From 4871fe4f0a594b7232b2f67f94af7c19076a6c84 Mon Sep 17 00:00:00 2001
From: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>
Date: Mon, 16 Jun 2025 17:22:33 -0400
Subject: [PATCH 1/4] Started using requests instead of pyURL

---
 .gitignore             |   3 +
 obiba_agate/console.py |   1 +
 obiba_agate/core.py    | 308 +++++++++++++++++++++++++++++------------
 obiba_agate/rest.py    |  63 +++++----
 poetry.lock            | 245 +++++++++++++++++++++++---------
 pyproject.toml         |   3 +-
 tests/test_restCall.py |  15 +-
 7 files changed, 446 insertions(+), 192 deletions(-)

diff --git a/.gitignore b/.gitignore
index ffdc42e..ededdd0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,3 +28,6 @@ coverage
 *.sw?
 
 __pycache__
+
+debug.py
+.history
\ No newline at end of file
diff --git a/obiba_agate/console.py b/obiba_agate/console.py
index f4f1324..15d294d 100755
--- a/obiba_agate/console.py
+++ b/obiba_agate/console.py
@@ -24,6 +24,7 @@ def add_agate_arguments(parser):
     parser.add_argument('--ssl-cert', '-sc', required=False, help='Certificate (public key) file')
     parser.add_argument('--ssl-key', '-sk', required=False, help='Private key file')
     parser.add_argument('--verbose', '-v', action='store_true', help='Verbose output')
+    parser.add_argument('--no-ssl-verify', '-nv', action='store_true', help='Do not verify SSL certificates for HTTPS.')
 
 
 def add_subcommand(subparsers, name, help, add_args_func, default_func):
diff --git a/obiba_agate/core.py b/obiba_agate/core.py
index f8388ec..5574e5e 100755
--- a/obiba_agate/core.py
+++ b/obiba_agate/core.py
@@ -4,11 +4,15 @@
 Curl options http://curl.haxx.se/libcurl/c/curl_easy_setopt.html
 """
 
-import pycurl
 import base64
 import json
 import os.path
 import getpass
+from requests import Session, Request
+import urllib3
+from http.client import HTTPConnection
+from http import HTTPStatus
+
 import urllib.request, urllib.parse, urllib.error
 from functools import reduce
 
@@ -19,21 +23,27 @@ class AgateClient:
     """
 
     def __init__(self, server=None):
-        self.curl_options = {}
+        self.session = Session()
         self.headers = {}
         self.base_url = self.__ensure_entry('Agate address', server)
 
+    def __del__(self):
+        self.close()
+
     @classmethod
     def build(cls, loginInfo):
         return AgateClient.buildWithAuthentication(loginInfo.data['server'], loginInfo.data['user'],
-                                                   loginInfo.data['password'], loginInfo.data['otp'])
+                                                   loginInfo.data['password'], loginInfo.data['otp'],
+                                                   loginInfo.data["no_ssl_verify"])
 
     @classmethod
-    def buildWithAuthentication(cls, server, user, password, otp=None):
+    def buildWithAuthentication(cls, server, user, password, otp=None, no_ssl_verify: bool = False):
         client = cls(server)
         if client.base_url.startswith('https:'):
-            client.verify_peer(0)
-            client.verify_host(0)
+            client.session.verify = not no_ssl_verify
+            if no_ssl_verify:
+                urllib3.disable_warnings()
+
         client.credentials(user, password, otp)
         return client
 
@@ -52,7 +62,8 @@ def credentials(self, user, password, otp):
         if otp:
             val = input("Enter 6-digits code: ")
             self.header('X-Obiba-TOTP', val)
-        return self.header('Authorization', 'Basic ' + base64.b64encode((u + ':' + p).encode("utf-8")).decode("utf-8"))
+
+        self.session.headers.update({"Authorization": "Basic %s" % base64.b64encode(("%s:%s" % (u, p)).encode("utf-8")).decode("utf-8")})
 
     def keys(self, cert_file, key_file, key_pwd=None, ca_certs=None):
         self.curl_option(pycurl.SSLCERT, cert_file)
@@ -64,26 +75,41 @@ def keys(self, cert_file, key_file, key_pwd=None, ca_certs=None):
         self.headers.pop('Authorization', None)
         return self
 
-    def verify_peer(self, verify):
-        return self.curl_option(pycurl.SSL_VERIFYPEER, verify)
-
-    def verify_host(self, verify):
-        return self.curl_option(pycurl.SSL_VERIFYHOST, verify)
-
-    def ssl_version(self, version):
-        return self.curl_option(pycurl.SSLVERSION, version)
+    def verify(self, value):
+        """
+        Ignore or validate certificate
 
