Fixing tests

.travis.yml

@@ -30,7 +30,15 @@ install:
   - pip install sphinx sphinx-bootstrap-theme coveralls 'ipython[all]==2.4.1'
   - travis_retry pip install . --process-dependency-links
   - 'echo "backend: Agg" > matplotlibrc'
-script:
+  # Install the biom plugin so we can run the analysis tests
+  - pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
+  - pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip --process-dependency-links
+  - export QIITA_SERVER_CERT=`pwd`/qiita_core/support_files/server.crt
+  - mkdir ~/.qiita_plugins
+  - cp $PWD/qiita_core/support_files/BIOM\ type_2.1.4.conf ~/.qiita_plugins
+before_script:
+    # Some of the tests rely on the plugin system to complete successfuly.
+    # Thus, we need a qiita webserver running to be able to execute the tests.
   - export MOI_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
   - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then
     export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test_travis.cfg;
@@ -39,6 +47,12 @@ script:
   - ipython profile create qiita-general --parallel
   - qiita-env start_cluster qiita-general
   - qiita-env make --no-load-ontologies
+  - |
+    if [ ${TEST_ADD_STUDIES} == "False" ]; then
+        qiita pet webserver --no-build-docs start &
+    fi
+script:
+  - sleep 5
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then qiita-cron-job ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita-test-install ; fi

qiita_core/support_files/BIOM type_2.1.4.conf

@@ -0,0 +1,13 @@
+[main]
+NAME = BIOM type
+VERSION = 2.1.4
+DESCRIPTION = The Biological Observation Matrix format
+ENVIRONMENT_SCRIPT = source activate qtp-biom
+START_SCRIPT = start_biom
+PLUGIN_TYPE = artifact definition
+PUBLICATIONS =
+
+[oauth2]
+SERVER_CERT = /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_core/support_files/server.crt
+CLIENT_ID = dHgaXDwq665ksFPqfIoD3Jt8KRXdSioTRa4lGa5mGDnz6JTIBf
+CLIENT_SECRET = xqx61SD4M2EWbaS0WYv3H1nIemkvEAMIn16XMLjy5rTCqi7opCcWbfLINEwtV48bQ

qiita_core/support_files/config_test.cfg

@@ -23,7 +23,7 @@ LOG_DIR =
 REQUIRE_APPROVAL = True
 
 # Base URL: DO NOT ADD TRAILING SLASH
-BASE_URL = https://localhost
+BASE_URL = https://localhost:21174
 
 # Download path files
 UPLOAD_DATA_DIR = /tmp/
@@ -35,7 +35,7 @@ WORKING_DIR = /tmp/
 MAX_UPLOAD_SIZE = 100
 
 # Path to the base directory where the data files are going to be stored
-BASE_DATA_DIR =
+BASE_DATA_DIR = /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_db/support_files/test_data/
 
 # Valid upload extension, comma separated. Empty for no uploads
 VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual

qiita_db/artifact.py

@@ -311,8 +311,7 @@ def create(cls, filepaths, artifact_type, name=None, prep_template=None,
         # them execute a set of common operations. Declare functions to avoid
         # code duplication. These functions should not be used outside of the
         # create function, hence declaring them here
-        def _common_creation_steps(atype, cmd_id, data_type, cmd_parameters,
-                                   fps, mv_files):
+        def _common_creation_steps(atype, cmd_id, data_type, cmd_parameters):
             gen_timestamp = datetime.now()
             visibility_id = qdb.util.convert_to_id("sandbox", "visibility")
             atype_id = qdb.util.convert_to_id(atype, "artifact_type")
@@ -328,15 +327,6 @@ def _common_creation_steps(atype, cmd_id, data_type, cmd_parameters,
                         cmd_parameters, visibility_id, atype_id, False]
             qdb.sql_connection.TRN.add(sql, sql_args)
             a_id = qdb.sql_connection.TRN.execute_fetchlast()
-            # Associate the artifact with its filepaths
-            fp_ids = qdb.util.insert_filepaths(
-                fps, a_id, atype, "filepath",
-                move_files=mv_files, copy=(not mv_files))
-            sql = """INSERT INTO qiita.artifact_filepath
-                        (artifact_id, filepath_id)
-                     VALUES (%s, %s)"""
-            sql_args = [[a_id, fp_id] for fp_id in fp_ids]
-            qdb.sql_connection.TRN.add(sql, sql_args, many=True)
             qdb.sql_connection.TRN.execute()
 
             return cls(a_id)
@@ -398,8 +388,7 @@ def _associate_with_analysis(instance, analysis_id):
 
                     instance = _common_creation_steps(
                         artifact_type, processing_parameters.command.id,
-                        dtypes.pop(), processing_parameters.dump(), filepaths,
-                        move_files)
+                        dtypes.pop(), processing_parameters.dump())
 
