diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py
index c7fd8cf71..7fff5cdf6 100644
--- a/qiita_db/test/test_meta_util.py
+++ b/qiita_db/test/test_meta_util.py
@@ -98,7 +98,7 @@ def test_validate_filepath_access_by_user(self):
self.assertTrue(qdb.meta_util.validate_filepath_access_by_user(
admin, i[0]))
- # returning to origina sharing
+ # returning to original sharing
qdb.study.Study(1).share(user)
qdb.analysis.Analysis(1).share(user)
qdb.study.Study.delete(study.id)
diff --git a/qiita_db/util.py b/qiita_db/util.py
index cbee92485..07fbc9167 100644
--- a/qiita_db/util.py
+++ b/qiita_db/util.py
@@ -896,12 +896,12 @@ def filepath_id_to_rel_path(filepath_id):
LEFT JOIN qiita.artifact_filepath USING (filepath_id)
WHERE filepath_id = %s"""
qdb.sql_connection.TRN.add(sql, [filepath_id])
+ # It should be only one row
mp, fp, sd, a_id = qdb.sql_connection.TRN.execute_fetchindex()[0]
if sd:
result = join(mp, str(a_id), fp)
else:
result = join(mp, fp)
- # It should be only one row
return result
diff --git a/qiita_pet/handlers/download.py b/qiita_pet/handlers/download.py
index bbf10699f..912471754 100644
--- a/qiita_pet/handlers/download.py
+++ b/qiita_pet/handlers/download.py
@@ -1,10 +1,13 @@
-from tornado.web import authenticated
+from tornado.web import authenticated, HTTPError
-from os.path import basename
+from os.path import basename, getsize, join
+from os import walk
+from datetime import datetime
from .base_handlers import BaseHandler
-from qiita_pet.exceptions import QiitaPetAuthorizationError
-from qiita_db.util import filepath_id_to_rel_path
+from qiita_pet.handlers.api_proxy import study_get_req
+from qiita_db.study import Study
+from qiita_db.util import filepath_id_to_rel_path, get_db_files_base_dir
from qiita_db.meta_util import validate_filepath_access_by_user
from qiita_core.util import execute_as_transaction
@@ -16,8 +19,9 @@ def get(self, filepath_id):
fid = int(filepath_id)
if not validate_filepath_access_by_user(self.current_user, fid):
- raise QiitaPetAuthorizationError(
- self.current_user, 'filepath id %s' % str(fid))
+ raise HTTPError(
+ 404, "%s doesn't have access to "
+ "filepath_id: %s" % (self.current_user.email, str(fid)))
relpath = filepath_id_to_rel_path(fid)
fname = basename(relpath)
@@ -37,3 +41,85 @@ def get(self, filepath_id):
'attachment; filename=%s' % fname)
self.finish()
+
+
+class DownloadStudyBIOMSHandler(BaseHandler):
+ @authenticated
+ @execute_as_transaction
+ def get(self, study_id):
+ study_id = int(study_id)
+ # Check access to study
+ study_info = study_get_req(study_id, self.current_user.id)
+
+ if study_info['status'] != 'success':
+ raise HTTPError(405, "%s: %s, %s" % (study_info['message'],
+ self.current_user.email,
+ str(study_id)))
+
+ study = Study(study_id)
+ user = self.current_user
+ basedir = get_db_files_base_dir()
+ basedir_len = len(basedir) + 1
+ # loop over artifacts and retrieve those that we have access to
+ to_download = []
+ vfabu = validate_filepath_access_by_user
+ for a in study.artifacts():
+ if a.artifact_type == 'BIOM':
+ to_add = True
+ for i, (fid, path, data_type) in enumerate(a.filepaths):
+ # validate access only of the first artifact filepath,
+ # the rest have the same permissions
+ if (i == 0 and not vfabu(user, fid)):
+ to_add = False
+ break
+ # ignore if tgz as they could create problems and the
+ # raw data is in the folder
+ if data_type == 'tgz':
+ continue
+ if data_type == 'directory':
+ # If we have a directory, we actually need to list
+ # all the files from the directory so NGINX can
+ # actually download all of them
+ for dp, _, fps in walk(path):
+ for fname in fps:
+ fullpath = join(dp, fname)
+ spath = fullpath
+ if fullpath.startswith(basedir):
+ spath = fullpath[basedir_len:]
+ to_download.append((fullpath, spath, spath))
+ elif path.startswith(basedir):
