Python Artifact.visibility方法代码示例

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def test_check_artifact_access(self):
        # "Study" artifact
        a = Artifact(1)
        # The user has access
        u = User('[email protected]')
        check_artifact_access(u, a)

        # Admin has access to everything
        admin = User('[email protected]')
        check_artifact_access(admin, a)

        # Demo user doesn't have access
        demo_u = User('[email protected]')
        with self.assertRaises(HTTPError):
            check_artifact_access(demo_u, a)

        # "Analysis" artifact
        a = Artifact(8)
        a.visibility = 'private'
        check_artifact_access(u, a)
        check_artifact_access(admin, a)
        with self.assertRaises(HTTPError):
            check_artifact_access(demo_u, a)
        check_artifact_access(User('[email protected]'), a)
        a.visibility = 'public'
        check_artifact_access(demo_u, a)

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def approve_study(self, study, user, callback):
        """Approves the current study if and only if the current user is admin

        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
        """
        if _approve(user.level):
            pd_id = int(self.get_argument('pd_id'))
            pd = Artifact(pd_id)
            pd.visibility = 'private'
            _propagate_visibility(pd)
            msg = "Processed data approved"
            msg_level = "success"
        else:
            msg = ("The current user does not have permission to approve "
                   "the processed data")
            msg_level = "danger"
        callback((msg, msg_level, "processed_data_tab", pd_id, None))

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
def artifact_status_put_req(artifact_id, user_id, visibility):
    """Set the status of the artifact given

    Parameters
    ----------
    artifact_id : int
        Artifact being acted on
    user_id : str
        The user requesting the action
    visibility : {'sandbox', 'awaiting_approval', 'private', 'public'}
        What to change the visibility to

    Returns
    -------
    dict
        Status of action, in the form {'status': status, 'message': msg}
        status: status of the action, either success or error
        message: Human readable message for status
    """
    if visibility not in get_visibilities():
        return {'status': 'error',
                'message': 'Unknown visiblity value: %s' % visibility}

    pd = Artifact(int(artifact_id))
    access_error = check_access(pd.study.id, user_id)
    if access_error:
        return access_error
    user = User(str(user_id))
    status = 'success'
    msg = 'Artifact visibility changed to %s' % visibility
    # Set the approval to private if needs approval and admin
    if visibility == 'private':
        if not qiita_config.require_approval:
            pd.visibility = 'private'
        # Set the approval to private if approval not required
        elif user.level == 'admin':
            pd.visibility = 'private'
        # Trying to set approval without admin privileges
        else:
            status = 'error'
            msg = 'User does not have permissions to approve change'
    else:
        pd.visibility = visibility

    return {'status': status,
            'message': msg}

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def test_propagate_visibility(self):
        a = Artifact(4)
        a.visibility = 'public'
        _propagate_visibility(a)
        self.assertEqual(Artifact(1).visibility, 'public')
        self.assertEqual(Artifact(2).visibility, 'public')
        self.assertEqual(Artifact(4).visibility, 'public')

        a.visibility = 'private'
        _propagate_visibility(a)
        self.assertEqual(Artifact(1).visibility, 'private')
        self.assertEqual(Artifact(2).visibility, 'private')
        self.assertEqual(Artifact(4).visibility, 'private')

        a = Artifact(2)
        a.visibility = 'public'
        _propagate_visibility(a)
        self.assertEqual(Artifact(1).visibility, 'private')
        self.assertEqual(Artifact(2).visibility, 'private')
        self.assertEqual(Artifact(4).visibility, 'private')

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def make_sandbox(self, study, user, callback):
        """Reverts the current study to the 'sandbox' status

        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
        """
        pd_id = int(self.get_argument('pd_id'))
        pd = Artifact(pd_id)
        pd.visibility = 'sandbox'
        _propagate_visibility(pd)
        msg = "Processed data reverted to sandbox"
        msg_level = "success"
        callback((msg, msg_level, "processed_data_tab", pd_id, None))

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def request_approval(self, study, user, callback):
        """Changes the status of the current study to "awaiting_approval"

        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
        """
        pd_id = int(self.get_argument('pd_id'))
        pd = Artifact(pd_id)
        pd.visibility = 'awaiting_approval'
        _propagate_visibility(pd)
        msg = "Processed data sent to admin for approval"
        msg_level = "success"
        callback((msg, msg_level, "processed_data_tab", pd_id, None))

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def make_public(self, study, user, callback):
        """Makes the current study public

