def render(self, raw_data_id, prep_template, study, files):
        rd = RawData(raw_data_id)
        raw_data_files = [(basename(fp), fp_type[4:])
                          for _, fp, fp_type in rd.get_filepaths()]
        filetype = rd.filetype
        fp_types = fp_type_by_ft[filetype]
        raw_data_link_status = rd.link_filepaths_status

        show_buttons = rd.status(study) == 'sandbox'
        link_msg = ""
        if show_buttons:
            # Define the message for the link status
            if raw_data_link_status == 'linking':
                link_msg = "Linking files..."
                show_buttons = False
            elif raw_data_link_status == 'unlinking':
                link_msg = "Unlinking files..."
                show_buttons = False
            elif raw_data_link_status.startswith('failed'):
                link_msg = "Error (un)linking files: %s" % raw_data_link_status

        link_msg = convert_text_html(link_msg)
        return self.render_string(
            "study_description_templates/raw_data_info.html",
            rd_id=raw_data_id,
            rd_filetype=rd.filetype,
            raw_data_files=raw_data_files,
            prep_template_id=prep_template.id,
            files=files,
            filepath_types=fp_types,
            filetype=filetype,
            link_msg=link_msg,
            show_buttons=show_buttons)

    def delete_raw_data(self, study, user, callback):
        """Delete the selected raw data

        Parameters
        ----------
        study : Study
            The current study object
        user : User
            The current user object
        callback : function
            The callback function to call with the results once the processing
            is done
        """
        raw_data_id = int(self.get_argument('raw_data_id'))
        prep_template_id = int(self.get_argument('prep_template_id'))

        try:
            RawData.delete(raw_data_id, prep_template_id)
            msg = ("Raw data %d has been deleted from prep_template %d"
                   % (raw_data_id, prep_template_id))
            msg_level = "success"
        except Exception as e:
            msg = "Couldn't remove raw data %d: %s" % (raw_data_id, str(e))
            msg_level = "danger"

        callback((msg, msg_level, "prep_template_tab", prep_template_id, None))

    def test_status_error(self):
        # Let's create a new study, so we can check that the error is raised
        # because the new study does not have access to the raw data
        info = {
            "timeseries_type_id": 1,
            "metadata_complete": True,
            "mixs_compliant": True,
            "number_samples_collected": 25,
            "number_samples_promised": 28,
            "portal_type_id": 3,
            "study_alias": "FCM",
            "study_description": "Microbiome of people who eat nothing but "
                                 "fried chicken",
            "study_abstract": "Exploring how a high fat diet changes the "
                              "gut microbiome",
            "emp_person_id": StudyPerson(2),
            "principal_investigator_id": StudyPerson(3),
            "lab_person_id": StudyPerson(1)
        }
        s = Study.create(User('[email protected]'), "Fried chicken microbiome",
                         [1], info)
        rd = RawData(1)

        with self.assertRaises(QiitaDBStatusError):
            rd.status(s)

    def delete_raw_data(self, study, user, callback):
        """Delete the selected raw data

        Parameters
        ----------
        study : Study
            The current study object
        user : User
            The current user object
        callback : function
            The callback function to call with the results once the processing
            is done
        """
        raw_data_id = int(self.get_argument('raw_data_id'))

        try:
            RawData.delete(raw_data_id, study.id)
            msg = ("Raw data %d has been deleted from study: "
                   "<b><i>%s</i></b>" % (raw_data_id, study.title))
            msg_level = "success"
            tab = 'study_information_tab'
            tab_id = None
        except Exception as e:
            msg = "Couldn't remove %d raw data: %s" % (raw_data_id, str(e))
            msg_level = "danger"
            tab = 'raw_data_tab'
            tab_id = raw_data_id

        callback((msg, msg_level, tab, tab_id, None))

def unlink_all_files(raw_data_id):
    """Removes all files from raw data

    Needs to be dispachable because it does I/O and a lot of DB calls
    """
    rd = RawData(raw_data_id)
    rd.clear_filepaths()

def add_files_to_raw_data(raw_data_id, filepaths):
    """Add files to raw data

    Needs to be dispachable because it moves large files
    """
    rd = RawData(raw_data_id)
    rd.add_filepaths(filepaths)

 def test_get_filepaths(self):
     """Correctly returns the filepaths to the raw files"""
     rd = RawData(1)
     obs = rd.get_filepaths()
     exp = [
         (join(self.db_test_raw_dir, '1_s_G1_L001_sequences.fastq.gz'), 1),
         (join(self.db_test_raw_dir,
               '1_s_G1_L001_sequences_barcodes.fastq.gz'), 2)]
     self.assertEqual(obs, exp)

