ for el in resp.root.findall("u:entry/u:gene/u:name", ns):
+ gene_name = {"name": el.text, "type": el.attrib["type"]}
gene_names.append(gene_name)
try:
- gene_id = resp.root.findall(
- 'u:entry/u:dbReference[@type="GeneID"]', ns)[0].attrib['id']
+ gene_id = resp.root.findall('u:entry/u:dbReference[@type="GeneID"]', ns)[
+ 0
+ ].attrib["id"]
except IndexError:
gene_id = None
- entry_name = resp.root.findall('u:entry/u:name', ns)[0].text
+ entry_name = resp.root.findall("u:entry/u:name", ns)[0].text
go_els = resp.root.findall('u:entry/u:dbReference[@type="GO"]', ns)
- accessions = [el.text for el in resp.root.findall('u:entry/u:accession', ns)]
+ accessions = [el.text for el in resp.root.findall("u:entry/u:accession", ns)]
molecular_functions = []
cellular_localisations = []
biological_processes = []
for go_el in go_els:
- term_property_value = go_el.findall(
- 'u:property[@type="term"]', ns)[0].attrib['value']
- if term_property_value[0:2] == 'F:':
- molecular_functions.append('GO_' + go_el.attrib['id'][3:])
- if term_property_value[0:2] == 'C:':
- cellular_localisations.append('GO_' + go_el.attrib['id'][3:])
- if term_property_value[0:2] == 'P:':
- biological_processes.append('GO_' + go_el.attrib['id'][3:])
+ term_property_value = go_el.findall('u:property[@type="term"]', ns)[0].attrib[
+ "value"
+ ]
+ if term_property_value[0:2] == "F:":
+ molecular_functions.append("GO_" + go_el.attrib["id"][3:])
+ if term_property_value[0:2] == "C:":
+ cellular_localisations.append("GO_" + go_el.attrib["id"][3:])
+ if term_property_value[0:2] == "P:":
+ biological_processes.append("GO_" + go_el.attrib["id"][3:])
citations = []
- for el in resp.root.findall('u:entry/u:reference', ns):
+ for el in resp.root.findall("u:entry/u:reference", ns):
try:
- doi = el.findall('u:citation/u:dbReference[@type="DOI"]', ns)[0].attrib['id']
- pmid = el.findall('u:citation/u:dbReference[@type="PubMed"]', ns)[0].attrib['id']
- citations.append({'doi': doi, 'pmid': pmid})
+ doi = el.findall('u:citation/u:dbReference[@type="DOI"]', ns)[0].attrib[
+ "id"
+ ]
+ pmid = el.findall('u:citation/u:dbReference[@type="PubMed"]', ns)[0].attrib[
+ "id"
+ ]
+ citations.append({"doi": doi, "pmid": pmid})
except IndexError:
continue
alternative_names = []
- for el in resp.root.findall('u:entry/u:protein/u:alternativeName', ns):
- alternative_name = {'full': el.findall('u:fullName', ns)[0].text}
- if el.findall('u:shortName', ns):
- alternative_name['short'] = el.findall('u:shortName', ns)[0].text
+ for el in resp.root.findall("u:entry/u:protein/u:alternativeName", ns):
+ alternative_name = {"full": el.findall("u:fullName", ns)[0].text}
+ if el.findall("u:shortName", ns):
+ alternative_name["short"] = el.findall("u:shortName", ns)[0].text
alternative_names.append(alternative_name)
db_references = resp.root.findall('u:entry/u:dbReference[@type="Pfam"]', ns)
@@ -280,21 +325,22 @@ def get_uniprot_info(uniprot_id):
name = db_reference.attrib["id"]
domains.append(name)
- return {'recommended_name': recommended_name,
- 'recommended_short_name': recommended_short_name,
- 'organism': int(organism),
- 'gene_id': int(gene_id) if gene_id else None,
- 'accessions': accessions,
- 'gene_names': gene_names,
- 'entry_name': entry_name,
- 'short_name': entry_name.split('_')[0],
- 'molecular_functions': molecular_functions,
- 'domains': domains,
- 'cellular_localisations': cellular_localisations,
- 'biological_processes': biological_processes,
- 'citations': citations,
- 'alternative_names': alternative_names
- }
+ return {
+ "recommended_name": recommended_name,
+ "recommended_short_name": recommended_short_name,
+ "organism": int(organism),
+ "gene_id": int(gene_id) if gene_id else None,
+ "accessions": accessions,
+ "gene_names": gene_names,
