fix #1999 (#2514)

* fix #1999

* fix template error

* rm maintenance conditional

* some improvements

* fix #1053

Author: antgonza

qiita_db/commands.py

@@ -186,45 +186,6 @@ def load_prep_template_from_cmd(prep_temp_path, study_id, data_type):
         prep_temp, qdb.study.Study(study_id), data_type)
 
 
-def load_parameters_from_cmd(name, fp, cmd_id):
-    """Add a new parameters entry on `table`
-
-    Parameters
-    ----------
-    fp : str
-        The filepath to the parameters file
-    cmd_id : int
-        The command to add the new default parameter set
-
-    Returns
-    -------
-    qiita_db.software.DefaultParameters
-        The newly parameter set object created
-
-    Raises
-    ------
-    ValueError
-        If the table does not exists on the DB
-        If the fp is not correctly formatted
-
-    Notes
-    -----
-    `fp` should be a tab-delimited text file following this format:
-        parameter_1<TAB>value
-        parameter_2<TAB>value
-        ...
-    """
-    cmd = qdb.software.Command(cmd_id)
-
-    try:
-        params = dict(tuple(l.strip().split('\t')) for l in open(fp, 'U'))
-    except ValueError:
-        raise ValueError("The format of the parameters files is not correct. "
-                         "The format is PARAMETER_NAME<tab>VALUE")
-
-    return qdb.software.DefaultParameters.create(name, cmd, **params)
-
-
 def update_artifact_from_cmd(filepaths, filepath_types, artifact_id):
     """Updates the artifact `artifact_id` with the given files
 

qiita_db/test/test_commands.py

@@ -211,29 +211,6 @@ def tearDown(self):
             if exists(fp):
                 remove(fp)
 
-    def test_load_parameters_from_cmd_error(self):
-        with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
-            qdb.commands.load_parameters_from_cmd(
-                "test", self.fp, 20000)
-
-    def test_load_parameters_from_cmd_error_format(self):
-        with self.assertRaises(ValueError):
-            qdb.commands.load_parameters_from_cmd(
-                "test", self.fp_wrong, 1)
-
-    def test_load_parameters_from_cmd(self):
-        new = qdb.commands.load_parameters_from_cmd(
-            "test", self.fp, 1)
-        obs = new.values
-        exp = {"barcode_type": "hamming_8", "max_bad_run_length": "3",
-               "phred_offset": "auto", "max_barcode_errors": "1.5",
-               "min_per_read_length_fraction": "0.75",
-               "phred_quality_threshold": "3", "sequence_max_n": "0",
-               "rev_comp": "False", "rev_comp_barcode": "False",
-               "rev_comp_mapping_barcodes": "False",
-               "sequence_max_n": "0"}
-        self.assertEqual(obs, exp)
-
 
 @qiita_test_checker()
 class TestPatch(TestCase):

qiita_pet/handlers/auth_handlers.py

@@ -7,7 +7,6 @@
 # -----------------------------------------------------------------------------
 
 from tornado.escape import url_escape, json_encode
-from tornado.web import HTTPError
 
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_core.qiita_settings import qiita_config, r_client
@@ -106,9 +105,6 @@ def get(self):
 
     @execute_as_transaction
     def post(self):
-        if r_client.get('maintenance') is not None:
-            raise HTTPError(503, reason="Site is down for maintenance")
-
         username = self.get_argument("username", "").strip().lower()
         passwd = self.get_argument("password", "")
         nextpage = self.get_argument("next", None)

qiita_pet/templates/change_lost_pass.html

@@ -8,7 +8,7 @@
 {%end%}
 
 {% block content %}
-  {% if level != 'danger' and maintenance is None %}
+  {% if level != 'danger' %}
     <div style='width: 50%;'>
     <h1>Password Reset</h1>
     <h3>Enter new password below</h3>

qiita_pet/templates/ebi_submission.html

@@ -11,7 +11,7 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
             and prep templates which will be submitted to EBI.
         </div>
 
-        {% if level != 'danger' and maintenance is None %}
+        {% if level != 'danger' %}
             <table class="table">
             {% for category, summary in stats %}
                 <tr>
@@ -27,7 +27,7 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
     The investigation type is: <b>{{investigation_type}}</b>
     <br/><br/>
     {% if investigation_type %}
-      {% if level != 'danger' and maintenance is None %}
+      {% if level != 'danger' %}
         {% if allow_submission %}
             <br/>
             What kind of submission do you want to do?