class QiitaBaseTest(TestCase):
    """Tests that the base class functions act correctly"""

    def setUp(self):
        # We need an actual subclass in order to test the equality functions
        self.tester = RawData(1)

    def test_init_base_error(self):
        """Raises an error when instantiating a base class directly"""
        with self.assertRaises(IncompetentQiitaDeveloperError):
            QiitaObject(1)

    def test_init_error_inexistent(self):
        """Raises an error when instantiating an object that does not exists"""
        with self.assertRaises(QiitaDBUnknownIDError):
            RawData(10)

    def test_check_subclass(self):
        """Nothing happens if check_subclass called from a subclass"""
        self.tester._check_subclass()

    def test_check_subclass_error(self):
        """check_subclass raises an error if called from a base class"""
        # Checked through the __init__ call
        with self.assertRaises(IncompetentQiitaDeveloperError):
            QiitaObject(1)
        with self.assertRaises(IncompetentQiitaDeveloperError):
            QiitaStatusObject(1)

    def test_check_id(self):
        """Correctly checks if an id exists on the database"""
        self.assertTrue(self.tester._check_id(1))
        self.assertFalse(self.tester._check_id(100))

    def test_equal_self(self):
        """Equality works with the same object"""
        self.assertEqual(self.tester, self.tester)

    def test_equal(self):
        """Equality works with two objects pointing to the same instance"""
        new = RawData(1)
        self.assertEqual(self.tester, new)

    def test_not_equal(self):
        """Not equals works with object of the same type"""
        new = RawData(2)
        self.assertNotEqual(self.tester, new)

    def test_not_equal_type(self):
        """Not equals works with object of different type"""
        new = Study(1)
        self.assertNotEqual(self.tester, new)

    def test_get_preprocess_fastq_cmd_per_sample_FASTQ_failure(self):
        metadata_dict = {
            'SKB8.640193': {'run_prefix': "sample1_failure", 'primer': 'A',
                            'barcode': 'A', 'center_name': 'ANL',
                            'platform': 'ILLUMINA',
                            'library_construction_protocol': 'A',
                            'experiment_design_description': 'A'}}
        md_template = pd.DataFrame.from_dict(metadata_dict, orient='index')
        prep_template = PrepTemplate.create(md_template, Study(1), '16S')

        # This part should fail
        fp1 = self.path_builder('sample1_failure.fastq')
        with open(fp1, 'w') as f:
            f.write('\n')
        self.files_to_remove.append(fp1)
        fp2 = self.path_builder('sample1_failure.barcodes.fastq.gz')
        with open(fp2, 'w') as f:
            f.write('\n')
        self.files_to_remove.append(fp2)
        forward_filepath_id = convert_to_id('raw_forward_seqs',
                                            'filepath_type')
        barcode_filepath_id = convert_to_id('raw_barcodes', 'filepath_type')

        fps = [(fp1, forward_filepath_id), (fp2, barcode_filepath_id)]

        filetype_id = get_filetypes()['per_sample_FASTQ']
        raw_data = RawData.create(filetype_id, [prep_template], fps)
        params = [p for p in list(PreprocessedIlluminaParams.iter())
                  if p.name == 'per sample FASTQ defaults'][0]

        with self.assertRaises(ValueError):
            _get_preprocess_fastq_cmd(raw_data, prep_template, params)

    def test_status(self):
        rd = RawData(1)
        s = Study(1)
        self.assertEqual(rd.status(s), 'private')

        # Since the status is inferred from the processed data, change the
        # status of the processed data so we can check how it changes in the
        # preprocessed data
        pd = ProcessedData(1)
        pd.status = 'public'
        self.assertEqual(rd.status(s), 'public')

        # Check that new raw data has sandbox as status since no
        # processed data exists for them
        rd = RawData.create(self.filetype, self.studies, self.filepaths)
        self.assertEqual(rd.status(s), 'sandbox')

    def test_move_filepaths_to_upload_folder(self):
        # setting up test, done here as this is the only test that uses these
        # files
        fd, seqs_fp = mkstemp(suffix='_seqs.fastq')
        close(fd)
        study_id = 1

        rd = RawData.create(2, [Study(study_id)], [(seqs_fp, 1)])
        filepaths = rd.get_filepaths()
        # deleting reference so we can directly call
        # move_filepaths_to_upload_folder
        for fid, _, _ in filepaths:
            self.conn_handler.execute(
                "DELETE FROM qiita.raw_filepath WHERE filepath_id=%s", (fid,))