+ "entry_name": entry_name,
+ "short_name": entry_name.split("_")[0],
+ "molecular_functions": molecular_functions,
+ "domains": domains,
+ "cellular_localisations": cellular_localisations,
+ "biological_processes": biological_processes,
+ "citations": citations,
+ "alternative_names": alternative_names,
+ }
def get_go_info(go_id):
@@ -307,11 +353,12 @@ def get_go_info(go_id):
:rtype: dict
"""
resp = requests.get(
- 'https://www.ebi.ac.uk/ols/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F{}'.format(
- go_id))
+ f"https://www.ebi.ac.uk/ols/api/ontologies/go/terms/"
+ f"http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F{go_id}"
+ )
data = resp.json()
- label = data['label']
- return {'label': label}
+ label = data["label"]
+ return {"label": label}
def get_taxonomy_info(taxonomy_id):
@@ -324,9 +371,9 @@ def get_taxonomy_info(taxonomy_id):
:rtype: dict
"""
eu = EUtils()
- r = eu.EFetch('taxonomy', taxonomy_id, retmode='dict')
- scientific_name = r['TaxaSet']['Taxon']['ScientificName']
- return {'scientific_name': scientific_name}
+ r = eu.EFetch("taxonomy", taxonomy_id, retmode="dict")
+ scientific_name = r["TaxaSet"]["Taxon"]["ScientificName"]
+ return {"scientific_name": scientific_name}
def get_pfam_info(pfam_acc):
@@ -338,15 +385,13 @@ def get_pfam_info(pfam_acc):
:return: Protein family metadata (id, description).
:rtype: dict
"""
- resp = requests.get(
- 'https://pfam.xfam.org/family/{}?output=xml'.format(pfam_acc))
+ resp = requests.get("https://pfam.xfam.org/family/{}?output=xml".format(pfam_acc))
root = ET.fromstring(resp.text)
- ns = {'pfam': 'https://pfam.xfam.org/'}
- entry = root.findall('pfam:entry', ns)[0]
- pfam_id = entry.attrib['id']
- description = entry.findall('pfam:description', ns)[0].text.strip()
- return {'id': pfam_id,
- 'description': description}
+ ns = {"pfam": "https://pfam.xfam.org/"}
+ entry = root.findall("pfam:entry", ns)[0]
+ pfam_id = entry.attrib["id"]
+ description = entry.findall("pfam:description", ns)[0].text.strip()
+ return {"id": pfam_id, "description": description}
def get_pdb_uniprot_mapping(pdb_id):
@@ -360,10 +405,11 @@ def get_pdb_uniprot_mapping(pdb_id):
"""
pdb_id = pdb_id.lower()
resp = requests.get(
- 'https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}'.format(pdb_id.lower()))
+ "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}".format(pdb_id.lower())
+ )
if resp.status_code != 200:
raise EntryNotFoundError(pdb_id, resp.status_code)
- uniprot_ids = list(resp.json()[pdb_id]['UniProt'].keys())
+ uniprot_ids = list(resp.json()[pdb_id]["UniProt"].keys())
return uniprot_ids
@@ -378,7 +424,8 @@ def pdb_entry_exists(pdb_id):
"""
""" """
resp = requests.get(
- 'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{}'.format(pdb_id.lower()))
+ "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{}".format(pdb_id.lower())
+ )
# EBI sends back either a 404 or an empty json if the PDB does not exist
if not (resp.ok):
return False
@@ -394,7 +441,8 @@ def convert_iupac_to_smiles_and_inchi(iupac):
if iupac is None:
raise EntryNotFoundError(iupac, 422)
resp = requests.get(
- 'https://opsin.ch.cam.ac.uk/opsin/{}'.format(urllib_parse.quote(iupac, safe='')))
+ "https://opsin.ch.cam.ac.uk/opsin/{}".format(urllib_parse.quote(iupac, safe=""))
+ )
if resp.status_code != 200:
raise EntryNotFoundError(iupac, resp.status_code)
ret = resp.json()
diff --git a/ippisite/requirements-dev.txt b/ippisite/requirements-dev.txt
index d2531e117fa2ec0f344fd73b065a59b05906c116..29824591a52c9b85cff19c09d2bdda3e1e8a042c 100644
--- a/ippisite/requirements-dev.txt
+++ b/ippisite/requirements-dev.txt
@@ -1,4 +1,7 @@
-r requirements-core.txt
+# linting and formatting
+flake8
+black
# documentation generation
sphinx
sphinx_rtd_theme