fix #3455

qiita_db/meta_util.py

@@ -22,7 +22,8 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from os import stat, rename
+from os import stat
+from shutil import move
 from os.path import join, relpath, basename
 from time import strftime, localtime
 import matplotlib.pyplot as plt
@@ -48,6 +49,8 @@
     "sName", "sVersion", "cID", "cName", "processing_job_id",
     "parameters", "samples", "columns", "input_size", "extra_info",
     "MaxRSSRaw", "ElapsedRaw", "Start", "node_name", "node_model"]
+RAW_DATA_ARTIFACT_TYPE = {
+        'SFF', 'FASTQ', 'FASTA', 'FASTA_Sanger', 'per_sample_FASTQ'}
 
 
 def _get_data_fpids(constructor, object_id):
@@ -118,9 +121,7 @@ def validate_filepath_access_by_user(user, filepath_id):
 
             if artifact.visibility == 'public':
                 # TODO: https://github.com/biocore/qiita/issues/1724
-                if artifact.artifact_type in ['SFF', 'FASTQ', 'FASTA',
-                                              'FASTA_Sanger',
-                                              'per_sample_FASTQ']:
+                if artifact.artifact_type in RAW_DATA_ARTIFACT_TYPE:
                     study = artifact.study
                     has_access = study.has_access(user, no_public=True)
                     if (not study.public_raw_download and not has_access):
@@ -469,7 +470,7 @@ def generate_biom_and_metadata_release(study_status='public'):
         for c in iter(lambda: f.read(4096), b""):
             md5sum.update(c)
 
-    rename(tgz_name, tgz_name_final)
+    move(tgz_name, tgz_name_final)
 
     vals = [
         ('filepath', tgz_name_final[len(working_dir):], r_client.set),
@@ -543,7 +544,7 @@ def generate_plugin_releases():
         md5sum = md5()
         for c in iter(lambda: f.read(4096), b""):
             md5sum.update(c)
-    rename(tgz_name, tgz_name_final)
+    move(tgz_name, tgz_name_final)
     vals = [
         ('filepath', tgz_name_final[len(working_dir):], r_client.set),
         ('md5sum', md5sum.hexdigest(), r_client.set),

qiita_db/support_files/populate_test_db.sql

@@ -88,6 +88,7 @@ INSERT INTO qiita.artifact_type VALUES (5, 'per_sample_FASTQ', NULL, true, false
 INSERT INTO qiita.artifact_type VALUES (7, 'BIOM', 'BIOM table', false, false, true);
 
 
+
 --
 -- Data for Name: data_type; Type: TABLE DATA; Schema: qiita; Owner: antoniog
 --

qiita_db/util.py

@@ -49,7 +49,7 @@
 from bcrypt import hashpw, gensalt
 from functools import partial
 from os.path import join, basename, isdir, exists, getsize
-from os import walk, remove, listdir, rename, stat, makedirs
+from os import walk, remove, listdir, stat, makedirs
 from glob import glob
 from shutil import move, rmtree, copy as shutil_copy
 from openpyxl import load_workbook
@@ -542,7 +542,7 @@ def move_upload_files_to_trash(study_id, files_to_move):
         new_fullpath = join(foldername, trash_folder, filename)
 
         if exists(fullpath):
-            rename(fullpath, new_fullpath)
+            move(fullpath, new_fullpath)
 
 
 def get_mountpoint(mount_type, retrieve_all=False, retrieve_subdir=False):
@@ -2297,7 +2297,9 @@ def send_email(to, subject, body):
     msg = MIMEMultipart()
     msg['From'] = qiita_config.smtp_email
     msg['To'] = to
-    msg['Subject'] = subject.strip()
+    # we need to do 'replace' because the subject can have
+    # new lines in the middle of the string
+    msg['Subject'] = subject.replace('\n', '')
     msg.attach(MIMEText(body, 'plain'))
 
     # connect to smtp server, using ssl if needed

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -21,6 +21,7 @@
 from qiita_db.processing_job import ProcessingJob
 from qiita_db.util import get_visibilities, send_email
 from qiita_db.logger import LogEntry
+from qiita_db.meta_util import RAW_DATA_ARTIFACT_TYPE
 
 
 PREP_TEMPLATE_KEY_FORMAT = 'prep_template_%s'
@@ -208,8 +209,7 @@ def artifact_summary_get_request(user, artifact_id):
     # TODO: https://github.com/biocore/qiita/issues/1724 Remove this hardcoded
     # values to actually get the information from the database once it stores
     # the information
-    if artifact_type in ['SFF', 'FASTQ', 'FASTA', 'FASTA_Sanger',
-                         'per_sample_FASTQ']:
+    if artifact_type in RAW_DATA_ARTIFACT_TYPE:
         # If the artifact is one of the "raw" types, only the owner of the
         # study and users that has been shared with can see the files
         study = artifact.study

setup.py

@@ -105,7 +105,8 @@
       install_requires=['psycopg2', 'click', 'bcrypt', 'pandas<2.0',
                         'biom-format', 'tornado<6.0', 'toredis', 'redis',
                         'scp', 'pyparsing', 'h5py',  'natsort', 'nose', 'pep8',
-                        'networkx', 'humanize', 'wtforms<3.0.0', 'nltk<=3.8.1',
+                        'networkx', 'humanize==4.11', 'wtforms<3.0.0',
+                        'nltk<=3.8.1',
                         'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx<3.0',
                         'gitpython', 'redbiom', 'pyzmq', 'sphinx_rtd_theme',
                         'paramiko', 'seaborn',  'matplotlib', 'scipy<=1.10.1',