Skip to content

WIP: Missing links #1662

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 7 commits into from
Feb 29, 2016
Merged

WIP: Missing links #1662

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
a8f8271
Fixing link in list_studies
josenavas Feb 23, 2016
690106f
Adding setUp to TestSearchStudiesAJAX
josenavas Feb 23, 2016
afcd709
Adding a test to TestSearchStudiesAJAX with different portal
josenavas Feb 23, 2016
ff469b9
Changing url in email sent to the user
josenavas Feb 24, 2016
4689470
Fixing link in sitebase.html
josenavas Feb 24, 2016
bbe27ca
Fixing moi call in analysis
josenavas Feb 25, 2016
11372c8
Fixing login_url in webserver config
josenavas Feb 25, 2016
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions qiita_pet/handlers/user_handlers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,12 @@ def post(self):
try:
send_email(user.id, "Qiita: Password Reset", "Please go to "
"the following URL to reset your password: \n"
"%s/auth/reset/%s \nYou "
"%s/%s/auth/reset/%s \nYou "
"have 30 minutes from the time you requested a "
"reset to change your password. After this period, "
"you will have to request another reset." %
(qiita_config.base_url, info["pass_reset_code"]))
(qiita_config.base_url, qiita_config.portal_dir,
info["pass_reset_code"]))
message = ("Check your email for the reset code.")
level = "success"
page = "index.html"
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/analysis_waiting.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi_list.js"></script>
<script type="text/javascript">
$(document).ready(function() {
moi_list.init("{{group_id}}");
moi_list.init("{{group_id}}", undefined, window.location.host + '{% raw qiita_config.portal_dir %}/moi-ws/');
});
</script>
{% end %}
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/list_studies.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@
}, targets: [1]},
// render the title cell
{"render": function ( data, type, row, meta ) {
return "<a href='#' data-toggle='modal' data-target='#study-abstract-modal' onclick=\"fillAbstract('studies-table', "+ meta.row +")\"><span class='glyphicon glyphicon-file' aria-hidden='true'></span></a> | <a href='/study/description/"+ row.study_id +"' id='study"+ meta.row +"-title'>"+ data +"</a>";
return "<a href='#' data-toggle='modal' data-target='#study-abstract-modal' onclick=\"fillAbstract('studies-table', "+ meta.row +")\"><span class='glyphicon glyphicon-file' aria-hidden='true'></span></a> | <a href='{% raw qiita_config.portal_dir %}/study/description/"+ row.study_id +"' id='study"+ meta.row +"-title'>"+ data +"</a>";
}, targets: [2]},
// render the metadata complete cell
{"render": function ( data, type, row, meta ) {
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/sitebase.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@
});

$("#analysis-drop-down").mouseover(function() {
$.getJSON("/analysis/dflt/sumary/", function(result){
$.getJSON("{% raw qiita_config.portal_dir %}/analysis/dflt/sumary/", function(result){
if(parseInt(result.studies) > 0){
$("#selected_samples_menu").removeClass('disabled');
$("#selected_samples_link").attr('href', '{% raw qiita_config.portal_dir %}/analysis/selected/');
Expand Down
256 changes: 145 additions & 111 deletions qiita_pet/test/test_study_handlers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from qiita_pet.handlers.base_handlers import BaseHandler
from qiita_pet.test.tornado_test_base import TestHandlerBase
from qiita_core.exceptions import IncompetentQiitaDeveloperError
from qiita_core.qiita_settings import qiita_config
from qiita_db.artifact import Artifact
from qiita_db.study import StudyPerson, Study
from qiita_db.util import get_count, check_count
Expand Down Expand Up @@ -470,118 +471,141 @@ def test_get_no_access(self):
class TestSearchStudiesAJAX(TestHandlerBase):
database = True

