Add artifact creation test handler

qiita_db/handlers/artifact.py

@@ -8,6 +8,7 @@
 
 from tornado.web import HTTPError
 from collections import defaultdict
+from json import loads
 
 import qiita_db as qdb
 from .oauth2 import OauthBaseHandler, authenticate_oauth
@@ -136,3 +137,43 @@ def patch(self, artifact_id):
                                  'supported operations: add' % req_op)
 
         self.finish()
+
+
+class ArtifactAPItestHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def post(self):
+        """Creates a new artifact
+
+        Parameters
+        ----------
+        filepaths : str
+            Json string with a list of filepaths and its types
+        type : str
+            The artifact type
+        prep_template: int
+            The id of the template that the new artifact belongs to
+        name : str, optional
+            The artifact name
+
+        Returns
+        -------
+        dict
+            'artifact': the id of the new artifact
+
+        See Also
+        --------
+        qiita_db.artifact.Artifact.create
+        """
+        filepaths = loads(self.get_argument('filepaths'))
+        artifact_type = self.get_argument('type')
+        prep_template = self.get_argument('prep')
+        name = self.get_argument('name', None)
+
+        if prep_template:
+            prep_template = qdb.metadata_template.prep_template.PrepTemplate(
+                prep_template)
+
+        a = qdb.artifact.Artifact.create(
+            filepaths, artifact_type, name=name, prep_template=prep_template)
+
+        self.write({'artifact': a.id})

qiita_db/handlers/oauth2.py

@@ -148,7 +148,11 @@ def write_error(self, status_code, **kwargs):
                 'ERROR:\n%s\nTRACE:\n%s\nHTTP INFO:\n%s\n' %
                 (error, trace_info, request_info))
 
-        self.finish(exc_info[1].log_message)
+        message = exc_info[1].message
+        if hasattr(exc_info[1], 'log_message'):
+            message = exc_info[1].log_message
+
+        self.finish(message)
 
     def head(self):
         """Adds proper response for head requests"""

qiita_db/handlers/tests/test_artifact.py

@@ -12,8 +12,10 @@
 from os.path import join, exists
 from os import close, remove
 from tempfile import mkstemp
+from json import dumps
 
 from tornado.web import HTTPError
+import pandas as pd
 
 from qiita_db.handlers.tests.oauthbase import OauthTestingBase
 import qiita_db as qdb
@@ -122,5 +124,78 @@ def test_patch(self):
         self.assertIn('No such file or directory', obs.body)
 
 
+class ArtifactAPItestHandlerTests(OauthTestingBase):
+    database = True
+
+    def setUp(self):
+        super(ArtifactAPItestHandlerTests, self).setUp()
+
+        metadata_dict = {
+            'SKB8.640193': {'center_name': 'ANL',
+                            'primer': 'GTGCCAGCMGCCGCGGTAA',
+                            'barcode': 'GTCCGCAAGTTA',
+                            'run_prefix': "s_G1_L001_sequences",
+                            'platform': 'ILLUMINA',
+                            'instrument_model': 'Illumina MiSeq',
+                            'library_construction_protocol': 'AAAA',
+                            'experiment_design_description': 'BBBB'}}
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
+        self.prep_template = \
+            qdb.metadata_template.prep_template.PrepTemplate.create(
+                metadata, qdb.study.Study(1), "16S")
+
+        self._clean_up_files = []
+
+    def tearDown(self):
+        super(ArtifactAPItestHandlerTests, self).tearDown()
+
+        for f in self._clean_up_files:
+            if exists(f):
+                remove(f)
+
+    def test_post(self):
+        fd, fp1 = mkstemp(suffix='_seqs.fastq')
+        close(fd)
+        self._clean_up_files.append(fp1)
+        with open(fp1, 'w') as f:
+            f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
+                    "NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
+                    "+\n"
+                    "#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
+
+        fd, fp2 = mkstemp(suffix='_barcodes.fastq')
+        close(fd)
+        self._clean_up_files.append(fp2)
+        with open(fp2, 'w') as f:
+            f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n"
+                    "NNNCNNNNNNNNN\n"
+                    "+\n"
+                    "#############\n")
+
+        data = {'filepaths': dumps([(fp1, 'raw_forward_seqs'),
+                                    (fp2, 'raw_barcodes')]),
+                'type': "FASTQ",
+                'name': "New test artifact",
+                'prep': self.prep_template.id}
+        obs = self.post('/apitest/artifact/', headers=self.header, data=data)
+        self.assertEqual(obs.code, 200)
+        obs = loads(obs.body)
+        self.assertEqual(obs.keys(), ['artifact'])
+
+        a = qdb.artifact.Artifact(obs['artifact'])
+        self._clean_up_files.extend([fp for _, fp, _ in a.filepaths])
+        self.assertEqual(a.name, "New test artifact")
+
+    def test_post_error(self):
+        data = {'filepaths': dumps([('Do not exist', 'raw_forward_seqs')]),
+                'type': "FASTQ",
+                'name': "New test artifact",
+                'prep': 1}
+        obs = self.post('/apitest/artifact/', headers=self.header, data=data)
+        self.assertEqual(obs.code, 500)
+        self.assertIn("Prep template 1 already has an artifact associated",
+                      obs.body)
+
+
 if __name__ == '__main__':
     main()

qiita_pet/webserver.py

@@ -44,7 +44,7 @@
 from qiita_db.handlers.processing_job import (
     JobHandler, HeartbeatHandler, ActiveStepHandler, CompleteHandler,
     ProcessingJobAPItestHandler)
-from qiita_db.handlers.artifact import ArtifactHandler
+from qiita_db.handlers.artifact import ArtifactHandler, ArtifactAPItestHandler
 from qiita_db.handlers.prep_template import (
     PrepTemplateDataHandler, PrepTemplateAPItestHandler,
     PrepTemplateDBHandler)
@@ -168,7 +168,8 @@ def __init__(self):
             test_handlers = [
                 (r"/apitest/processing_job/", ProcessingJobAPItestHandler),
                 (r"/apitest/reset/", ResetAPItestHandler),
-                (r"/apitest/prep_template/", PrepTemplateAPItestHandler)
+                (r"/apitest/prep_template/", PrepTemplateAPItestHandler),
+                (r"/apitest/artifact/", ArtifactAPItestHandler)
             ]
             handlers.extend(test_handlers)