httpx fixes - removed SSL verification

Belapi was failing due to SSL verification issues. Removed that
from the httpx client and updated everything to use that httpx Client.

bel/edge/edges.py

@@ -14,7 +14,6 @@
 from typing import Any, List, Mapping, MutableSequence
 
 # Third Party Imports
-import httpx
 import structlog
 
 # Local Imports
@@ -23,6 +22,7 @@
 import bel.lang.belobj
 import bel.utils as utils
 from bel.Config import config
+from bel.utils import http_client
 
 log = structlog.getLogger(__name__)
 
@@ -442,7 +442,7 @@ def orthologize_context(
     """
 
     url = f'{config["bel_api"]["servers"]["api_url"]}/terms/{orthologize_target}'
-    r = httpx.get(url)
+    r = http_client.get(url)
     species_label = r.json().get("label", "unlabeled")
 
     orthologized_from = {}

bel/edge/pipeline.py

@@ -15,14 +15,14 @@
 import urllib
 
 # Third Party Imports
-import httpx
 import structlog
 
 # Local Imports
 import bel.db.arangodb as arangodb
 import bel.edge.edges
 import bel.nanopub.files as files
 import bel.utils as utils
+from bel.utils import http_client
 
 log = structlog.getLogger(__name__)
 
@@ -71,7 +71,7 @@ def process_nanopub(
     if token:
         headers = {"Authorization": f"Bearer {token}"}
 
-    r = httpx.get(nanopub_url, headers=headers)
+    r = http_client.get(nanopub_url, headers=headers)
 
     nanopub = r.json()
 

bel/lang/ast.py

@@ -16,15 +16,14 @@
 from typing import Any, List, Mapping
 
 # Third Party Imports
-import httpx
 import structlog
 import yaml
 
 # Local Imports
 import bel.terms.orthologs
 import bel.terms.terms
 from bel.Config import config
-from bel.utils import url_path_param_quoting
+from bel.utils import http_client, url_path_param_quoting
 
 log = structlog.getLogger(__name__)
 
@@ -718,7 +717,7 @@ def convert_nsarg(
 
     request_url = api_url.format(url_path_param_quoting(nsarg))
 
-    r = httpx.get(request_url, params=params, timeout=10)
+    r = http_client.get(request_url, params=params, timeout=10)
 
     if r and r.status_code == 200:
         nsarg = r.json().get("term_id", nsarg)

bel/lang/bel_specification.py

@@ -22,14 +22,14 @@
 from typing import Any, List, Mapping
 
 # Third Party Imports
-import httpx
 import jinja2
 import structlog
 import tatsu
 import yaml
 
 # Local Imports
 from bel.Config import config
+from bel.utils import http_client
 
 log = structlog.getLogger(__name__)
 
@@ -222,7 +222,7 @@ def github_belspec_files(spec_dir, force: bool = False):
     if github_access_token:
         params = {"access_token": github_access_token}
 
-    r = httpx.get(repo_url, params=params)
+    r = http_client.get(repo_url, params=params)
     if r.status_code == 200:
         results = r.json()
         for f in results:
@@ -232,7 +232,7 @@ def github_belspec_files(spec_dir, force: bool = False):
             if "yaml" not in fn and "yml" in fn:
                 fn = fn.replace("yml", "yaml")
 
-            r = httpx.get(url, params=params, allow_redirects=True)
+            r = http_client.get(url, params=params, allow_redirects=True)
             if r.status_code == 200:
                 open(f"{spec_dir}/{fn}", "wb").write(r.content)
             else:
@@ -561,7 +561,7 @@ def get_ebnf_template():
 
     try:
         # Get download url for template file
-        r = httpx.get(repo_url, params=params)
+        r = http_client.get(repo_url, params=params)
 
         if r.status_code == 200:
             template_url = r.json()["download_url"]
@@ -570,7 +570,7 @@ def get_ebnf_template():
 
         # Get template file
         try:
-            r = httpx.get(template_url, params=params, allow_redirects=True)
+            r = http_client.get(template_url, params=params, allow_redirects=True)
             if r.status_code == 200:
                 open(local_fp, "wt").write(r.text)
             else:

bel/lang/completion.py

@@ -15,14 +15,13 @@
 from typing import Any, List, Mapping, Optional, Tuple
 
 # Third Party Imports
-import httpx
 from structlog import get_logger
 
 # Local Imports
 import bel.lang.bel_specification as bel_specification
 import bel.lang.partialparse as pparse
 from bel.Config import config
-from bel.utils import url_path_param_quoting
+from bel.utils import http_client, url_path_param_quoting
 
 log = get_logger()
 
@@ -215,7 +214,7 @@ def nsarg_completions(
         }
         log.info("NSArg completion", api_url=config["bel_api"]["servers"]["api_url"], url=url)
 
-        r = httpx.get(url, params=params)
+        r = http_client.get(url, params=params)
 
         if r.status_code == 200:
             ns_completions = r.json()

bel/lang/semantics.py

@@ -5,12 +5,11 @@
 from typing import List, Tuple
 
 # Third Party Imports
-import httpx
 import structlog
 
 # Local Imports
 from bel.lang.ast import BELAst, Function, NSArg, StrArg
-from bel.utils import url_path_param_quoting
+from bel.utils import http_client, url_path_param_quoting
 
 log = structlog.getLogger()
 
