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Merged
merged 4 commits into from
Feb 23, 2018
Merged

fix #1999 #2514

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55b864e
fix #1999
antgonza Feb 22, 2018
8a40823
fix template error
antgonza Feb 23, 2018
4f40b63
rm maintenance conditional
antgonza Feb 23, 2018
be097a2
some improvements
antgonza Feb 23, 2018
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39 changes: 0 additions & 39 deletions qiita_db/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
23 changes: 0 additions & 23 deletions qiita_db/test/test_commands.py
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Expand Up @@ -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):
Expand Down
4 changes: 0 additions & 4 deletions qiita_pet/handlers/auth_handlers.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
9 changes: 1 addition & 8 deletions qiita_pet/templates/sitebase.html
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Original file line number Diff line number Diff line change
Expand Up @@ -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() %}
Expand All @@ -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 %}
Expand Down Expand Up @@ -427,7 +422,6 @@
</li>
</ul>
<!-- otherwise show the login form -->
{% elif maintenance is None %}
<ul class="nav navbar-nav">
<li>
<a href="{% raw qiita_config.portal_dir %}/auth/forgot/">Forgot Password</a>
Expand All @@ -445,7 +439,6 @@
</div>
<button tabindex="3" type="submit" class="btn btn-success">Sign in</button>
</form>
{% end %}
<ul class="nav navbar-nav">
<!-- generic elements -->
<li class="dropdown">
Expand Down
20 changes: 0 additions & 20 deletions qiita_pet/test/test_user_handlers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand All @@ -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'],
Expand Down
137 changes: 0 additions & 137 deletions scripts/qiita
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Expand Up @@ -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
# #############################################################################
Expand Down Expand Up @@ -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))
Expand Down Expand Up @@ -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),
Expand All @@ -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')
Expand All @@ -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:
Expand Down
16 changes: 1 addition & 15 deletions test_data_studies/commands.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -47,24 +47,10 @@ for i in ${studies[@]}; do
pt_id=`echo -e "${output}" | cut -d " " -f 10`
echo "Ok"

# Loading raw data
echo "\tloading raw data... "
echo -e ">seq\nAAAA" > temp/seqs.fna
output="`qiita db load_artifact --fp temp/seqs.fna --fp_type raw_forward_seqs --artifact_type FASTQ --prep_template $pt_id`"
raw_id=`echo -e "${output}" | cut -d " " -f 2`
echo "Ok"

# Loading preprocessed data
echo "\tloading preprocessed data... "
echo -e ">seq\nAAAA" > temp/seqs.fna
output=`qiita db load_artifact --artifact_type FASTA_Sanger --dflt_params 1 --fp temp/ --fp_type preprocessed_fasta --parents ${raw_id}`
ppd_id=`echo -e "${output}" | cut -d " " -f 2`
echo "Ok"

# Loading processed data
echo "\tloading processed data... "
cp $otu_table ${otu_table}_backup
output="`qiita db load_artifact --artifact_type BIOM --fp $otu_table --fp_type biom --dflt_params 2 --parents ${ppd_id}`"
output="`qiita db load_artifact --artifact_type BIOM --fp $otu_table --fp_type biom --prep_template $pt_id`"
pd_id=`echo -e "${output}" | cut -d " " -f 2`
mv ${otu_table}_backup $otu_table
echo "Ok"
Expand Down