        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
        """
        pd_id = int(self.get_argument('pd_id'))
        pd = Artifact(pd_id)
        pd.visibility = 'public'
        _propagate_visibility(pd)
        msg = "Processed data set to public"
        msg_level = "success"
        callback((msg, msg_level, "processed_data_tab", pd_id, None))

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
                           req_from=None):
    """Modifies an attribute of the artifact

    Parameters
    ----------
    user : qiita_db.user.User
        The user performing the patch operation
    artifact_id : int
        Id of the artifact in which the patch operation is being performed
    req_op : str
        The operation to perform on the artifact
    req_path : str
        The prep information and attribute to patch
    req_value : str, optional
        The value that needs to be modified
    req_from : str, optional
        The original path of the element

    Raises
    ------
    QiitaHTTPError
        If `req_op` != 'replace'
        If the path parameter is incorrect
        If missing req_value
        If the attribute to replace is not known
    """
    if req_op == 'replace':
        req_path = [v for v in req_path.split('/') if v]
        if len(req_path) != 1:
            raise QiitaHTTPError(404, 'Incorrect path parameter')

        attribute = req_path[0]

        # Check if the user actually has access to the artifact
        artifact = Artifact(artifact_id)
        check_artifact_access(user, artifact)

        if not req_value:
            raise QiitaHTTPError(404, 'Missing value to replace')

        if attribute == 'name':
            artifact.name = req_value
            return
        elif attribute == 'visibility':
            if req_value not in get_visibilities():
                raise QiitaHTTPError(400, 'Unknown visibility value: %s'
                                          % req_value)

            if (req_value == 'private' and qiita_config.require_approval
                    and not user.level == 'admin'):
                raise QiitaHTTPError(403, 'User does not have permissions '
                                          'to approve change')

            try:
                artifact.visibility = req_value
            except Exception as e:
                raise QiitaHTTPError(403, str(e).replace('\n', '<br/>'))

            if artifact.visibility == 'awaiting_approval':
                email_to = '[email protected]'
                sid = artifact.study.id
                subject = ('QIITA: Artifact %s awaiting_approval. Study %d, '
                           'Prep %d' % (artifact_id, sid,
                                        artifact.prep_templates[0].id))
                message = ('%s requested approval. <a '
                           'href="https://qiita.ucsd.edu/study/description/'
                           '%d">Study %d</a>.' % (user.email, sid, sid))
                try:
                    send_email(email_to, subject, message)
                except Exception:
                    msg = ("Couldn't send email to admins, please email us "
                           "directly to <a href='mailto:{0}'>{0}</a>.".format(
                               email_to))
                    raise QiitaHTTPError(400, msg)
        else:
            # We don't understand the attribute so return an error
            raise QiitaHTTPError(404, 'Attribute "%s" not found. Please, '
                                      'check the path parameter' % attribute)
    else:
        raise QiitaHTTPError(400, 'Operation "%s" not supported. Current '
                                  'supported operations: replace' % req_op)

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def test_artifact_summary_get_request(self):
        # Artifact w/o summary
        obs = artifact_summary_get_request('[email protected]', 1)
        exp_p_jobs = [
            ['063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
             'queued', None, None],
            ['bcc7ebcd-39c1-43e4-af2d-822e3589f14d', 'Split libraries',
             'running', 'demultiplexing', None]]
        exp_files = [
            (1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
            (2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
        exp = {'status': 'success',
               'message': '',
               'name': 'Raw data 1',
               'summary': None,
               'job': None,
               'processing_jobs': exp_p_jobs,
               'errored_jobs': [],
               'visibility': 'private',
               'buttons': '<button onclick="if (confirm(\'Are you sure you '
                          'want to make public artifact id: 1?\')) { '
                          'set_artifact_visibility(\'public\', 1) }" '
                          'class="btn btn-primary btn-sm">Make public</button>'
                          ' <button onclick="if (confirm(\'Are you sure you '
                          'want to revert to sandbox artifact id: 1?\')) '
                          '{ set_artifact_visibility(\'sandbox\', 1) }" '
                          'class="btn btn-primary btn-sm">Revert to '
                          'sandbox</button>',
               'files': exp_files,
               'editable': True}
        self.assertEqual(obs, exp)