-    def curl_option(self, opt, value):
-        self.curl_options[opt] = value
+        :param value = True/False to validation or not. Value can also be a CA_BUNDLE file or directory (e.g. 'verify=/etc/ssl/certs/ca-certificates.crt')
+        """
+        self.session.verify = value
         return self
 
     def header(self, key, value):
-        self.headers[key] = value
+        """
+        Adds a header to session headers used by the request
+
+        :param key - header key
+        :param value - header value
+        """
+        header = {}
+        header[key] = value
+
+        self.session.headers.update(header)
         return self
 
     def new_request(self):
         return AgateRequest(self)
 
+    def close(self):
+        """
+        Closes client session and request to close Agate server session
+        """
+        try:
+            self.new_request().resource("/auth/session/_current").delete().send()
+            self.session.close()
+        except Exception as e:
+            pass
+
     class LoginInfo:
         data = None
 
@@ -92,18 +118,17 @@ def parse(cls, args):
             data = {}
             argv = vars(args)
 
+            data["no_ssl_verify"] = argv.get("no_ssl_verify")
+
             if argv.get('agate'):
                 data['server'] = argv['agate']
             else:
                 raise Exception('Agate server information is missing.')
 
             if argv.get('user') and argv.get('password'):
-                data['user'] = argv['user']
-                data['password'] = argv['password']
-                data['otp'] = argv['otp']
-            elif argv.get('ssl_cert') and argv.get('ssl_key'):
-                data['cert'] = argv['ssl_cert']
-                data['key'] = argv['ssl_key']
+                data["user"] = argv["user"]
+                data["password"] = argv["password"]
+                data["otp"] = argv["otp"]
             else:
                 raise Exception('Invalid login information. Requires user-password or certificate-key information')
 
@@ -123,37 +148,55 @@ class AgateRequest:
 
     def __init__(self, agate_client):
         self.client = agate_client
-        self.curl_options = {}
+        self.options = {}
         self.headers = {'Accept': 'application/json'}
-        self._verbose = False
+        self.params = {}
+        self._fail_on_error = False
+        self.files = None
+        self.data = None
 
-    def curl_option(self, opt, value):
-        self.curl_options[opt] = value
-        return self
 
     def timeout(self, value):
-        return self.curl_option(pycurl.TIMEOUT, value)
+        """
+        Sets the connection and read timeout
+        Note: value can be a tupple to have different timeouts for connection and reading (connTimout, readTimeout)
 
-    def connection_timeout(self, value):
-        return self.curl_option(pycurl.CONNECTTIMEOUT, value)
+        :param value - connection/read timout
+        """
+        self.options["timeout"] = value
+        return self
 
     def verbose(self):
+        """
+        Enables the verbose mode
+        """
+        HTTPConnection.debuglevel = 1
         self._verbose = True
-        return self.curl_option(pycurl.VERBOSE, True)
+        return self
 
     def fail_on_error(self):
-        return self.curl_option(pycurl.FAILONERROR, True)
+        self._fail_on_error = True
+        return self
 
     def header(self, key, value):
+        """
+        Adds a header to session headers used by the request
+
+        :param key - header key
+        :param value - header value
+        """
         if value:
-            self.headers[key] = value
+            header = {}
+            header[key] = value
+            self.headers.update(header)
         return self
 
     def accept(self, value):
-        return self.header('Accept', value)
+        self.headers.update({"Accept": value})
+        return self
 
     def content_type(self, value):
-        return self.header('Content-Type', value)
+        return self.accept("application/json")
 
     def accept_json(self):
         return self.accept('application/json')
@@ -162,12 +205,17 @@ def content_type_json(self):
         return self.content_type('application/json')
 
     def method(self, method):
+        """
+        Sets a HTTP method
+
+        :param method - any of ['GET', 'DELETE', 'PUT', 'POST', 'OPTIONS']
+        """
         if not method:
-            self.method = 'GET'
-        elif method in ['GET', 'DELETE', 'PUT', 'POST', 'OPTIONS']:
+            self.method = "GET"
+        elif method in ["GET", "DELETE", "PUT", "POST", "OPTIONS"]:
             self.method = method
         else:
-            raise Exception('Not a valid method: ' + method)
+            raise ValueError("Not a valid method: " + method)
         return self
 