qiita_pet/templates/sitebase.html

@@ -2,7 +2,6 @@
 {% from qiita_core.util import get_qiita_version, get_release_info %}
 {% from qiita_pet import allowed_min_browser_versions %}
 {% from qiita_pet.portal import portal_styling %}
-{% set maintenance = r_client.get('maintenance') %}
 {% set sysmessage = r_client.get('sysmessage') %}
 {% set user = current_user %}
 {% set qiita_version, qiita_sha = get_qiita_version() %}
@@ -13,11 +12,7 @@
     {% set level = 'info' %}
 {% end %}
 {% set message = globals().get('message', '') %}
-{% if maintenance is not None %}
-  {# maintenance mode takes precedence #}
-  {% set level = 'danger' %}
-  {% set message = maintenance %}
-{% elif sysmessage is not None %}
+{% if sysmessage is not None %}
   {# since this is a systemwide message, allow regular messages as well #}
   {% set message = sysmessage + "<br />" + str(message) %}
 {% end %}
@@ -427,7 +422,7 @@
               </li>
             </ul>
             <!-- otherwise show the login form -->
-            {% elif  maintenance is None %}
+            {% else %}
             <ul class="nav navbar-nav">
               <li>
                 <a href="{% raw qiita_config.portal_dir %}/auth/forgot/">Forgot Password</a>

qiita_pet/templates/vamps_submission.html

@@ -10,7 +10,7 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
             and prep templates which will be submitted to VAMPS.
         </div>
 
-        {% if level != 'danger' and maintenance is None  %}
+        {% if level != 'danger' %}
             <table class="table">
             {% for category, summary in stats %}
                 <tr>
@@ -26,7 +26,7 @@ <h1>Submission summary for study: <b>{{study_title}}</b></h1>
     The investigation type is: <b>{{investigation_type}}</b>
     <br/><br/>
 
-    {% if level != 'danger' and maintenance is None %}
+    {% if level != 'danger' %}
       {% if allow_submission %}
         <input type="submit" class="btn btn-primary" value="Submit to VAMPS">
       {% else %}

qiita_pet/test/test_user_handlers.py

@@ -8,8 +8,6 @@
 
 from unittest import main
 
-from qiita_core.qiita_settings import r_client
-
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 
 
@@ -33,24 +31,6 @@ def test_post_password(self):
         response = self.post('/profile/', post_args)
         self.assertEqual(response.code, 200)
 
-    def test_post_select_samples(self):
-        # just making sure that the key is not set in redis
-        r_client.delete('maintenance')
-        response = self.get('/auth/reset/')
-        self.assertEqual(response.code, 200)
-        self.assertIn(('<label for="newpass2" class="col-sm-2 '
-                       'control-label">Repeat New Password'
-                       '</label>'), response.body)
-
-        # not displaying due to maintenance
-        r_client.set('maintenance', 'This is my error message')
-        response = self.get('/auth/reset/')
-        self.assertEqual(response.code, 200)
-        self.assertNotIn(('<label for="newpass2" class="col-sm-2 '
-                          'control-label">Repeat New Password'
-                          '</label>'), response.body)
-        r_client.delete('maintenance')
-
     def test_post_profile(self):
         post_args = {
             'action': ['profile'],

scripts/qiita

@@ -90,22 +90,11 @@ def plugins():
     pass
 
 
-# The private group holds commands that should never be called by the user
-# since they are used internally by Qiita to be able to distribute compute
-@qiita.group()
-def private():
-    pass
-
-
 @ware.group()
 def ebi():
     pass
 
 
-@db.group()
-def portal():
-    pass
-
 # #############################################################################
 # DB COMMANDS
 # #############################################################################
@@ -165,23 +154,6 @@ def load_artifact(fp, fp_type, artifact_type, prep_template, parents,
     click.echo("Artifact %s successfully created" % artifact.id)
 
 
-@db.command()
-@click.option('--fp', required=True, type=click.Path(resolve_path=True,
-              readable=True, exists=True), multiple=True,
-              help='Path to the artifact files. This option can be used '
-              'multiple times if there are multiple artifact files.')
-@click.option('--fp_type', required=True, multiple=True, help='Describes the '
-              'contents of the file. Pass one fp_type per fp.',
-              type=click.Choice(qdb.util.get_filepath_types().keys()))
-@click.option('--artifact_id', required=True,
-              help="The artifact to update",
-              type=click.IntRange(1))
-def update_artifact(fp, fp_type, artifact_id):
-    """Updates an artifact from the database"""
-    artifact = qdb.commands.update_artifact_from_cmd(fp, fp_type, artifact_id)
-    click.echo("Artifact %s successfully updated" % artifact.id)
-
-
 @db.command()
 @click.argument('fp', required=True,
                 type=click.Path(resolve_path=True, readable=True, exists=True))
@@ -210,96 +182,10 @@ def load_prep_template(fp, study, data_type):
                % prep_template.id)
 
