--- a
+++ b/qiita_ware/test/test_commands.py
@@ -0,0 +1,280 @@
+# -----------------------------------------------------------------------------
+# 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 unittest import TestCase, main, skipIf
+from os.path import join, basename, exists
+from tempfile import mkdtemp
+import pandas as pd
+from datetime import datetime
+from shutil import rmtree, copyfile
+from os import path
+from glob import glob
+from paramiko.ssh_exception import AuthenticationException
+
+from h5py import File
+from qiita_files.demux import to_hdf5
+
+from qiita_ware.exceptions import ComputeError
+from qiita_ware.commands import submit_EBI, list_remote, download_remote
+from qiita_db.util import get_mountpoint
+from qiita_db.study import Study, StudyPerson
+from qiita_db.software import DefaultParameters, Parameters
+from qiita_db.artifact import Artifact
+from qiita_db.metadata_template.prep_template import PrepTemplate
+from qiita_db.metadata_template.sample_template import SampleTemplate
+from qiita_db.user import User
+from qiita_core.util import qiita_test_checker
+from qiita_core.qiita_settings import qiita_config
+
+
+@qiita_test_checker()
+class SSHTests(TestCase):
+    def setUp(self):
+        self.self_dir_path = path.dirname(path.abspath(__file__))
+        self.remote_dir_path = join(self.self_dir_path,
+                                    'test_data/test_remote_dir/')
+        self.test_ssh_key = join(self.self_dir_path, 'test_data/test_key')
+        self.test_wrong_key = join(self.self_dir_path, 'test_data/random_key')
+        self.temp_local_dir = mkdtemp()
+        self.exp_files = ['test_0.fastq.gz', 'test_1.txt']
+
+    def tearDown(self):
+        rmtree(self.temp_local_dir)
+
+    def _get_valid_files(self, folder):
+        files = []
+        for x in qiita_config.valid_upload_extension:
+            files.extend([basename(f) for f in glob(join(folder, '*.%s' % x))])
+        return files
+
+    def test_list_scp_wrong_key(self):
+        with self.assertRaises(AuthenticationException):
+            list_remote('scp://runner@localhost:'+self.remote_dir_path,
+                        self.test_wrong_key)
+
+    def test_list_scp_nonexist_key(self):
+        with self.assertRaises(IOError):
+            list_remote('scp://runner@localhost:'+self.remote_dir_path,
+                        join(self.self_dir_path, 'nokey'))
+
+    def test_list_scp(self):
+        kpath = join(self.temp_local_dir, 'tmp-key')
+        copyfile(self.test_ssh_key, kpath)
+        read_file_list = list_remote(
+            'scp://runner@localhost:'+self.remote_dir_path, kpath)
+        self.assertCountEqual(read_file_list, self.exp_files)
+
+    def test_download_scp(self):
+        kpath = join(self.temp_local_dir, 'tmp-key')
+        copyfile(self.test_ssh_key, kpath)
+        download_remote('scp://runner@localhost:'+self.remote_dir_path,
+                        kpath, self.temp_local_dir)
+        local_files = self._get_valid_files(self.temp_local_dir)
+        self.assertCountEqual(local_files, self.exp_files)
+        self.assertFalse(exists(kpath))
+
+
+class CommandsTests(TestCase):
+    def setUp(self):
+        self.files_to_remove = []
+        self.temp_dir = mkdtemp()
+        self.files_to_remove.append(self.temp_dir)
+        _, self.base_fp = get_mountpoint("preprocessed_data")[0]
+
+    def write_demux_files(self, prep_template, generate_hdf5=True):
+        """Writes a demux test file to avoid duplication of code"""
+        fna_fp = join(self.temp_dir, 'seqs.fna')
+        demux_fp = join(self.temp_dir, 'demux.seqs')
+        if generate_hdf5:
+            with open(fna_fp, 'w') as f:
+                f.write(FASTA_EXAMPLE)
+            with File(demux_fp, "w") as f:
+                to_hdf5(fna_fp, f)
+        else:
+            with open(demux_fp, 'w') as f:
+                f.write('')
+
+        if prep_template.artifact is None:
+            ppd = Artifact.create(
+                [(demux_fp, 6)], "Demultiplexed", prep_template=prep_template)
+        else:
+            params = Parameters.from_default_params(
+                DefaultParameters(1),
+                {'input_data': prep_template.artifact.id})
+            ppd = Artifact.create(
+                [(demux_fp, 6)], "Demultiplexed",
+                parents=[prep_template.artifact], processing_parameters=params)
+        return ppd
+
+    def generate_new_study_with_preprocessed_data(self):
+        """Creates a new study up to the processed data for testing"""
+        info = {
+            "timeseries_type_id": 1,
+            "metadata_complete": True,
+            "mixs_compliant": True,
+            "study_alias": "Test EBI",
+            "study_description": "Study for testing EBI",
+            "study_abstract": "Study for testing EBI",
+            "principal_investigator_id": StudyPerson(3),
+            "lab_person_id": StudyPerson(1)
+        }
+        study = Study.create(User('test@foo.bar'), "Test EBI study", info)
+        metadata_dict = {
+            'Sample1': {'collection_timestamp': datetime(2015, 6, 1, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 1'},