     def get(self):
@@ -186,68 +234,86 @@ def options(self):
         return self.method('OPTIONS')
 
     def __build_request(self):
-        curl = pycurl.Curl()
-        # curl options
-        for o in self.client.curl_options:
-            curl.setopt(o, self.client.curl_options[o])
-        for o in self.curl_options:
-            curl.setopt(o, self.curl_options[o])
-            # headers
-        hlist = []
-        for h in self.client.headers:
-            hlist.append(h + ": " + self.client.headers[h])
-        for h in self.headers:
-            hlist.append(h + ": " + self.headers[h])
-        curl.setopt(pycurl.HTTPHEADER, hlist)
-        if self.method:
-            curl.setopt(pycurl.CUSTOMREQUEST, self.method)
+        """
+        Builder method creating a Request object to be sent by the client session object
+        """
+        request = Request()
+        request.method = self.method if self.method else "GET"
+
+        for option in self.options:
+            setattr(request, option, self.options[option])
+
+        # Combine the client and the request headers
+        request.headers = {}
+        request.headers.update(self.client.session.headers)
+        request.headers.update(self.headers)
+
         if self.resource:
-            curl.setopt(pycurl.URL, self.client.base_url + '/ws' + self.resource)
+            path = self.resource
+            request.url = self.client.base_url + "/ws" + path
+
+            if self.params:
+                request.params = self.params
         else:
-            raise Exception('Resource is missing')
-        return curl
+            raise ValueError("Resource is missing")
+
+        if self.files is not None:
+            request.files = self.files
+
+        if self.data is not None:
+            request.data = self.data
+
+        return request
+
 
     def resource(self, ws):
         self.resource = ws
         return self
 
+    def form(self, parameters):
+        """
+        Stores the request's body as a form
+        Note: no need to transform parameters in key=value pairs
+
+        :param parametes - parameters as a dict value
+        """
+        return self.content(parameters)
+
     def content(self, content):
+        """
+        Stores the request body
+
+        :param content - request body
+        """
         if self._verbose:
-            print('* Content:')
+            print("* Content:")
             print(content)
-        encodedContent = content.encode('utf-8')
-        self.curl_option(pycurl.POST, 1)
-        self.curl_option(pycurl.POSTFIELDSIZE, len(encodedContent))
-        self.curl_option(pycurl.POSTFIELDS, encodedContent)
-        return self
 
-    def content_file(self, filename):
-        if self._verbose:
-            print('* File Content:')
-            print('[file=' + filename + ', size=' + str(os.path.getsize(filename)) + ']')
-        self.curl_option(pycurl.POST, 1)
-        self.curl_option(pycurl.POSTFIELDSIZE, os.path.getsize(filename))
-        reader = open(filename, 'rb')
-        self.curl_option(pycurl.READFUNCTION, reader.read)
+        self.data = content
         return self
 
+
     def content_upload(self, filename):
+        """
+        Sets the file associate with the upload
+
+        Note: Requests library takes care of mutlti-part setting in the header
+        """
         if self._verbose:
-            print('* File Content:')
-            print('[file=' + filename + ', size=' + str(os.path.getsize(filename)) + ']')
-            # self.curl_option(pycurl.POST,1)
-        self.curl_option(pycurl.HTTPPOST, [("file1", (pycurl.FORM_FILE, filename))])
+            print("* File Content:")
+            print("[file=" + filename + ", size=" + str(os.path.getsize(filename)) + "]")
+        self.files = {"file": (filename, open(filename, "rb"))}
         return self
 
     def send(self):
-        curl = self.__build_request()
-        hbuf = HeaderStorage()
-        cbuf = Storage()
-        curl.setopt(curl.WRITEFUNCTION, cbuf.store)
-        curl.setopt(curl.HEADERFUNCTION, hbuf.store)
-        curl.perform()
-        response = AgateResponse(curl.getinfo(pycurl.HTTP_CODE), hbuf.headers, cbuf.content)
-        curl.close()
+        """
+        Sends the request via client session object
+        """
+        request = self.__build_request()
+        response = AgateResponse(self.client.session.send(request.prepare()))
+
+        if self._fail_on_error and response.code >= 400:
+            raise HTTPError(response)
 
         return response
 
@@ -298,20 +364,56 @@ class AgateResponse:
     Response from Agate: code, headers and content
     """
 