        # moving filepaths
        move_filepaths_to_upload_folder(study_id, filepaths, self.conn_handler)

        # check that they do not exist in the old path but do in the new one
        path_for_removal = join(get_mountpoint("uploads")[0][1], str(study_id))
        for _, fp, _ in filepaths:
            self.assertFalse(exists(fp))
            new_fp = join(path_for_removal, basename(fp).split('_', 1)[1])
            self.assertTrue(exists(new_fp))

            self.files_to_remove.append(new_fp)

 def test_clear_filepaths(self):
     rd = RawData.create(self.filetype, self.studies, self.filepaths)
     self.assertTrue(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE raw_data_id=%s)", (rd.id,))[0])
     rd.clear_filepaths()
     self.assertFalse(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE raw_data_id=%s)", (rd.id,))[0])

 def test_remove_filepath(self):
     rd = RawData.create(self.filetype, self.studies, self.filepaths)
     fp = join(self.db_test_raw_dir, "3_%s" % basename(self.seqs_fp))
     rd.remove_filepath(fp)
     self.assertFalse(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE filepath_id=17)")[0])
     self.assertTrue(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE filepath_id=18)")[0])

 def test_link_filepaths_status_setter(self):
     rd = RawData(1)
     self.assertEqual(rd.link_filepaths_status, 'idle')
     rd._set_link_filepaths_status('linking')
     self.assertEqual(rd.link_filepaths_status, 'linking')
     rd._set_link_filepaths_status('unlinking')
     self.assertEqual(rd.link_filepaths_status, 'unlinking')
     rd._set_link_filepaths_status('failed: error')
     self.assertEqual(rd.link_filepaths_status, 'failed: error')

    def test_create(self):
        """Correctly creates all the rows in the DB for the raw data"""
        # Check that the returned object has the correct id
        exp_id = get_count("qiita.raw_data") + 1
        obs = RawData.create(self.filetype, self.prep_templates,
                             self.filepaths)
        self.assertEqual(obs.id, exp_id)

        # Check that the raw data have been correctly added to the DB
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.raw_data WHERE raw_data_id=%d" % exp_id)
        # raw_data_id, filetype, link_filepaths_status
        self.assertEqual(obs, [[exp_id, 2, 'idle']])

        # Check that the raw data has been correctly linked with the prep
        # templates
        sql = """SELECT prep_template_id
                 FROM qiita.prep_template
                 WHERE raw_data_id = %s
                 ORDER BY prep_template_id"""
        obs = self.conn_handler.execute_fetchall(sql, (exp_id,))
        self.assertEqual(obs, [[self.pt1.id], [self.pt2.id]])

        # Check that the files have been copied to right location
        exp_seqs_fp = join(self.db_test_raw_dir,
                           "%d_%s" % (exp_id, basename(self.seqs_fp)))
        self.assertTrue(exists(exp_seqs_fp))
        self._clean_up_files.append(exp_seqs_fp)

        exp_bc_fp = join(self.db_test_raw_dir,
                         "%d_%s" % (exp_id, basename(self.barcodes_fp)))
        self.assertTrue(exists(exp_bc_fp))
        self._clean_up_files.append(exp_bc_fp)

        # Check that the filepaths have been correctly added to the DB
        top_id = self.conn_handler.execute_fetchone(
            "SELECT count(1) FROM qiita.filepath")[0]
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.filepath WHERE filepath_id=%d or "
            "filepath_id=%d" % (top_id - 1, top_id))
        exp_seqs_fp = "%d_%s" % (exp_id, basename(self.seqs_fp))
        exp_bc_fp = "%d_%s" % (exp_id, basename(self.barcodes_fp))
        # filepath_id, path, filepath_type_id
        exp = [[top_id - 1, exp_seqs_fp, 1, '852952723', 1, 5],
               [top_id, exp_bc_fp, 2, '852952723', 1, 5]]
        self.assertEqual(obs, exp)

        # Check that the raw data have been correctly linked with the filepaths
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.raw_filepath WHERE raw_data_id=%d" % exp_id)
        # raw_data_id, filepath_id
        self.assertEqual(obs, [[exp_id, top_id - 1], [exp_id, top_id]])

    def create_raw_data(self, study, user, callback):
        """Adds a (new) raw data to the study

        Parameters
        ----------
        study : Study
            The current study object
        user : User
            The current user object
        callback : function
            The callback function to call with the results once the processing
            is done
        """
        msg = "Raw data successfully added"
        msg_level = "success"