        # Artifact with summary being generated
        job = ProcessingJob.create(
            User('[email protected]'),
            Parameters.load(Command(7), values_dict={'input_data': 1})
        )
        job._set_status('queued')
        obs = artifact_summary_get_request('[email protected]', 1)
        exp = {'status': 'success',
               'message': '',
               'name': 'Raw data 1',
               'summary': None,
               'job': [job.id, 'queued', None],
               'processing_jobs': exp_p_jobs,
               'errored_jobs': [],
               'visibility': 'private',
               'buttons': '<button onclick="if (confirm(\'Are you sure you '
                          'want to make public artifact id: 1?\')) { '
                          'set_artifact_visibility(\'public\', 1) }" '
                          'class="btn btn-primary btn-sm">Make public</button>'
                          ' <button onclick="if (confirm(\'Are you sure you '
                          'want to revert to sandbox artifact id: 1?\')) { '
                          'set_artifact_visibility(\'sandbox\', 1) }" '
                          'class="btn btn-primary btn-sm">Revert to '
                          'sandbox</button>',
               'files': exp_files,
               'editable': True}
        self.assertEqual(obs, exp)

        # Artifact with summary
        fd, fp = mkstemp(suffix=".html")
        close(fd)
        with open(fp, 'w') as f:
            f.write('<b>HTML TEST - not important</b>\n')
        a = Artifact(1)
        a.html_summary_fp = fp
        self._files_to_remove.extend([fp, a.html_summary_fp[1]])
        exp_files.append(
            (a.html_summary_fp[0],
             '%s (html summary)' % basename(a.html_summary_fp[1])))
        obs = artifact_summary_get_request('[email protected]', 1)
        exp = {'status': 'success',
               'message': '',
               'name': 'Raw data 1',
               'summary': '<b>HTML TEST - not important</b>\n',
               'job': None,
               'processing_jobs': exp_p_jobs,
               'errored_jobs': [],
               'visibility': 'private',
               'buttons': '<button onclick="if (confirm(\'Are you sure you '
                          'want to make public artifact id: 1?\')) { '
                          'set_artifact_visibility(\'public\', 1) }" '
                          'class="btn btn-primary btn-sm">Make public</button>'
                          ' <button onclick="if (confirm(\'Are you sure you '
                          'want to revert to sandbox artifact id: 1?\')) { '
                          'set_artifact_visibility(\'sandbox\', 1) }" '
                          'class="btn btn-primary btn-sm">Revert to '
                          'sandbox</button>',
               'files': exp_files,
               'editable': True}
        self.assertEqual(obs, exp)

        # No access
        obs = artifact_summary_get_request('[email protected]', 1)
        exp = {'status': 'error',
               'message': 'User does not have access to study'}
        self.assertEqual(obs, exp)

        # A non-owner/share user can't see the files
#.........这里部分代码省略.........

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
                           req_from=None):
    """Modifies an attribute of the artifact

    Parameters
    ----------
    user : qiita_db.user.User
        The user performing the patch operation
    artifact_id : int
        Id of the artifact in which the patch operation is being performed
    req_op : str
        The operation to perform on the artifact
    req_path : str
        The prep information and attribute to patch
    req_value : str, optional
        The value that needs to be modified
    req_from : str, optional
        The original path of the element

    Raises
    ------
    QiitaHTTPError
        If `req_op` != 'replace'
        If the path parameter is incorrect
        If missing req_value
        If the attribute to replace is not known
    """
    if req_op == 'replace':
        req_path = [v for v in req_path.split('/') if v]
        if len(req_path) != 1:
            raise QiitaHTTPError(404, 'Incorrect path parameter')

        attribute = req_path[0]

        # Check if the user actually has access to the artifact
        artifact = Artifact(artifact_id)
        check_artifact_access(user, artifact)

        if not req_value:
            raise QiitaHTTPError(404, 'Missing value to replace')

        if attribute == 'name':
            artifact.name = req_value
            return
        elif attribute == 'visibility':
            if req_value not in get_visibilities():
                raise QiitaHTTPError(400, 'Unknown visibility value: %s'
                                          % req_value)
            # Set the approval to private if needs approval and admin
            if req_value == 'private':
                if not qiita_config.require_approval:
                    artifact.visibility = 'private'
                # Set the approval to private if approval not required
                elif user.level == 'admin':
                    artifact.visibility = 'private'
                # Trying to set approval without admin privileges
                else:
                    raise QiitaHTTPError(403, 'User does not have permissions '
                                              'to approve change')
            else:
                artifact.visibility = req_value
        else:
            # We don't understand the attribute so return an error
            raise QiitaHTTPError(404, 'Attribute "%s" not found. Please, '
                                      'check the path parameter' % attribute)
    else:
        raise QiitaHTTPError(400, 'Operation "%s" not supported. Current '
                                  'supported operations: replace' % req_op)