+ spath = path[basedir_len:]
+ to_download.append((path, spath, spath))
+ else:
+ # We are not aware of any case that can trigger this
+ # situation, but we wanted to be overly cautious
+ # There is no test for this line cause we don't know
+ # how to trigger it
+ to_download.append((path, path, path))
+
+ if to_add:
+ for pt in a.prep_templates:
+ qmf = pt.qiime_map_fp
+ if qmf is not None:
+ sqmf = qmf
+ if qmf.startswith(basedir):
+ sqmf = qmf[basedir_len:]
+ to_download.append(
+ (qmf, sqmf, 'mapping_files/%s_mapping_file.txt'
+ % a.id))
+
+ # If we don't have nginx, write a file that indicates this
+ all_files = '\n'.join(["- %s /protected/%s %s" % (getsize(fp), sfp, n)
+ for fp, sfp, n in to_download])
+ self.write("%s\n" % all_files)
+
+ zip_fn = 'study_%d_%s.zip' % (
+ study_id, datetime.now().strftime('%m%d%y-%H%M%S'))
+
+ self.set_header('Content-Description', 'File Transfer')
+ self.set_header('Expires', '0')
+ self.set_header('Cache-Control', 'no-cache')
+ self.set_header('X-Archive-Files', 'zip')
+ self.set_header('Content-Disposition',
+ 'attachment; filename=%s' % zip_fn)
+ self.finish()
diff --git a/qiita_pet/nginx_example.conf b/qiita_pet/nginx_example.conf
index f0cca6f81..27dd4d0f5 100644
--- a/qiita_pet/nginx_example.conf
+++ b/qiita_pet/nginx_example.conf
@@ -18,7 +18,7 @@ http {
internal;
# CHANGE ME: This should match the BASE_DATA_DIR in your qiita
- # config. E.g.,
+ # config. E.g.,
# alias /Users/username/qiita/qiita_db/support_files/test_data/;
alias ;
}
@@ -30,6 +30,7 @@ http {
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header Accept-Encoding identity;
}
}
}
diff --git a/qiita_pet/templates/study_base.html b/qiita_pet/templates/study_base.html
index 3e16e9fa9..34b604bf4 100644
--- a/qiita_pet/templates/study_base.html
+++ b/qiita_pet/templates/study_base.html
@@ -239,6 +239,7 @@
Upload Files
{% end %}
+ All QIIME maps and BIOMs
diff --git a/qiita_pet/test/test_download.py b/qiita_pet/test/test_download.py
new file mode 100644
index 000000000..5fbc5a4d8
--- /dev/null
+++ b/qiita_pet/test/test_download.py
@@ -0,0 +1,142 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from unittest import main
+from mock import Mock
+from os.path import exists, isdir, join
+from os import remove, makedirs
+from shutil import rmtree
+from tempfile import mkdtemp
+
+from biom.util import biom_open
+from biom import example_table as et
+
+from qiita_pet.test.tornado_test_base import TestHandlerBase
+from qiita_pet.handlers.base_handlers import BaseHandler
+from qiita_db.user import User
+from qiita_db.artifact import Artifact
+from qiita_db.software import Parameters, Command
+
+
+class TestDownloadHandler(TestHandlerBase):
+
+ def setUp(self):
+ super(TestDownloadHandler, self).setUp()
+
+ def tearDown(self):
+ super(TestDownloadHandler, self).tearDown()
+
+ def test_download(self):
+ # check success
+ response = self.get('/download/1')
+ self.assertEqual(response.code, 200)
+ self.assertEqual(response.body, (
+ "This installation of Qiita was not equipped with nginx, so it "
+ "is incapable of serving files. The file you attempted to "
+ "download is located at raw_data/1_s_G1_L001_sequences.fastq.gz"))
+
+ # failure
+ response = self.get('/download/1000')
+ self.assertEqual(response.code, 404)
+
+
+class TestDownloadStudyBIOMSHandler(TestHandlerBase):
+
+ def setUp(self):
+ super(TestDownloadStudyBIOMSHandler, self).setUp()
+ self._clean_up_files = []
+
+ def tearDown(self):
+ super(TestDownloadStudyBIOMSHandler, self).tearDown()
+ for fp in self._clean_up_files:
+ if exists(fp):
+ if isdir(fp):
+ rmtree(fp)
+ else:
+ remove(fp)
+
+ def test_download_study(self):
+ tmp_dir = mkdtemp()
+ self._clean_up_files.append(tmp_dir)
+
+ biom_fp = join(tmp_dir, 'otu_table.biom')
+ smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
