HTTPS

qiita_core/configuration_manager.py

@@ -171,6 +171,15 @@ def _get_main(self, config):
             self.valid_upload_extension = []
             print 'No files will be allowed to be uploaded.'
 
+        self.certificate_file = config.get('main', 'CERTIFICATE_FILE')
+        if not self.certificate_file:
+            self.certificate_file = join(install_dir, 'qiita_core',
+                                         'support_files', 'server.crt')
+        self.key_file = config.get('main', 'KEY_FILE')
+        if not self.key_file:
+            self.key_file = join(install_dir, 'qiita_core', 'support_files',
+                                 'server.key')
+
     def _get_postgres(self, config):
         """Get the configuration of the postgres section"""
         self.user = config.get('postgres', 'USER')

qiita_core/support_files/config_test.cfg

@@ -22,7 +22,7 @@ LOG_PATH =
 REQUIRE_APPROVAL = True
 
 # Base URL: DO NOT ADD TRAILING SLASH
-BASE_URL = http://localhost
+BASE_URL = https://localhost
 
 # Download path files
 UPLOAD_DATA_DIR = /tmp/
@@ -39,12 +39,16 @@ BASE_DATA_DIR =
 # Valid upload extension, comma separated. Empty for no uploads
 VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual
 
-#Portal the site is working under
+# Portal the site is working under
 PORTAL = QIITA
 
-#Script used for launching plugins
+# Script used for launching plugins
 PLUGIN_LAUNCHER = qiita-plugin-launcher
 
+# Webserver certificate files
+CERTIFICATE_FILE =
+KEY_FILE =
+
 # ----------------------------- SMTP settings -----------------------------
 [smtp]
 # The hostname to connect to

qiita_core/support_files/server.crt

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

qiita_core/support_files/server.csr

@@ -0,0 +1,17 @@
+-----BEGIN CERTIFICATE REQUEST-----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+-----END CERTIFICATE REQUEST-----

qiita_core/support_files/server.key

@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----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+-----END RSA PRIVATE KEY-----

qiita_pet/templates/compute_wait.html

@@ -4,7 +4,8 @@
 <script type="text/javascript">
     $(document).ready(function() {
 
-        var host = 'ws://' + window.location.host + '/consumer/';
+        var socket_protocol = window.location.protocol == "https:" ? 'wss://' : 'ws://'
+        var host = socket_protocol + window.location.host + '/consumer/';
         var websocket = new WebSocket(host);
 
         // When the socket is opened, send a message from the client to the

qiita_plugins/target_gene/tgp/pick_otus.py

@@ -10,10 +10,7 @@
 from functools import partial
 from glob import glob
 
-import requests
-
-from tgp.util import (update_job_step, execute_request_retry, system_call,
-                      format_payload)
+from tgp.util import update_job_step, system_call, format_payload
 
 
 def write_parameters_file(fp, parameters):
@@ -109,13 +106,13 @@ def generate_artifact_info(pick_out):
     return [['BIOM', filepaths, True, True]]
 
 
-def pick_closed_reference_otus(server_url, job_id, parameters, out_dir):
+def pick_closed_reference_otus(qclient, job_id, parameters, out_dir):
     """Run split libraries fastq with the given parameters
 
     Parameters
     ----------
-    server_url : str
-        The URL of the server
+    qclient : tgp.qiita_client.QiitaClient
+        The Qiita server client
     job_id : str
         The job id
     parameters : dict
@@ -133,10 +130,9 @@ def pick_closed_reference_otus(server_url, job_id, parameters, out_dir):
     ValueError
         If there is any error gathering the information from the server
     """
-    update_job_step(server_url, job_id, "Step 1 of 3: Collecting information")
+    update_job_step(qclient, job_id, "Step 1 of 3: Collecting information")
     artifact_id = parameters['input_data']
-    url = "%s/qiita_db/artifacts/%s/filepaths/" % (server_url, artifact_id)
-    fps_info = execute_request_retry(requests.get, url)
+    fps_info = qclient.get("/qiita_db/artifacts/%s/filepaths/" % artifact_id)
     if not fps_info or not fps_info['success']:
         error_msg = "Could not get artifact filepath information: %s"
         if fps_info:
@@ -147,8 +143,7 @@ def pick_closed_reference_otus(server_url, job_id, parameters, out_dir):
     fps = fps_info['filepaths']
 
     reference_id = parameters['reference']
-    url = "%s/qiita_db/references/%s/filepaths/" % (server_url, reference_id)
-    ref_info = execute_request_retry(requests.get, url)
+    ref_info = qclient.get("/qiita_db/references/%s/filepaths/" % reference_id)
     if not ref_info or not ref_info['success']:
         error_msg = "Could not get artifact filepath information: %s"
         if ref_info:
@@ -158,11 +153,11 @@ def pick_closed_reference_otus(server_url, job_id, parameters, out_dir):
         raise ValueError(error_msg)
     reference_fps = ref_info['filepaths']
 