        # Get the arguments needed to create a raw data object
        filetype = self.get_argument('filetype', None)
        previous_raw_data = self.get_argument('previous_raw_data', None)

        if filetype and previous_raw_data:
            # The user selected a filetype and an existing raw data
            msg = ("You can not specify both a new raw data and a previously "
                   "used one")
            msg_level = "danger"
        elif filetype:
            # We are creating a new raw data object
            try:
                rd_id = RawData.create(filetype, [study]).id
            except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
                    QiitaDBDuplicateError, IOError, ValueError, KeyError,
                    CParserError) as e:
                msg = html_error_message % (
                    "creating a new raw data object for study:",
                    str(study.id), str(e))
                msg_level = "danger"
        elif previous_raw_data:
            previous_raw_data = previous_raw_data.split(',')
            raw_data = [RawData(rd) for rd in previous_raw_data]
            study.add_raw_data(raw_data)
            rd_id = raw_data[0].id
        else:
            # The user did not provide a filetype neither an existing raw data
            # If using the interface, we should never reach this if, but
            # better be safe than sorry
            msg = ("You should choose a filetype for a new raw data or "
                   "choose a raw data previously used")
            msg_level = "danger"
            rd_id = None

        callback((msg, msg_level, 'raw_data_tab', rd_id, None))

    def setUp(self):
        metadata_dict = {
            'SKB8.640193': {'center_name': 'ANL',
                            'center_project_name': 'Test Project',
                            'ebi_submission_accession': None,
                            'EMP_status_id': 1,
                            'data_type_id': 2,
                            'str_column': 'Value for sample 1'},
            'SKD8.640184': {'center_name': 'ANL',
                            'center_project_name': 'Test Project',
                            'ebi_submission_accession': None,
                            'EMP_status_id': 1,
                            'data_type_id': 2,
                            'str_column': 'Value for sample 2'},
            'SKB7.640196': {'center_name': 'ANL',
                            'center_project_name': 'Test Project',
                            'ebi_submission_accession': None,
                            'EMP_status_id': 1,
                            'data_type_id': 2,
                            'str_column': 'Value for sample 3'}
            }
        self.metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
        self.test_raw_data = RawData(1)

        fd, seqs_fp = mkstemp(suffix='_seqs.fastq')
        close(fd)
        fd, barcodes_fp = mkstemp(suffix='_barcodes.fastq')
        close(fd)
        filepaths = [(seqs_fp, 1), (barcodes_fp, 2)]
        with open(seqs_fp, "w") as f:
            f.write("\n")
        with open(barcodes_fp, "w") as f:
            f.write("\n")
        self.new_raw_data = RawData.create(2, filepaths, [Study(1)])
        db_test_raw_dir = join(get_db_files_base_dir(), 'raw_data')
        db_seqs_fp = join(db_test_raw_dir, "3_%s" % basename(seqs_fp))
        db_barcodes_fp = join(db_test_raw_dir, "3_%s" % basename(barcodes_fp))
        self._clean_up_files = [db_seqs_fp, db_barcodes_fp]

        self.tester = PrepTemplate(1)
        self.exp_sample_ids = {'SKB1.640202', 'SKB2.640194', 'SKB3.640195',
                               'SKB4.640189', 'SKB5.640181', 'SKB6.640176',
                               'SKB7.640196', 'SKB8.640193', 'SKB9.640200',
                               'SKD1.640179', 'SKD2.640178', 'SKD3.640198',
                               'SKD4.640185', 'SKD5.640186', 'SKD6.640190',
                               'SKD7.640191', 'SKD8.640184', 'SKD9.640182',
                               'SKM1.640183', 'SKM2.640199', 'SKM3.640197',
                               'SKM4.640180', 'SKM5.640177', 'SKM6.640187',
                               'SKM7.640188', 'SKM8.640201', 'SKM9.640192'}

 def test_remove_filepath(self):
     top_id = self.conn_handler.execute_fetchone(
         "SELECT count(1) FROM qiita.raw_filepath")[0]
     raw_id = self.conn_handler.execute_fetchone(
         "SELECT count(1) FROM qiita.raw_data")[0]
     rd = RawData.create(self.filetype, self.studies, self.filepaths)
     fp = join(self.db_test_raw_dir, "%d_%s" % (raw_id + 1,
                                                basename(self.seqs_fp)))
     rd.remove_filepath(fp)
     self.assertFalse(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE filepath_id=%d)" % (top_id - 1))[0])
     self.assertTrue(self.conn_handler.execute_fetchone(
         "SELECT EXISTS(SELECT * FROM qiita.raw_filepath "
         "WHERE filepath_id=%d)" % (top_id - 2))[0])