+            'Sample2': {'collection_timestamp': datetime(2015, 6, 2, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 2'},
+            'Sample3': {'collection_timestamp': datetime(2015, 6, 3, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 3'}
+        }
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
+                                          dtype=str)
+        SampleTemplate.create(metadata, study)
+        metadata_dict = {
+            'Sample1': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTC',
+                        'center_name': 'KnightLab',
+                        'platform': 'Illumina',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 1"},
+            'Sample2': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTA',
+                        'center_name': 'KnightLab',
+                        'platform': 'Illumina',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 2"},
+            'Sample3': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTT',
+                        'center_name': 'KnightLab',
+                        'platform': 'Illumina',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 3"},
+        }
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
+                                          dtype=str)
+        pt = PrepTemplate.create(metadata, study, "16S", 'Metagenomics')
+        fna_fp = join(self.temp_dir, 'seqs.fna')
+        demux_fp = join(self.temp_dir, 'demux.seqs')
+        with open(fna_fp, 'w') as f:
+            f.write(FASTA_EXAMPLE_2.format(study.id))
+        with File(demux_fp, 'w') as f:
+            to_hdf5(fna_fp, f)
+
+        ppd = Artifact.create(
+            [(demux_fp, 6)], "Demultiplexed", prep_template=pt)
+
+        return ppd
+
+    def test_submit_EBI_step_2_failure(self):
+        ppd = self.write_demux_files(PrepTemplate(1), True)
+        pid = ppd.id
+
+        with self.assertRaises(ComputeError):
+            submit_EBI(pid, 'VALIDATE', True)
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
+
+    @skipIf(
+        qiita_config.ebi_seq_xfer_pass == '', 'skip: ascp not configured')
+    def test_submit_EBI_parse_EBI_reply_failure(self):
+        ppd = self.write_demux_files(PrepTemplate(1))
+        pid = ppd.id
+
+        with self.assertRaises(ComputeError) as error:
+            submit_EBI(pid, 'VALIDATE', True)
+        error = str(error.exception)
+        self.assertIn('EBI Submission failed! Log id:', error)
+        self.assertIn('The EBI submission failed:', error)
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
+
+    @skipIf(
+        qiita_config.ebi_seq_xfer_pass == '', 'skip: ascp not configured')
+    def test_full_submission(self):
+        artifact = self.generate_new_study_with_preprocessed_data()
+        self.assertEqual(
+            artifact.study.ebi_submission_status, 'not submitted')
+        aid = artifact.id
+        submit_EBI(aid, 'VALIDATE', True, test=True)
+        self.assertEqual(artifact.study.ebi_submission_status, 'submitted')
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
+
+    def test_max_ebiena_curl_error(self):
+        artifact = self.generate_new_study_with_preprocessed_data()
+        self.assertEqual(
+            artifact.study.ebi_submission_status, 'not submitted')
+        aid = artifact.id
+        with self.assertRaises(ComputeError) as error:
+            submit_EBI(aid, 'VALIDATE', True, test_size=True)
+        error = str(error.exception)
+        self.assertIn('is too large. Before cleaning:', error)
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
+
+
+FASTA_EXAMPLE = """>1.SKB2.640194_1 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKB2.640194_2 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKB2.640194_3 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKM4.640180_4 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKM4.640180_5 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKB3.640195_6 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKB6.640176_7 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKD6.640190_8 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKM6.640187_9 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKD9.640182_10 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKM8.640201_11 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>1.SKM2.640199_12 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+"""
+
+FASTA_EXAMPLE_2 = """>{0}.Sample1_1 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample1_2 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample1_3 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample2_4 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample2_5 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample2_6 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample3_7 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample3_8 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+>{0}.Sample3_9 X orig_bc=X new_bc=X bc_diffs=0
+CCACCCAGTAAC
+"""
+
+
+if __name__ == '__main__':
+    main()