@@ -275,7 +274,7 @@ def validate_arg_values(ast, bo):
         else:
             request_url = bo.api_url + "/terms/{}".format(url_path_param_quoting(term_id))
             log.info(f"Validate Arg Values url {request_url}")
-            r = httpx.get(request_url)
+            r = http_client.get(request_url)
             if r and r.status_code == 200:
                 result = r.json()
                 # function signature term value_types doesn't match up with API term entity_types

bel/nanopub/nanopubs.py

@@ -4,14 +4,14 @@
 from typing import Any, Iterable, List, Mapping, Tuple
 
 # Third Party Imports
-import httpx
 import jsonschema
 from cityhash import CityHash64
 
 # Local Imports
 import bel.edge.edges
 import bel.lang.belobj
 from bel.Config import config
+from bel.utils import http_client
 
 log = logging.getLogger(__name__)
 
@@ -98,7 +98,7 @@ def validate_context(self, context: Mapping[str, Any]) -> Tuple[bool, List[Tuple
 
         url = f'{self.endpoint}/terms/{context["id"]}'
 
-        res = httpx.get(url)
+        res = http_client.get(url)
         if res.status_code == 200:
             return (True, [])
         else:

bel/nanopub/pubmed.py

@@ -15,14 +15,13 @@
 from typing import Any, Mapping
 
 # Third Party Imports
-import httpx
 import structlog
 from lxml import etree
 
 # Local Imports
 import bel.lang.ast as bel_ast
 from bel.Config import config
-from bel.utils import url_path_param_quoting
+from bel.utils import http_client, url_path_param_quoting
 
 log = structlog.getLogger(__name__)
 
@@ -69,7 +68,7 @@ def get_pubtator(pmid):
     Re-configure the denotations into an annotation dictionary format
     and collapse duplicate terms so that their spans are in a list.
     """
-    r = httpx.get(PUBTATOR_TMPL.replace("PMID", pmid), timeout=10)
+    r = http_client.get(PUBTATOR_TMPL.replace("PMID", pmid), timeout=10)
     if r and r.status_code == 200:
         pubtator = r.json()[0]
     else:
@@ -283,7 +282,7 @@ def get_pubmed(pmid: str) -> Mapping[str, Any]:
 
     try:
         pubmed_url = PUBMED_TMPL.replace("PMID", str(pmid))
-        r = httpx.get(pubmed_url)
+        r = http_client.get(pubmed_url)
         content = r.content
         log.info(f"Getting Pubmed URL {pubmed_url}")
         root = etree.fromstring(content)
@@ -332,7 +331,7 @@ def enhance_pubmed_annotations(pubmed: Mapping[str, Any]) -> Mapping[str, Any]:
     for nsarg in pubmed["annotations"]:
         url = f'{config["bel_api"]["servers"]["api_url"]}/terms/{url_path_param_quoting(nsarg)}'
         log.info(f"URL: {url}")
-        r = httpx.get(url)
+        r = http_client.get(url)
         log.info(f"Result: {r}")
         new_nsarg = ""
         if r and r.status_code == 200:

bel/utils.py

@@ -20,6 +20,15 @@
 log = get_logger()
 
 
+def get_http_client():
+    """Client for http requests"""
+
+    return httpx.Client(verify=False)
+
+
+http_client = get_http_client()
+
+
 def timespan(start_time):
     """Return time in milliseconds from start_time"""
 
@@ -31,7 +40,7 @@ def timespan(start_time):
 def download_file(url):
     """Download file"""
 
-    response = httpx.get(url, stream=True)
+    response = http_client.get(url, stream=True)
     fp = tempfile.NamedTemporaryFile()
     for chunk in response.iter_content(chunk_size=1024):
         if chunk:  # filter out keep-alive new chunks

tests/lang/test_completion.py

@@ -165,7 +165,10 @@ def test_completion_arg_fn_5():
 
 def test_completion_arg_ns_prefix():
 
-    if bel.httpx.get(f"{config['bel_api']['servers']['api_url']}/simple_status").status_code != 200:
+    if (
+        bel.http_client.get(f"{config['bel_api']['servers']['api_url']}/simple_status").status_code
+        != 200
+    ):
         pytest.xfail("BEL.bio API Test environment is not setup")
 
     completions = bel.lang.completion.bel_completion(
@@ -181,7 +184,10 @@ def test_completion_arg_ns_prefix():
 
 def test_completion_arg_ns_val():
 
-    if bel.httpx.get(f"{config['bel_api']['servers']['api_url']}/simple_status").status_code != 200:
+    if (
+        bel.http_client.get(f"{config['bel_api']['servers']['api_url']}/simple_status").status_code
+        != 200
+    ):
         pytest.xfail("BEL.bio API Test environment is not setup")
 
     completions = bel.lang.completion.bel_completion(