-    def __init__(self, code, headers, content):
-        self.code = code
-        self.headers = headers
-        self.content = content
+    def __init__(self, response):
+        self.response = response
+
+    @property
+    def code(self):
+        return self.response.status_code
+
+    @property
+    def headers(self):
+        return self.response.headers
+
+    @property
+    def content(self):
+        return self.response.content
+
+    @property
+    def version(self):
+        return self.headers.get("X-Agate-Version", None)
+
+    @property
+    def version_info(self):
+        agateVersion = self.version
+        if agateVersion is not None:
+            info = {}
+            [info["major"], info["minor"], info["patch"]] = self.version.split(".")
+            return info
+        return None
 
     def as_json(self):
-        return json.loads(self.content)
+        """
+        Returns response body as a JSON document
+        """
+        if self.response is None or self.response.content is None:
+            return None
+
+        try:
+            return self.response.json()
+        except Exception as e:
+            if type(self.response.content) == str:
+                return self.response.content
+            else:
+                # FIXME silently fail
+                return None
 
     def pretty_json(self):
+        """
+        Beatifies the JSON response
+        """
         return json.dumps(self.as_json(), sort_keys=True, indent=2)
 
-    def __str__(self):
-        return self.content
-
 
 class UriBuilder:
     """
@@ -357,3 +459,25 @@ def concat_query(q, p):
 
     def build(self):
         return self.__str__()
+
+class HTTPError(Exception):
+    """
+    HTTP related error class
+    """
+
+    def __init__(self, response: AgateResponse, message: str = None):
+        # Call the base class constructor with the parameters it needs
+        super().__init__(message if message else "HTTP Error: %s" % response.code)
+        self.code = response.code
+        http_status = [x for x in list(HTTPStatus) if x.value == response.code][0]
+        self.message = message if message else "%s: %s" % (http_status.phrase, http_status.description)
+        self.error = response.as_json() if response.content else {"code": response.code, "status": self.message}
+        # case the reported error is not a dict
+        if type(self.error) != dict:
+            self.error = {"code": response.code, "status": self.error}
+
+    def is_client_error(self) -> bool:
+        return self.code >= 400 and self.code < 500
+
+    def is_server_error(self) -> bool:
+        return self.code >= 500
\ No newline at end of file
diff --git a/obiba_agate/rest.py b/obiba_agate/rest.py
index eb9e2e3..a2a45ef 100755
--- a/obiba_agate/rest.py
+++ b/obiba_agate/rest.py
@@ -24,32 +24,37 @@ def do_command(args):
     Execute REST command
     """
     # Build and send request
-    request = core.AgateClient.build(core.AgateClient.LoginInfo.parse(args)).new_request()
-    request.fail_on_error()
-
-    if args.accept:
-        request.accept(args.accept)
-    else:
-        request.accept_json()
-
-    if args.content_type:
-        request.content_type(args.content_type)
-        print('Enter content:')
-        request.content(sys.stdin.read())
-
-    if args.verbose:
-        request.verbose()
-
-    # send request
-    request.method(args.method).resource(args.ws)
-    response = request.send()
-
-    # format response
-    res = response.content
-    if args.json:
-        res = response.pretty_json()
-    elif args.method in ['OPTIONS']:
-        res = response.headers['Allow']
-
-    # output to stdout
-    print(res)
+    client = core.AgateClient.build(core.AgateClient.LoginInfo.parse(args))
+
+    try:
+        request = client.new_request()
+        request.fail_on_error()
+
+        if args.accept:
+            request.accept(args.accept)
+        else:
+            request.accept_json()
+
+        if args.content_type:
+            request.content_type(args.content_type)
+            print('Enter content:')
+            request.content(sys.stdin.read())
+
+        if args.verbose:
+            request.verbose()
+
+        # send request
+        request.method(args.method).resource(args.ws)
+        response = request.send()
+
+        # format response
+        res = response.content
+        if args.json:
+            res = response.pretty_json()
+        elif args.method in ['OPTIONS']:
+            res = response.headers['Allow']
+
+        # output to stdout
+        print(res)
+    finally:
+        client.close()
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 77308b9..bd536f7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,13 +1,126 @@
-# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+
+[[package]]
+name = "certifi"
+version = "2025.6.15"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "certifi-2025.6.15-py3-none-any.whl", hash = "sha256:2e0c7ce7cb5d8f8634ca55d2ba7e6ec2689a2fd6537d8dec1296a477a4910057"},
+    {file = "certifi-2025.6.15.tar.gz", hash = "sha256:d747aa5a8b9bbbb1bb8c22bb13e22bd1f18e9796defa16bab421f7f7a317323b"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.4.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "charset_normalizer-3.4.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7c48ed483eb946e6c04ccbe02c6b4d1d48e51944b6db70f697e089c193404941"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b2d318c11350e10662026ad0eb71bb51c7812fc8590825304ae0bdd4ac283acd"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:9cbfacf36cb0ec2897ce0ebc5d08ca44213af24265bd56eca54bee7923c48fd6"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:18dd2e350387c87dabe711b86f83c9c78af772c748904d372ade190b5c7c9d4d"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8075c35cd58273fee266c58c0c9b670947c19df5fb98e7b66710e04ad4e9ff86"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:5bf4545e3b962767e5c06fe1738f951f77d27967cb2caa64c28be7c4563e162c"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:7a6ab32f7210554a96cd9e33abe3ddd86732beeafc7a28e9955cdf22ffadbab0"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:b33de11b92e9f75a2b545d6e9b6f37e398d86c3e9e9653c4864eb7e89c5773ef"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-musllinux_1_2_ppc64le.whl", hash = "sha256:8755483f3c00d6c9a77f490c17e6ab0c8729e39e6390328e42521ef175380ae6"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-musllinux_1_2_s390x.whl", hash = "sha256:68a328e5f55ec37c57f19ebb1fdc56a248db2e3e9ad769919a58672958e8f366"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:21b2899062867b0e1fde9b724f8aecb1af14f2778d69aacd1a5a1853a597a5db"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-win32.whl", hash = "sha256:e8082b26888e2f8b36a042a58307d5b917ef2b1cacab921ad3323ef91901c71a"},
+    {file = "charset_normalizer-3.4.2-cp310-cp310-win_amd64.whl", hash = "sha256:f69a27e45c43520f5487f27627059b64aaf160415589230992cec34c5e18a509"},
+    {file = "charset_normalizer-3.4.2-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:be1e352acbe3c78727a16a455126d9ff83ea2dfdcbc83148d2982305a04714c2"},
+    {file = "charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:aa88ca0b1932e93f2d961bf3addbb2db902198dca337d88c89e1559e066e7645"},
+    {file = "charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:d524ba3f1581b35c03cb42beebab4a13e6cdad7b36246bd22541fa585a56cccd"},
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+]
 