json = {
'iTotalRecords': 1, 'sEcho': 1021, 'iTotalDisplayRecords': 1,
'aaData': [{
'study_id': 1,
'status': 'private',
'study_abstract':
'This is a preliminary study to examine the microbiota '
'associated with the Cannabis plant. Soils samples '
'from the bulk soil, soil associated with the roots, '
'and the rhizosphere were extracted and the DNA '
'sequenced. Roots from three independent plants of '
'different strains were examined. These roots were '
'obtained November 11, 2011 from plants that had been '
'harvested in the summer. Future studies will attempt '
'to analyze the soils and rhizospheres from the same '
'location at different time points in the plant '
'lifecycle.',
'metadata_complete': True,
'study_title':
'Identification of the Microbiomes for Cannabis Soils',
'num_raw_data': 1,
'number_samples_collected': 27,
'shared':
'<a target="_blank" href="mailto:shared@foo.bar">Shared</a>',
'publication_doi':
'<a target="_blank" href="http://dx.doi.org/10.100/123456">'
'10.100/123456</a>, <a target="_blank" '
'href="http://dx.doi.org/10.100/7891011">10.100/7891011</a>',
'pmid': '<a target="_blank" href="http://www.ncbi.nlm.nih.gov'
'/pubmed/7891011">7891011</a>, <a target="_blank" href='
'"http://www.ncbi.nlm.nih.gov/pubmed/123456">123456</a>',
'pi': '<a target="_blank" href="mailto:PI_dude@foo.bar">'
'PIDude</a>',
'proc_data_info': [{
'pid': 4,
'processed_date': '2012-10-02 17:30:00',
'data_type': '18S',
'algorithm': 'sortmerna',
'reference_name': 'Greengenes',
'reference_version': '13_8',
'taxonomy_filepath': 'GreenGenes_13_8_97_otu_taxonomy.txt',
'sequence_filepath': 'GreenGenes_13_8_97_otus.fasta',
'tree_filepath': 'GreenGenes_13_8_97_otus.tree',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']
}, {
'pid': 5,
'processed_date': '2012-10-02 17:30:00',
'data_type': '18S',
'algorithm': 'sortmerna',
'reference_name': 'Greengenes',
'reference_version': '13_8',
'taxonomy_filepath': 'GreenGenes_13_8_97_otu_taxonomy.txt',
'sequence_filepath': 'GreenGenes_13_8_97_otus.fasta',
'tree_filepath': 'GreenGenes_13_8_97_otus.tree',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']
}, {
'pid': 6,
'processed_date': '2012-10-02 17:30:00',
'data_type': '16S',
'algorithm': 'sortmerna',
'reference_name': 'Silva',
'reference_version': 'test',
'taxonomy_filepath': 'Silva_97_otu_taxonomy.txt',
'sequence_filepath': 'Silva_97_otus.fasta',
'tree_filepath': '',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']
def setUp(self):
super(TestSearchStudiesAJAX, self).setUp()
self.json = {
'iTotalRecords': 1, 'sEcho': 1021, 'iTotalDisplayRecords': 1,
'aaData': [{
'study_id': 1,
'status': 'private',
'study_abstract':
'This is a preliminary study to examine the microbiota '
'associated with the Cannabis plant. Soils samples '
'from the bulk soil, soil associated with the roots, '
'and the rhizosphere were extracted and the DNA '
'sequenced. Roots from three independent plants of '
'different strains were examined. These roots were '
'obtained November 11, 2011 from plants that had been '
'harvested in the summer. Future studies will attempt '
'to analyze the soils and rhizospheres from the same '
'location at different time points in the plant '
'lifecycle.',
'metadata_complete': True,
'study_title':
'Identification of the Microbiomes for Cannabis Soils',
'num_raw_data': 1,
'number_samples_collected': 27,
'shared': '<a target="_blank" href="mailto:shared@foo.bar">'
'Shared</a>',
'publication_doi':
'<a target="_blank" href="http://dx.doi.org/10.100/123456"'
'>10.100/123456</a>, <a target="_blank" href='
'"http://dx.doi.org/10.100/7891011">10.100/7891011</a>',
'pmid': '<a target="_blank" href="http://www.ncbi.nlm.nih.gov'
'/pubmed/7891011">7891011</a>, <a target="_blank" href'
'="http://www.ncbi.nlm.nih.gov/pubmed/123456">123456'
'</a>',
'pi': '<a target="_blank" href="mailto:PI_dude@foo.bar">'
'PIDude</a>',
'proc_data_info': [{
'pid': 4,
'processed_date': '2012-10-02 17:30:00',
'data_type': '18S',
'algorithm': 'sortmerna',
'reference_name': 'Greengenes',
'reference_version': '13_8',
'taxonomy_filepath': 'GreenGenes_13_8_97_otu_taxonomy.txt',
'sequence_filepath': 'GreenGenes_13_8_97_otus.fasta',
'tree_filepath': 'GreenGenes_13_8_97_otus.tree',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194',
'1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179',
'1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186',
'1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180',
'1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201',
'1.SKM9.640192']
}, {
'pid': 5,
'processed_date': '2012-10-02 17:30:00',
'data_type': '18S',
'algorithm': 'sortmerna',
'reference_name': 'Greengenes',
'reference_version': '13_8',
'taxonomy_filepath': 'GreenGenes_13_8_97_otu_taxonomy.txt',
'sequence_filepath': 'GreenGenes_13_8_97_otus.fasta',
'tree_filepath': 'GreenGenes_13_8_97_otus.tree',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194',
'1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179',
'1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186',
'1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180',
'1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201',
'1.SKM9.640192']
}, {
'pid': 6,
'processed_date': '2012-10-02 17:30:00',
'data_type': '16S',
'algorithm': 'sortmerna',
'reference_name': 'Silva',
'reference_version': 'test',
'taxonomy_filepath': 'Silva_97_otu_taxonomy.txt',
'sequence_filepath': 'Silva_97_otus.fasta',
'tree_filepath': '',
'similarity': 0.97,
'sortmerna_max_pos': 10000,
'sortmerna_e_value': 1,
'sortmerna_coverage': 0.97,
'threads': 1,
'samples': ['1.SKB1.640202', '1.SKB2.640194',
'1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179',
'1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186',
'1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180',
'1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201',
'1.SKM9.640192']
}]
}]
}]
}
empty = {'aaData': [],
'iTotalDisplayRecords': 0,
'iTotalRecords': 0,
'sEcho': 1021}
}
self.empty = {'aaData': [],
'iTotalDisplayRecords': 0,
'iTotalRecords': 0,
'sEcho': 1021}
self.portal = qiita_config.portal

def tearDown(self):
super(TestSearchStudiesAJAX, self).tearDown()
qiita_config.portal = self.portal

def test_get(self):
response = self.get('/study/search/', {
Expand Down Expand Up @@ -620,6 +644,16 @@ def test_get_failure(self):
})
self.assertEqual(response.code, 403)

def test_get_emp_portal(self):
qiita_config.portal = "EMP"
response = self.get('/study/search/', {
'user': 'test@foo.bar',
'query': '',
'sEcho': '1021'
})
self.assertEqual(response.code, 200)
self.assertEqual(loads(response.body), self.empty)


class TestMetadataSummaryHandler(TestHandlerBase):
def test_error_prep_and_sample(self):
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/webserver.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,7 @@ def __init__(self):
"template_path": TEMPLATE_PATH,
"debug": DEBUG,
"cookie_secret": COOKIE_SECRET,
"login_url": "/auth/login/",
"login_url": "%s/auth/login/" % qiita_config.portal_dir,
"ui_modules": uimodules,
}
tornado.web.Application.__init__(self, handlers, **settings)