-    update_job_step(server_url, job_id, "Step 2 of 3: Generating command")
+    update_job_step(qclient, job_id, "Step 2 of 3: Generating command")
     command, pick_out = generate_pick_closed_reference_otus_cmd(
         fps, out_dir, parameters, reference_fps)
 
-    update_job_step(server_url, job_id, "Step 3 of 3: Executing OTU picking")
+    update_job_step(qclient, job_id, "Step 3 of 3: Executing OTU picking")
     std_out, std_err, return_value = system_call(command)
     if return_value != 0:
         error_msg = ("Error running OTU picking:\nStd out: %s\nStd err: %s"

qiita_plugins/target_gene/tgp/plugin.py

@@ -11,10 +11,8 @@
 from os.path import exists
 from os import makedirs
 
-import requests
-
-from tgp.util import (start_heartbeat, complete_job, execute_request_retry,
-                      format_payload)
+from tgp.qiita_client import QiitaClient
+from tgp.util import start_heartbeat, complete_job, format_payload
 from tgp.split_libraries import split_libraries, split_libraries_fastq
 from tgp.pick_otus import pick_closed_reference_otus
 
@@ -40,27 +38,27 @@ def execute_job(server_url, job_id, output_dir):
     RuntimeError
         If there is a problem gathering the job information
     """
+    qclient = QiitaClient(server_url)
     # Request job information
-    url = "%s/qiita_db/jobs/%s" % (server_url, job_id)
-    job_info = execute_request_retry(requests.get, url)
+    job_info = qclient.get("/qiita_db/jobs/%s" % job_id)
     # Check if we have received the job information so we can start it
-    if job_info['success']:
+    if job_info and job_info['success']:
         # Starting the heartbeat
-        start_heartbeat(server_url, job_id)
+        start_heartbeat(qclient, job_id)
         # Execute the given task
         task_name = job_info['command']
         task = TASK_DICT[task_name]
 
         if not exists(output_dir):
             makedirs(output_dir)
         try:
-            payload = task(server_url, job_id, job_info['parameters'],
+            payload = task(qclient, job_id, job_info['parameters'],
                            output_dir)
         except Exception:
             exc_str = repr(traceback.format_exception(*sys.exc_info()))
             error_msg = ("Error executing %s:\n%s" % (task_name, exc_str))
             payload = format_payload(False, error_msg=error_msg)
         # The job completed
-        complete_job(server_url, job_id, payload)
+        complete_job(qclient, job_id, payload)
     else:
         raise RuntimeError("Can't get job (%s) information" % job_id)

qiita_plugins/target_gene/tgp/qiita_client.py

@@ -0,0 +1,116 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from os.path import join, dirname, abspath
+from os import environ
+from future import standard_library
+
+import requests
+
+with standard_library.hooks():
+    from configparser import ConfigParser
+
+
+class QiitaClient(object):
+    """Client of the Qiita RESTapi
+
+    Parameters
+    ----------
+    server_url : str
+        The url of the Qiita server
+
+    Methods
+    -------
+    get
+    post
+    """
+    def __init__(self, server_url):
+        self._server_url = server_url
+
+        try:
+            conf_fp = environ['QP_TARGET_GENE_CONFIG_FP']
+        except KeyError:
+            conf_fp = join(dirname(abspath(__file__)), 'support_files',
+                           'config_file.cfg')
+
+        config = ConfigParser()
+        with open(conf_fp, 'U') as conf_file:
+            config.readfp(conf_file)
+
+        server_cert = config.get('main', 'SERVER_CERT')
+        if not server_cert:
+            # The server certificate is not provided, use standard certificate
+            # verification methods
+            self._verify = True
+        else:
+            # The server certificate is provided, use it to verify the identity
+            # of the server
+            self._verify = server_cert
+
+    def _request_retry(self, req, url, **kwargs):
+        """Executes a request retrying it 3 times in case of failure
+
+        Parameters
+        ----------
+        req : function
+            The request to execute
+        url : str
+            The url to access in the server
+        kwargs : dict
+            The request kwargs
+
+        Returns
+        -------
+        dict
+            The JSON information in the request reply
+        """
+        url = self._server_url + url
+        retries = 3
+        json_reply = None
+        while retries > 0:
+            retries -= 1
+            r = req(url, verify=self._verify, **kwargs)
+            r.close()
+            if r.status_code == 200:
+                json_reply = r.json()
+                break
+        return json_reply
+
+    def get(self, url, **kwargs):
+        """Execute a get against the Qiita server
+
+        Parameters
+        ----------
+        url : str
+            The url to access in the server
+        kwargs : dict
+            The request kwargs
+
+        Returns
+        -------
+        dict
+            The JSON response from the server
+        """
+        return self._request_retry(requests.get, url, **kwargs)
+
+    def post(self, url, **kwargs):
+        """Execute a post against the Qiita server
+
+        Parameters
+        ----------
+        url : str
+            The url to access in the server
+        kwargs : dict
+            The request kwargs
+
+        Returns
+        -------
+        dict
+            The JSON response from the server
+        """
+        return self._request_retry(requests.post, url, **kwargs)