 [[package]]
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
-groups = ["test"]
-markers = "sys_platform == \"win32\""
 files = [
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@@ -17,10 +130,9 @@ files = [
 name = "exceptiongroup"
 version = "1.3.0"
 description = "Backport of PEP 654 (exception groups)"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
-markers = "python_version < \"3.11\""
 files = [
     {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"},
     {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"},
@@ -32,14 +144,28 @@ typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "idna"
+version = "3.10"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
+]
+
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "importlib-metadata"
 version = "6.7.0"
 description = "Read metadata from Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
-markers = "python_version == \"3.7\""
 files = [
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@@ -52,15 +178,15 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3) ; python_version < \"3.9\"", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\"", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
 files = [
     {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
@@ -70,9 +196,9 @@ files = [
 name = "packaging"
 version = "24.0"
 description = "Core utilities for Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
 files = [
     {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
     {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
@@ -82,9 +208,9 @@ files = [
 name = "pluggy"
 version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
 files = [
     {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
     {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
@@ -97,54 +223,13 @@ importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
-[[package]]
-name = "pycurl"
-version = "7.45.6"
-description = "PycURL -- A Python Interface To The cURL library"
-optional = false
-python-versions = ">=3.5"
-groups = ["main"]
-files = [
-    {file = "pycurl-7.45.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c31b390f1e2cd4525828f1bb78c1f825c0aab5d1588228ed71b22c4784bdb593"},
-    {file = "pycurl-7.45.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:942b352b69184cb26920db48e0c5cb95af39874b57dbe27318e60f1e68564e37"},
-    {file = "pycurl-7.45.6-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:3441ee77e830267aa6e2bb43b29fd5f8a6bd6122010c76a6f0bf84462e9ea9c7"},
-    {file = "pycurl-7.45.6-cp310-cp310-manylinux_2_28_x86_64.whl", hash = "sha256:2a21e13278d7553a04b421676c458449f6c10509bebf04993f35154b06ee2b20"},
-    {file = "pycurl-7.45.6-cp310-cp310-win32.whl", hash = "sha256:d0b5501d527901369aba307354530050f56cd102410f2a3bacd192dc12c645e3"},
-    {file = "pycurl-7.45.6-cp310-cp310-win_amd64.whl", hash = "sha256:abe1b204a2f96f2eebeaf93411f03505b46d151ef6d9d89326e6dece7b3a008a"},
-    {file = "pycurl-7.45.6-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6f57ad26d6ab390391ad5030790e3f1a831c1ee54ad3bf969eb378f5957eeb0a"},
-    {file = "pycurl-7.45.6-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:c6fd295f03c928da33a00f56c91765195155d2ac6f12878f6e467830b5dce5f5"},
-    {file = "pycurl-7.45.6-cp311-cp311-manylinux_2_28_aarch64.whl", hash = "sha256:334721ce1ccd71ff8e405470768b3d221b4393570ccc493fcbdbef4cd62e91ed"},
-    {file = "pycurl-7.45.6-cp311-cp311-manylinux_2_28_x86_64.whl", hash = "sha256:0cd6b7794268c17f3c660162ed6381769ce0ad260331ef49191418dfc3a2d61a"},
-    {file = "pycurl-7.45.6-cp311-cp311-win32.whl", hash = "sha256:357ea634395310085b9d5116226ac5ec218a6ceebf367c2451ebc8d63a6e9939"},
-    {file = "pycurl-7.45.6-cp311-cp311-win_amd64.whl", hash = "sha256:878ae64484db18f8f10ba99bffc83fefb4fe8f5686448754f93ec32fa4e4ee93"},
-    {file = "pycurl-7.45.6-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:c872d4074360964697c39c1544fe8c91bfecbff27c1cdda1fee5498e5fdadcda"},
-    {file = "pycurl-7.45.6-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:56d1197eadd5774582b259cde4364357da71542758d8e917f91cc6ed7ed5b262"},
-    {file = "pycurl-7.45.6-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:8a99e56d2575aa74c48c0cd08852a65d5fc952798f76a34236256d5589bf5aa0"},