    def test_get_preprocess_fastq_cmd_per_sample_FASTQ(self):
        metadata_dict = {
            'SKB8.640193': {'run_prefix': "sample1", 'primer': 'A',
                            'barcode': 'A', 'center_name': 'ANL',
                            'platform': 'ILLUMINA',
                            'instrument_model': 'Illumina MiSeq',
                            'library_construction_protocol': 'A',
                            'experiment_design_description': 'A'},
            'SKD8.640184': {'run_prefix': "sample2", 'primer': 'A',
                            'barcode': 'A', 'center_name': 'ANL',
                            'platform': 'ILLUMINA',
                            'instrument_model': 'Illumina MiSeq',
                            'library_construction_protocol': 'A',
                            'experiment_design_description': 'A'}}
        md_template = pd.DataFrame.from_dict(metadata_dict, orient='index')
        prep_template = PrepTemplate.create(md_template, Study(1), '16S')

        fp1 = self.path_builder('sample1.fastq')
        with open(fp1, 'w') as f:
            f.write('\n')
        self.files_to_remove.append(fp1)
        fp2 = self.path_builder('sample2.fastq.gz')
        with open(fp2, 'w') as f:
            f.write('\n')
        self.files_to_remove.append(fp2)
        filepath_id = convert_to_id('raw_forward_seqs', 'filepath_type')

        fps = [(fp1, filepath_id), (fp2, filepath_id)]

        filetype_id = get_filetypes()['per_sample_FASTQ']
        raw_data = RawData.create(filetype_id, [prep_template], fps)
        params = [p for p in list(PreprocessedIlluminaParams.iter())
                  if p.name == 'per sample FASTQ defaults'][0]

        obs_cmd, obs_output_dir = _get_preprocess_fastq_cmd(raw_data,
                                                            prep_template,
                                                            params)

        raw_fps = ','.join([fp for _, fp, _ in
                            sorted(raw_data.get_filepaths())])
        exp_cmd = (
            "split_libraries_fastq.py --store_demultiplexed_fastq -i "
            "{} --sample_ids 1.SKB8.640193,1.SKD8.640184 -o {} --barcode_type "
            "not-barcoded --max_bad_run_length 3 --max_barcode_errors 1.5 "
            "--min_per_read_length_fraction 0.75 --phred_quality_threshold 3 "
            "--sequence_max_n 0").format(raw_fps, obs_output_dir)
        self.assertEqual(obs_cmd, exp_cmd)

    def test_create(self):
        """Correctly creates all the rows in the DB for the raw data"""
        # Check that the returned object has the correct id
        obs = RawData.create(self.filetype, self.studies, self.filepaths)
        self.assertEqual(obs.id, 3)

        # Check that the raw data have been correctly added to the DB
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.raw_data WHERE raw_data_id=3")
        # raw_data_id, filetype, link_filepaths_status
        self.assertEqual(obs, [[3, 2, 'idle']])

        # Check that the raw data have been correctly linked with the study
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.study_raw_data WHERE raw_data_id=3")
        # study_id , raw_data_id
        self.assertEqual(obs, [[1, 3]])

        # Check that the files have been copied to right location
        exp_seqs_fp = join(self.db_test_raw_dir,
                           "3_%s" % basename(self.seqs_fp))
        self.assertTrue(exists(exp_seqs_fp))
        self._clean_up_files.append(exp_seqs_fp)

        exp_bc_fp = join(self.db_test_raw_dir,
                         "3_%s" % basename(self.barcodes_fp))
        self.assertTrue(exists(exp_bc_fp))
        self._clean_up_files.append(exp_bc_fp)

        # Check that the filepaths have been correctly added to the DB
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.filepath WHERE filepath_id=17 or "
            "filepath_id=18")
        exp_seqs_fp = "3_%s" % basename(self.seqs_fp)
        exp_bc_fp = "3_%s" % basename(self.barcodes_fp)
        # filepath_id, path, filepath_type_id
        exp = [[17, exp_seqs_fp, 1, '852952723', 1, 5],
               [18, exp_bc_fp, 2, '852952723', 1, 5]]
        self.assertEqual(obs, exp)

        # Check that the raw data have been correctly linked with the filepaths
        obs = self.conn_handler.execute_fetchall(
            "SELECT * FROM qiita.raw_filepath WHERE raw_data_id=3")
        # raw_data_id, filepath_id
        self.assertEqual(obs, [[3, 17], [3, 18]])