Merge pull request #1800 from josenavas/fix-rest-api-target-gene

Fix target gene plugin

qiita_plugins/target_gene/tgp/pick_otus.py

@@ -11,8 +11,6 @@
 from glob import glob
 from tarfile import open as taropen
 
-from qiita_client import format_payload
-
 from tgp.util import system_call
 
 
@@ -156,24 +154,10 @@ def pick_closed_reference_otus(qclient, job_id, parameters, out_dir):
     qclient.update_job_step(job_id, "Step 1 of 4: Collecting information")
     artifact_id = parameters['input_data']
     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:
-            error_msg = error_msg % fps_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
     fps = fps_info['filepaths']
 
     reference_id = parameters['reference']
     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:
-            error_msg = error_msg % ref_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
     reference_fps = ref_info['filepaths']
 
     qclient.update_job_step(job_id, "Step 2 of 4: Generating command")
@@ -185,16 +169,16 @@ def pick_closed_reference_otus(qclient, job_id, parameters, out_dir):
     if return_value != 0:
         error_msg = ("Error running OTU picking:\nStd out: %s\nStd err: %s"
                      % (std_out, std_err))
-        return format_payload(False, error_msg=error_msg)
+        return False, None, error_msg
 
     qclient.update_job_step(job_id,
                             "Step 4 of 4: Generating tgz sortmerna folder")
     try:
         generate_sortmerna_tgz(pick_out)
     except Exception as e:
         error_msg = ("Error while tgz failures:\nError: %s" % str(e))
-        return format_payload(False, error_msg=error_msg)
+        return False, None, error_msg
 
     artifacts_info = generate_artifact_info(pick_out)
 
-    return format_payload(True, artifacts_info=artifacts_info)
+    return True, artifacts_info, ""

qiita_plugins/target_gene/tgp/plugin.py

@@ -12,7 +12,7 @@
 from os import makedirs, environ
 from future import standard_library
 
-from qiita_client import QiitaClient, format_payload
+from qiita_client import QiitaClient
 
 from tgp.split_libraries import split_libraries, split_libraries_fastq
 from tgp.pick_otus import pick_closed_reference_otus
@@ -43,39 +43,35 @@ def execute_job(server_url, job_id, output_dir):
         If there is a problem gathering the job information
     """
     # Set up the Qiita Client
-    try:
-        conf_fp = environ['QP_TARGET_GENE_CONFIG_FP']
-    except KeyError:
-        conf_fp = join(dirname(abspath(__file__)), 'support_files',
-                       'config_file.cfg')
-
+    dflt_conf_fp = join(dirname(abspath(__file__)), 'support_files',
+                        'config_file.cfg')
+    conf_fp = environ.get('QP_TARGET_GENE_CONFIG_FP', dflt_conf_fp)
     config = ConfigParser()
     with open(conf_fp, 'U') as conf_file:
         config.readfp(conf_file)
+
     qclient = QiitaClient(server_url, config.get('main', 'CLIENT_ID'),
                           config.get('main', 'CLIENT_SECRET'),
                           server_cert=config.get('main', 'SERVER_CERT'))
 
-    # Request job information
+    # Request job information. If there is a problem retrieving the job
+    # information, the QiitaClient already raises an error
     job_info = qclient.get_job_info(job_id)
-    # Check if we have received the job information so we can start it
-    if job_info and job_info['success']:
-        # Starting the heartbeat
-        qclient.start_heartbeat(job_id)
-        # Execute the given task
-        task_name = job_info['command']
-        task = TASK_DICT[task_name]
+    # Starting the heartbeat
+    qclient.start_heartbeat(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(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
-        qclient.complete_job(job_id, payload)
-    else:
-        raise RuntimeError("Can't get job (%s) information" % job_id)
+    if not exists(output_dir):
+        makedirs(output_dir)
+    try:
+        success, artifacts_info, error_msg = 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))
+        success = False
+    # The job completed
+    qclient.complete_job(job_id, success, error_msg=error_msg,
+                         artifacts_info=artifacts_info)

qiita_plugins/target_gene/tgp/split_libraries/split_libraries.py

@@ -8,8 +8,6 @@
 
 from os.path import join, basename, splitext
 
-from qiita_client import format_payload
-
 from tgp.util import system_call
 from .util import (get_artifact_information, split_mapping_file,
                    generate_demux_file, generate_artifact_info)
@@ -290,4 +288,4 @@ def split_libraries(qclient, job_id, parameters, out_dir):
 
     artifacts_info = generate_artifact_info(output_dir)
 