-    {file = "pycurl-7.45.6-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:c04230b9e9cfdca9cf3eb09a0bec6cf2f084640f1f1ca1929cca51411af85de2"},
-    {file = "pycurl-7.45.6-cp312-cp312-win32.whl", hash = "sha256:ae893144b82d72d95c932ebdeb81fc7e9fde758e5ecd5dd10ad5b67f34a8b8ee"},
-    {file = "pycurl-7.45.6-cp312-cp312-win_amd64.whl", hash = "sha256:56f841b6f2f7a8b2d3051b9ceebd478599dbea3c8d1de8fb9333c895d0c1eea5"},
-    {file = "pycurl-7.45.6-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:7c09b7180799af70fc1d4eed580cfb1b9f34fda9081f73a3e3bc9a0e5a4c0e9b"},
-    {file = "pycurl-7.45.6-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:361bf94b2a057c7290f9ab84e935793ca515121fc012f4b6bef6c3b5e4ea4397"},
-    {file = "pycurl-7.45.6-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:bb9eff0c7794af972da769a887c87729f1bcd8869297b1c01a2732febbb75876"},
-    {file = "pycurl-7.45.6-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:26839d43dc7fff6b80e0067f185cc1d0e9be2ae6e2e2361ae8488cead5901c04"},
-    {file = "pycurl-7.45.6-cp313-cp313-win32.whl", hash = "sha256:a721c2696a71b1aa5ecf82e6d0ade64bc7211b7317f1c9c66e82f82e2264d8b4"},
-    {file = "pycurl-7.45.6-cp313-cp313-win_amd64.whl", hash = "sha256:f0198ebcda8686b3a0c66d490a687fa5fd466f8ecc2f20a0ed0931579538ae3d"},
-    {file = "pycurl-7.45.6-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a554a2813d415a7bb9a996a6298f3829f57e987635dcab9f1197b2dccd0ab3b2"},
-    {file = "pycurl-7.45.6-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9f721e3394e5bd7079802ec1819b19c5be4842012268cc45afcb3884efb31cf0"},
-    {file = "pycurl-7.45.6-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:81005c0f681d31d5af694d1d3c18bbf1bed0bc8b2bb10fb7388cb1378ba9bd6a"},
-    {file = "pycurl-7.45.6-cp39-cp39-manylinux_2_28_x86_64.whl", hash = "sha256:3fc0b505c37c7c54d88ced27e1d9e3241130987c24bf1611d9bbd9a3e499e07c"},
-    {file = "pycurl-7.45.6-cp39-cp39-win32.whl", hash = "sha256:1309fc0f558a80ca444a3a5b0bdb1572a4d72b195233f0e65413b4d4dd78809b"},
-    {file = "pycurl-7.45.6-cp39-cp39-win_amd64.whl", hash = "sha256:2d1a49418b8b4c61f52e06d97b9c16142b425077bd997a123a2ba9ef82553203"},
-    {file = "pycurl-7.45.6.tar.gz", hash = "sha256:2b73e66b22719ea48ac08a93fc88e57ef36d46d03cb09d972063c9aa86bb74e6"},
-]
-
 [[package]]
 name = "pytest"
 version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
 files = [
     {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
     {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
@@ -162,14 +247,35 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "requests"
+version = "2.31.0"
+description = "Python HTTP for Humans."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
+    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+]
+
+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
-markers = "python_version < \"3.11\""
 files = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -179,23 +285,38 @@ files = [
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
-markers = "python_version < \"3.11\""
 files = [
     {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
+[[package]]
+name = "urllib3"
+version = "1.26.15"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+files = [
+    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
+    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
+socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+
 [[package]]
 name = "zipp"
 version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
-groups = ["test"]
-markers = "python_version == \"3.7\""
 files = [
     {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
     {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
@@ -203,9 +324,9 @@ files = [
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8 ; python_version < \"3.12\"", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\""]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
-lock-version = "2.1"
+lock-version = "2.0"
 python-versions = "^3.7"
-content-hash = "62f3bc5253b6427b5e6c14a397459c9045060a937dd39e1f553c1b2446698f52"
+content-hash = "1ed0e72a1b6f9dc1b844998404d35939579ca909d881179bc4f6e22bc072371c"
diff --git a/pyproject.toml b/pyproject.toml
index 5e5ee24..9a9aa44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,8 @@ packages = [{include = "obiba_agate"}]
 