+ log_dir = join(smr_dir, 'seqs_otus.log')
+ tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
+
+ with biom_open(biom_fp, 'w') as f:
+ et.to_hdf5(f, "test")
+ makedirs(smr_dir)
+ with open(log_dir, 'w') as f:
+ f.write('\n')
+ with open(tgz, 'w') as f:
+ f.write('\n')
+
+ self._clean_up_files.append(tmp_dir)
+
+ files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
+
+ params = Parameters.from_default_params(
+ Command(3).default_parameter_sets.next(), {'input_data': 1})
+ a = Artifact.create(files_biom, "BIOM", parents=[Artifact(2)],
+ processing_parameters=params)
+ for _, fp, _ in a.filepaths:
+ self._clean_up_files.append(fp)
+
+ response = self.get('/download_study_bioms/1')
+ self.assertEqual(response.code, 200)
+ exp = (
+ '- 1256812 /protected/processed_data/1_study_1001_closed_'
+ 'reference_otu_table.biom processed_data/1_study_1001_closed_'
+ 'reference_otu_table.biom\n'
+ '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
+ '[0-9]*.txt mapping_files/4_mapping_file.txt\n'
+ '- 1256812 /protected/processed_data/'
+ '1_study_1001_closed_reference_otu_table.biom processed_data/'
+ '1_study_1001_closed_reference_otu_table.biom\n'
+ '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
+ '[0-9]*.txt mapping_files/5_mapping_file.txt\n'
+ '- 1256812 /protected/processed_data/'
+ '1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
+ '/1_study_1001_closed_reference_otu_table_Silva.biom\n'
+ '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
+ '[0-9]*.txt mapping_files/6_mapping_file.txt\n'
+ '- 36615 /protected/templates/1_prep_2_qiime_[0-9]*-'
+ '[0-9]*.txt mapping_files/7_mapping_file.txt\n'
+ '- 39752 /protected/BIOM/{0}/otu_table.biom '
+ 'BIOM/{0}/otu_table.biom\n'
+ '- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
+ 'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
+ '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
+ 'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
+ self.assertRegexpMatches(response.body, exp)
+
+ response = self.get('/download_study_bioms/200')
+ self.assertEqual(response.code, 405)
+
+ # changing user so we can test the failures
+ BaseHandler.get_current_user = Mock(
+ return_value=User("demo@microbio.me"))
+ response = self.get('/download_study_bioms/1')
+ self.assertEqual(response.code, 405)
+
+ a.visibility = 'public'
+ response = self.get('/download_study_bioms/1')
+ self.assertEqual(response.code, 200)
+ exp = (
+ '- 39752 /protected/BIOM/{0}/otu_table.biom '
+ 'BIOM/{0}/otu_table.biom\n'
+ '- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
+ 'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
+ '- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
+ 'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
+ self.assertRegexpMatches(response.body, exp)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py
index 42952d478..15185601d 100644
--- a/qiita_pet/webserver.py
+++ b/qiita_pet/webserver.py
@@ -38,7 +38,8 @@
from qiita_pet.handlers.logger_handlers import LogEntryViewerHandler
from qiita_pet.handlers.upload import UploadFileHandler, StudyUploadFileHandler
from qiita_pet.handlers.stats import StatsHandler
-from qiita_pet.handlers.download import DownloadHandler
+from qiita_pet.handlers.download import (
+ DownloadHandler, DownloadStudyBIOMSHandler)
from qiita_pet.handlers.prep_template import PrepTemplateHandler
from qiita_pet.handlers.ontology import OntologyHandler
from qiita_db.handlers.processing_job import (
@@ -144,6 +145,7 @@ def __init__(self):
(r"/check_study/", CreateStudyAJAX),
(r"/stats/", StatsHandler),
(r"/download/(.*)", DownloadHandler),
+ (r"/download_study_bioms/(.*)", DownloadStudyBIOMSHandler),
(r"/vamps/(.*)", VAMPSHandler),
# Plugin handlers - the order matters here so do not change
# qiita_db/jobs/(.*) should go after any of the