-    return format_payload(True, artifacts_info=artifacts_info)
+    return False, artifacts_info, ""

qiita_plugins/target_gene/tgp/split_libraries/split_libraries_fastq.py

@@ -10,7 +10,6 @@
 import re
 
 import pandas as pd
-from qiita_client import format_payload
 
 from tgp.util import system_call
 from .util import (get_artifact_information, split_mapping_file,
@@ -267,4 +266,4 @@ def split_libraries_fastq(qclient, job_id, parameters, out_dir):
 
     artifacts_info = generate_artifact_info(sl_out)
 
-    return format_payload(True, artifacts_info=artifacts_info)
+    return True, artifacts_info, ""

qiita_plugins/target_gene/tgp/split_libraries/tests/test_util.py

@@ -50,17 +50,15 @@ def test_get_artifact_information(self):
             httpretty.GET,
             "https://test_server.com/qiita_db/artifacts/1/filepaths/",
             body='{"filepaths": [["forward_seqs.fastq.gz", "raw_forward_seqs"]'
-                 ', ["barcodes.fastq.gz", "raw_barcodes"]], "success": true, '
-                 '"error": ""}')
+                 ', ["barcodes.fastq.gz", "raw_barcodes"]]}')
         httpretty.register_uri(
             httpretty.GET,
             "https://test_server.com/qiita_db/artifacts/1/mapping/",
-            body='{"mapping": "mapping_file.txt", "success": true, '
-                 '"error": ""}')
+            body='{"mapping": "mapping_file.txt"}')
         httpretty.register_uri(
             httpretty.GET,
             "https://test_server.com/qiita_db/artifacts/1/type/",
-            body='{"type": "FASTQ", "success": true, "error": ""}')
+            body='{"type": "FASTQ"}')
 
         obs_fps, obs_mf, obs_at = get_artifact_information(self.qclient, 1)
 
@@ -70,17 +68,6 @@ def test_get_artifact_information(self):
         self.assertEqual(obs_mf, "mapping_file.txt")
         self.assertEqual(obs_at, "FASTQ")
 
-    @httpretty.activate
-    def test_get_artifact_error(self):
-        # Mock the URIs
-        httpretty.register_uri(
-            httpretty.GET,
-            "https://test_server.com/qiita_db/artifacts/1/filepaths/",
-            body='{"filepaths": '', "success": false, "error": "some error"}')
-
-        with self.assertRaises(ValueError):
-            get_artifact_information(self.qclient, 1)
-
     def test_split_mapping_file_single(self):
         out_dir = mkdtemp()
         self._clean_up_files.append(out_dir)

qiita_plugins/target_gene/tgp/split_libraries/util.py

@@ -42,36 +42,15 @@ def get_artifact_information(qclient, artifact_id):
     """
     # Get the artifact filepath information
     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:
-            error_msg = error_msg % fps_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
     fps = fps_info['filepaths']
 
     # Get the artifact metadata
     metadata_info = qclient.get(
         "/qiita_db/artifacts/%s/mapping/" % artifact_id)
-    if not metadata_info or not metadata_info['success']:
-        error_msg = "Could not get artifact metadata information %s"
-        if metadata_info:
-            error_msg = error_msg % metadata_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
     mapping_file = metadata_info['mapping']
 
     # Get the artifact type
     type_info = qclient.get("/qiita_db/artifacts/%s/type/" % artifact_id)
-    if not type_info or not type_info['success']:
-        error_msg = "Could not get artifact metadata information %s"
-        if type_info:
-            error_msg = error_msg % type_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
     artifact_type = type_info['type']
 
     return fps, mapping_file, artifact_type