 [tool.poetry.dependencies]
 python = "^3.7"
-pycurl = "^7.45.2"
+requests = "^2.31.0"
+urllib3 = "1.26.15"
 
 [tool.poetry.group.test.dependencies]
 pytest = "^7.2.2"
diff --git a/tests/test_restCall.py b/tests/test_restCall.py
index 14c59ed..6342476 100644
--- a/tests/test_restCall.py
+++ b/tests/test_restCall.py
@@ -33,14 +33,13 @@ def test_sendRest(self):
             self.fail(e)
 
     def test_sendSecuredRest(self):
-        if exists(self.SSL_CERTIFICATE):
-            try:
-                client = AgateClient.buildWithCertificate(server=self.SERVER,
-                                                        cert=self.SSL_CERTIFICATE,
-                                                        key=self.SSL_KEY)
-                self.__sendSimpleRequest(client.new_request())
-            except Exception as e:
-                self.fail(e)
+        try:
+            client = AgateClient.buildWithAuthentication(server='https://localhost:8444',
+                                                    user='administrator',
+                                                    password='password', no_ssl_verify=True)
+            self.__sendSimpleRequest(client.new_request())
+        except Exception as e:
+            self.fail(e)
 
     def test_validAuthLoginInfo(self):
         try:

From 40c8314630298f5fe74fb76ce2943947a82709d1 Mon Sep 17 00:00:00 2001
From: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>
Date: Tue, 17 Jun 2025 09:37:52 -0400
Subject: [PATCH 2/4] Removed any references to pycurl

---
 obiba_agate/core.py | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

diff --git a/obiba_agate/core.py b/obiba_agate/core.py
index 5574e5e..eaa820b 100755
--- a/obiba_agate/core.py
+++ b/obiba_agate/core.py
@@ -1,7 +1,5 @@
 """
-Based on PyCurl http://pycurl.sourceforge.net/
-See also http://www.angryobjects.com/2011/10/15/http-with-python-pycurl-by-example/
-Curl options http://curl.haxx.se/libcurl/c/curl_easy_setopt.html
+Based on Python Request library https://docs.python-requests.org/en/latest/index.html
 """
 
 import base64
@@ -12,8 +10,7 @@
 import urllib3
 from http.client import HTTPConnection
 from http import HTTPStatus
-
-import urllib.request, urllib.parse, urllib.error
+import urllib.parse
 from functools import reduce
 
 
@@ -65,16 +62,6 @@ def credentials(self, user, password, otp):
 
         self.session.headers.update({"Authorization": "Basic %s" % base64.b64encode(("%s:%s" % (u, p)).encode("utf-8")).decode("utf-8")})
 