# 需要导入模块: from qiita_db.artifact import Artifact [as 别名]
# 或者: from qiita_db.artifact.Artifact import visibility [as 别名]
    def test_artifact_summary_get_request(self):
        user = User('[email protected]')
        # Artifact w/o summary
        obs = artifact_summary_get_request(user, 1)
        exp_files = [
            (1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
            (2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
        exp = {'name': 'Raw data 1',
               'artifact_id': 1,
               'artifact_type': 'FASTQ',
               'artifact_timestamp': '2012-10-01 09:10',
               'visibility': 'private',
               'editable': True,
               'buttons': ('<button onclick="if (confirm(\'Are you sure you '
                           'want to make public artifact id: 1?\')) { '
                           'set_artifact_visibility(\'public\', 1) }" '
                           'class="btn btn-primary btn-sm">Make public'
                           '</button> <button onclick="if (confirm(\'Are you '
                           'sure you want to revert to sandbox artifact id: '
                           '1?\')) { set_artifact_visibility(\'sandbox\', 1) '
                           '}" class="btn btn-primary btn-sm">Revert to '
                           'sandbox</button>'),
               'processing_info': {},
               'files': exp_files,
               'is_from_analysis': False,
               'summary': None,
               'job': None,
               'errored_summary_jobs': []}
        self.assertEqual(obs, exp)

        # Artifact with summary being generated
        job = ProcessingJob.create(
            User('[email protected]'),
            Parameters.load(Command(7), values_dict={'input_data': 1})
        )
        job._set_status('queued')
        obs = artifact_summary_get_request(user, 1)
        exp = {'name': 'Raw data 1',
               'artifact_id': 1,
               'artifact_type': 'FASTQ',
               'artifact_timestamp': '2012-10-01 09:10',
               'visibility': 'private',
               'editable': True,
               'buttons': ('<button onclick="if (confirm(\'Are you sure you '
                           'want to make public artifact id: 1?\')) { '
                           'set_artifact_visibility(\'public\', 1) }" '
                           'class="btn btn-primary btn-sm">Make public'
                           '</button> <button onclick="if (confirm(\'Are you '
                           'sure you want to revert to sandbox artifact id: '
                           '1?\')) { set_artifact_visibility(\'sandbox\', 1) '
                           '}" class="btn btn-primary btn-sm">Revert to '
                           'sandbox</button>'),
               'processing_info': {},
               'files': exp_files,
               'is_from_analysis': False,
               'summary': None,
               'job': [job.id, 'queued', None],
               'errored_summary_jobs': []}
        self.assertEqual(obs, exp)

        # Artifact with summary
        fd, fp = mkstemp(suffix=".html")
        close(fd)
        with open(fp, 'w') as f:
            f.write('<b>HTML TEST - not important</b>\n')
        a = Artifact(1)
        a.set_html_summary(fp)
        self._files_to_remove.extend([fp, a.html_summary_fp[1]])
        exp_files.append(
            (a.html_summary_fp[0],
             '%s (html summary)' % basename(a.html_summary_fp[1])))
        exp_summary_path = relpath(
            a.html_summary_fp[1], qiita_config.base_data_dir)
        obs = artifact_summary_get_request(user, 1)
        exp = {'name': 'Raw data 1',
               'artifact_id': 1,
               'artifact_type': 'FASTQ',
               'artifact_timestamp': '2012-10-01 09:10',
               'visibility': 'private',
               'editable': True,
               'buttons': ('<button onclick="if (confirm(\'Are you sure you '
                           'want to make public artifact id: 1?\')) { '
                           'set_artifact_visibility(\'public\', 1) }" '
                           'class="btn btn-primary btn-sm">Make public'
                           '</button> <button onclick="if (confirm(\'Are you '
                           'sure you want to revert to sandbox artifact id: '
                           '1?\')) { set_artifact_visibility(\'sandbox\', 1) '
                           '}" class="btn btn-primary btn-sm">Revert to '
                           'sandbox</button>'),
               'processing_info': {},
               'files': exp_files,
               'is_from_analysis': False,
               'summary': exp_summary_path,
               'job': None,
               'errored_summary_jobs': []}
        self.assertEqual(obs, exp)

        # No access
        demo_u = User('[email protected]')
        with self.assertRaises(QiitaHTTPError):
#.........这里部分代码省略.........