                     _associate_with_study(instance, study_id)
                 else:
@@ -411,8 +400,7 @@ def _associate_with_analysis(instance, analysis_id):
                                  if len(dtypes) > 1 else dtypes.pop())
                     instance = _common_creation_steps(
                         artifact_type, processing_parameters.command.id,
-                        data_type, processing_parameters.dump(), filepaths,
-                        move_files)
+                        data_type, processing_parameters.dump())
                     _associate_with_analysis(instance, analysis_id)
 
                 # Associate the artifact with its parents
@@ -436,20 +424,28 @@ def _associate_with_analysis(instance, analysis_id):
                 # This artifact is uploaded by the user in the
                 # processing pipeline
                 instance = _common_creation_steps(
-                    artifact_type, None, prep_template.data_type(), None,
-                    filepaths, move_files)
+                    artifact_type, None, prep_template.data_type(), None)
                 # Associate the artifact with the prep template
                 prep_template.artifact = instance
                 # Associate the artifact with the study
                 _associate_with_study(instance, prep_template.study_id)
             else:
                 # This artifact is an initial artifact of an analysis
                 instance = _common_creation_steps(
-                    artifact_type, None, data_type, None, filepaths,
-                    move_files)
+                    artifact_type, None, data_type, None)
                 # Associate the artifact with the analysis
                 analysis.add_artifact(instance)
 
+            # Associate the artifact with its filepaths
+            fp_ids = qdb.util.insert_filepaths(
+                filepaths, instance.id, artifact_type, "filepath",
+                move_files=move_files, copy=(not move_files))
+            sql = """INSERT INTO qiita.artifact_filepath
+                        (artifact_id, filepath_id)
+                     VALUES (%s, %s)"""
+            sql_args = [[instance.id, fp_id] for fp_id in fp_ids]
+            qdb.sql_connection.TRN.add(sql, sql_args, many=True)
+
             if name:
                 instance.name = name
 

qiita_db/handlers/tests/test_plugin.py

@@ -56,7 +56,9 @@ def test_get(self):
                            'for performing microbiome analysis from raw DNA '
                            'sequencing data',
             'commands': ['Split libraries FASTQ', 'Split libraries',
-                         'Pick closed-reference OTUs'],
+                         'Pick closed-reference OTUs', 'Summarize Taxa',
+                         'Beta Diversity', 'Alpha Rarefaction',
+                         'Single Rarefaction'],
             'publications': [{'DOI': '10.1038/nmeth.f.303',
                               'PubMed': '20383131'}],
             'default_workflows': ['FASTQ upstream workflow',

qiita_db/metadata_template/test/test_prep_template.py

@@ -930,7 +930,6 @@ def test_create_data_type_id(self):
     def test_create_warning(self):
         """Warns if a required columns is missing for a given functionality
         """
-        fp_count = qdb.util.get_count("qiita.filepath")
         del self.metadata['barcode']
         pt = npt.assert_warns(
             qdb.exceptions.QiitaDBWarning,

qiita_db/test/test_analysis.py

@@ -66,6 +66,8 @@ def tearDown(self):
     def _wait_for_jobs(self, analysis):
         for j in analysis.jobs:
             wait_for_processing_job(j.id)
+            if j.status == 'error':
+                print j.log.msg
 
     def _create_analyses_with_samples(self, user='demo@microbio.me',
                                       merge=False):
@@ -129,21 +131,11 @@ def test_can_be_publicized(self):
         analysis = qdb.analysis.Analysis(1)
         self.assertFalse(analysis.can_be_publicized)
         a4 = qdb.artifact.Artifact(4)
-        a5 = qdb.artifact.Artifact(5)
-        a6 = qdb.artifact.Artifact(6)
 
         a4.visibility = 'public'
-        self.assertFalse(analysis.can_be_publicized)
-
-        a5.visibility = 'public'
-        self.assertFalse(analysis.can_be_publicized)
-
-        a6.visibility = 'public'
         self.assertTrue(analysis.can_be_publicized)
 
         a4.visibility = 'private'
-        a5.visibility = 'private'
-        a6.visibility = 'private'
         self.assertFalse(analysis.can_be_publicized)
 
     def test_add_artifact(self):

qiita_db/test/test_setup.py

@@ -36,7 +36,7 @@ def test_study_experimental_factor(self):
         self.assertEqual(get_count("qiita.study_experimental_factor"), 1)
 
     def test_filepath(self):
-        self.assertEqual(get_count("qiita.filepath"), 26)
+        self.assertEqual(get_count("qiita.filepath"), 25)
 
     def test_filepath_type(self):
         self.assertEqual(get_count("qiita.filepath_type"), 21)
@@ -66,7 +66,7 @@ def test_analysis(self):
         self.assertEqual(get_count("qiita.analysis"), 10)
 
     def test_analysis_filepath(self):
-        self.assertEqual(get_count("qiita.analysis_filepath"), 2)
+        self.assertEqual(get_count("qiita.analysis_filepath"), 1)
 
     def test_analysis_sample(self):
         self.assertEqual(get_count("qiita.analysis_sample"), 31)