-    def keys(self, cert_file, key_file, key_pwd=None, ca_certs=None):
-        self.curl_option(pycurl.SSLCERT, cert_file)
-        self.curl_option(pycurl.SSLKEY, key_file)
-        if key_pwd:
-            self.curl_option(pycurl.KEYPASSWD, key_pwd)
-        if ca_certs:
-            self.curl_option(pycurl.CAINFO, ca_certs)
-        self.headers.pop('Authorization', None)
-        return self
-
     def verify(self, value):
         """
         Ignore or validate certificate

From 13233bb6f235925a4329ce749734428297c479d5 Mon Sep 17 00:00:00 2001
From: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>
Date: Tue, 17 Jun 2025 13:31:02 -0400
Subject: [PATCH 3/4] Completed using requests

---
 obiba_agate/core.py    |  6 ++++--
 tests/test_restCall.py | 10 ++++++----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/obiba_agate/core.py b/obiba_agate/core.py
index eaa820b..b6d5149 100755
--- a/obiba_agate/core.py
+++ b/obiba_agate/core.py
@@ -137,6 +137,7 @@ def __init__(self, agate_client):
         self.client = agate_client
         self.options = {}
         self.headers = {'Accept': 'application/json'}
+        self._verbose = False
         self.params = {}
         self._fail_on_error = False
         self.files = None
@@ -183,13 +184,14 @@ def accept(self, value):
         return self
 
     def content_type(self, value):
-        return self.accept("application/json")
+        return self.headers.update({"Content-Type": value})
 
     def accept_json(self):
         return self.accept('application/json')
 
     def content_type_json(self):
-        return self.content_type('application/json')
+        self.content_type('application/json')
+        return self
 
     def method(self, method):
         """
diff --git a/tests/test_restCall.py b/tests/test_restCall.py
index 6342476..0d0c456 100644
--- a/tests/test_restCall.py
+++ b/tests/test_restCall.py
@@ -27,16 +27,18 @@ def test_sendRestBadCredentials(self):
     def test_sendRest(self):
         try:
             client = AgateClient.buildWithAuthentication(server=self.SERVER, user='administrator',
-                                                        password='password')
+                                                        password='password', no_ssl_verify=True)
             self.__sendSimpleRequest(client.new_request())
         except Exception as e:
             self.fail(e)
 
     def test_sendSecuredRest(self):
         try:
-            client = AgateClient.buildWithAuthentication(server='https://localhost:8444',
-                                                    user='administrator',
-                                                    password='password', no_ssl_verify=True)
+            client = AgateClient.buildWithAuthentication(server=self.SERVER,
+                                                        user='administrator',
+                                                        password='password')
+            # place a valid CRT to verify the SERVER SSL certificate
+            #client.verify('<PATH_TO_YOUR_CRT>')
             self.__sendSimpleRequest(client.new_request())
         except Exception as e:
             self.fail(e)

From 21c114e6a06469bd252ebd502184bf3e337131e5 Mon Sep 17 00:00:00 2001
From: Ramin Haeri Azad <rhaeri@maelstrom-reseach.org>
Date: Tue, 17 Jun 2025 17:05:27 -0400
Subject: [PATCH 4/4] Corrected PR comments

---
 obiba_agate/core.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/obiba_agate/core.py b/obiba_agate/core.py
index b6d5149..f46da28 100755
--- a/obiba_agate/core.py
+++ b/obiba_agate/core.py
@@ -184,7 +184,7 @@ def accept(self, value):
         return self
 
     def content_type(self, value):
-        return self.headers.update({"Content-Type": value})
+        return self.header('Content-Type', value)
 
     def accept_json(self):
         return self.accept('application/json')
@@ -291,7 +291,8 @@ def content_upload(self, filename):
         if self._verbose:
             print("* File Content:")
             print("[file=" + filename + ", size=" + str(os.path.getsize(filename)) + "]")
-        self.files = {"file": (filename, open(filename, "rb"))}
+        with open(filename, "rb") as file:
+            self.files = {"file": (filename, file.read())}
         return self
 
     def send(self):
@@ -377,8 +378,13 @@ def version_info(self):
         agateVersion = self.version
         if agateVersion is not None:
             info = {}
-            [info["major"], info["minor"], info["patch"]] = self.version.split(".")
-            return info
+            version_parts = self.version.split(".")
+            if len(version_parts) == 3:
+                info["major"], info["minor"], info["patch"] = version_parts
+                return info
+            else:
+                # Handle malformed version string
+                return None
         return None
 
     def as_json(self):