 
-@db.command()
-@click.option('--name', required=True, type=str,
-              help='The name of the new reference database')
-@click.option('--version', required=True, type=str,
-              help='The version of the reference database')
-@click.option('--seq_fp', required=True,
-              type=click.Path(resolve_path=True, readable=True, exists=True),
-              help="Path to the reference sequences file")
-@click.option('--tax_fp', required=False,
-              type=click.Path(resolve_path=True, readable=True, exists=True),
-              help="Path to the reference taxonomy file")
-@click.option('--tree_fp', required=False,
-              type=click.Path(resolve_path=True, readable=True, exists=True),
-              help="Path to the reference tree file")
-def load_reference_db(name, version, seq_fp, tax_fp, tree_fp):
-    """Loads a reference db to the database"""
-    reference = qdb.reference.Reference.create(
-        name, version, seq_fp, tax_fp, tree_fp)
-    click.echo("Reference db successfully added to the database with id %s"
-               % reference.id)
-
-
-@db.command()
-@click.argument('fp', required=True,
-                type=click.Path(resolve_path=True, readable=True, exists=True))
-@click.option('--cmd-id', required=True,
-              type=click.IntRange(1, None),
-              help='The command to add the parameter set')
-@click.option('--name', required=True, type=str,
-              help='The name of the parameters set')
-def load_parameters(fp, cmd_id, name):
-    """Loads a parameter set to the database"""
-    param = qdb.commands.load_parameters_from_cmd(name, fp, cmd_id)
-    click.echo("Parameters successfully added to the command %s with id %s"
-               % (cmd_id, param.id))
-
-
-# #############################################################################
-# PORTAL COMMANDS
-# #############################################################################
-
-
-@portal.command(name="add-analyses")
-@click.argument('portal', required=True,
-                type=click.Choice(qdb.portal.Portal.list_portals()))
-@click.argument('analyses', required=True, type=int, nargs=-1)
-def add_analysis(portal, analyses):
-    try:
-        qdb.portal.Portal(portal).add_analyses(analyses)
-    except qdb.exceptions.QiitaDBError as e:
-        raise click.BadOptionUsage("analyses", str(e))
-
-
-@portal.command(name="remove-analyses")
-@click.argument('portal', required=True,
-                type=click.Choice(qdb.portal.Portal.list_portals()))
-@click.argument('analyses', required=True, type=int, nargs=-1)
-def remove_analysis(portal, analyses):
-    try:
-        qdb.portal.Portal(portal).remove_analyses(analyses)
-    except qdb.exceptions.QiitaDBError as e:
-        raise click.BadOptionUsage("analyses", str(e))
-
-
-@portal.command(name="add-studies")
-@click.argument('portal', required=True,
-                type=click.Choice(qdb.portal.Portal.list_portals()))
-@click.argument('studies', required=True, type=int, nargs=-1)
-def add_study(portal, studies):
-    try:
-        qdb.portal.Portal(portal).add_studies(studies)
-    except qdb.exceptions.QiitaDBError as e:
-        raise click.BadOptionUsage("studies", str(e))
-
-
-@portal.command(name="remove-studies")
-@click.argument('portal', required=True,
-                type=click.Choice(qdb.portal.Portal.list_portals()))
-@click.argument('studies', required=True, type=int, nargs=-1)
-def remove_study(portal, studies):
-    try:
-        qdb.portal.Portal(portal).remove_studies(studies)
-    except qdb.exceptions.QiitaDBError as e:
-        raise click.BadOptionUsage("studies", str(e))
-
 # #############################################################################
 # EBI COMMANDS
 # #############################################################################
 
-
 @ebi.command()
 @click.option('--preprocessed_data_id', required=True, type=int)
 @click.option('--action', type=click.Choice(EBISubmission.valid_ebi_actions),
@@ -317,21 +203,6 @@ def submit(preprocessed_data_id, action, send):
 # MAINTENANCE COMMANDS
 # #############################################################################
 
-
-@maintenance.command()
-@click.option('--time', required=True, type=int,
-              help='The amount of time to lock the site, in hours')
-@click.option('--message', required=True, type=str,
-              help="Message to show users")
-def lock(message, time):
-    r_client.setex('maintenance', message, time * 60 * 60)
-
-
-@maintenance.command()
-def unlock():
-    r_client.delete('maintenance')
-
-
 @maintenance.command()
 @click.option('--time', required=True, type=int,
               help='The amount of time to show message, in hours')
@@ -355,16 +226,8 @@ def clear_sysmessage():
 
 @maintenance.command()
 def status():
-    maint_status = r_client.get('maintenance')
     sys_status = r_client.get('sysmessage')
 
-    if maint_status is None:
-        click.echo("Site is not in maintenance mode")
-    else:
-        click.echo("Site is in maintenance mode:")
-        click.echo(maint_status)
-        click.echo(r_client.ttl('maintenance'), "seconds remaining")
-
     if sys_status is None:
         click.echo("Site has no system message")
     else: