def _summary_demultiplexed(artifact_type, filepaths):
"""Generates the HTML summary for Demultiplexed artifacts
Parameters
----------
artifact_type : str
The artifact type
filepaths : [(str, str)]
A list of string pairs where the first element is the filepath and the
second is the filepath type
Returns
-------
list
A list of strings with the html summary
"""
# loop over each of the fps/fps_type pairs to find the demux_fp
demux_fps = filepaths.get('preprocessed_demux', None)
if demux_fps is None:
return None
# If demux_fps exists, it should contain only a single file
demux_fp = demux_fps[0]
# generating html summary
artifact_information = []
sn, smax, smin, smean, sstd, smedian, shist, shist_edge = demux_stats(
demux_fp)
artifact_information.append("<h3>Features</h3>")
artifact_information.append('<b>Total</b>: %d' % sn)
artifact_information.append("<br/>")
artifact_information.append('<b>Max</b>: %d' % smax)
artifact_information.append("<br/>")
artifact_information.append('<b>Mean</b>: %d' % smean)
artifact_information.append("<br/>")
artifact_information.append('<b>Standard deviation</b>: %d' % sstd)
artifact_information.append("<br/>")
artifact_information.append('<b>Median</b>: %d' % smedian)
artifact_information.append("<br/>")
# taken from http://stackoverflow.com/a/9141911
plt.bar(shist_edge[:-1], shist, width=1)
plt.xlim(min(shist_edge), max(shist_edge))
plt.xlabel('Sequence Length')
plt.ylabel('Number of sequences')
plot = BytesIO()
plt.savefig(plot, format='png')
plot.seek(0)
artifact_information.append(
'<img src = "data:image/png;base64,{}"/>'.format(
b64encode(plot.getvalue()).decode('utf-8')))
return artifact_information
def _summary_demultiplexed(artifact_type, filepaths):
"""Generates the HTML summary for Demultiplexed artifacts
Parameters
----------
artifact_type : str
The artifact type
filepaths : [(str, str)]
A list of string pairs where the first element is the filepath and the
second is the filepath type
Returns
-------
list
A list of strings with the html summary
"""
# loop over each of the fps/fps_type pairs to find the demux_fp
demux_fps = filepaths.get('preprocessed_demux', None)
if demux_fps is None:
return None
# If demux_fps exists, it should contain only a single file
demux_fp = demux_fps[0]
# generating html summary
artifact_information = []
sn, smax, smin, smean, sstd, smedian, shist, shist_edge = demux_stats(
demux_fp)
artifact_information.append("<h3>Features</h3>")
artifact_information.append('<b>Total</b>: %d' % sn)
artifact_information.append("<br/>")
artifact_information.append('<b>Max</b>: %d' % smax)
artifact_information.append("<br/>")
artifact_information.append('<b>Mean</b>: %d' % smean)
artifact_information.append("<br/>")
artifact_information.append('<b>Standard deviation</b>: %d' % sstd)
artifact_information.append("<br/>")
artifact_information.append('<b>Median</b>: %d' % smedian)
artifact_information.append("<br/>")
# taken from http://stackoverflow.com/a/9141911
plt.bar(shist_edge[:-1], shist, width=1)
plt.xlim(min(shist_edge), max(shist_edge))
plt.xlabel('Sequence Length')
plt.ylabel('Number of sequences')
plot = StringIO()
plt.savefig(plot, format='png')
plot.seek(0)
uri = 'data:image/png;base64,' + quote(b64encode(plot.buf))
artifact_information.append('<img src = "%s"/>' % uri)
return artifact_information
def display_template(self, artifact_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
artifact_id = int(artifact_id)
try:
artifact = Artifact(artifact_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
artifact_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/EBISubmitHandler: %s!" % user.id)
prep_templates = artifact.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = artifact.study
sample_template = study.sample_template
stats = {
'Number of samples': len(prep_template),
'Number of metadata headers': len(sample_template.categories()),
'Number of sequences': 'N/A',
'Total forward': 'N/A',
'Total reverse': 'N/A'
}
artifact_type = artifact.artifact_type
if artifact_type not in VALID_SUBMISSION_TYPES:
msg = "You can only submit: '%s' and this artifact is '%s'" % (
', '.join(VALID_SUBMISSION_TYPES), artifact_type)
msg_level = 'danger'
elif artifact_type == 'Demultiplexed':
demux = [x['fp'] for x in artifact.filepaths
if x['fp_type'] == 'preprocessed_demux']
demux_length = len(demux)
if demux_length > 1:
msg = "Study appears to have multiple demultiplexed files!"
msg_level = 'danger'
else:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats['Number of sequences'] = demux_file_stats.n
msg_level = 'success'
elif artifact_type == 'per_sample_FASTQ':
raw_forward_seqs = []
raw_reverse_seqs = []
for x in artifact.filepaths:
if x['fp_type'] == 'raw_forward_seqs':
raw_forward_seqs.append(x['fp'])
elif x['fp_type'] == 'raw_reverse_seqs':
raw_reverse_seqs.append(x['fp'])
stats['Total forward'] = len(raw_forward_seqs)
stats['Total reverse'] = len(raw_reverse_seqs)
msg_level = 'success'
# Check if the templates have all the required columns for EBI
pt_missing_cols = prep_template.check_restrictions(
[PREP_TEMPLATE_COLUMNS['EBI']])
st_missing_cols = sample_template.check_restrictions(
[SAMPLE_TEMPLATE_COLUMNS['EBI']])
allow_submission = (len(pt_missing_cols) == 0 and
len(st_missing_cols) == 0 and allow_submission)
if not allow_submission:
if len(pt_missing_cols) > 0:
msg_list.append("Columns missing in prep template: %s"
% ', '.join(pt_missing_cols))
if len(st_missing_cols) > 0:
msg_list.append("Columns missing in sample template: %s"
% ', '.join(st_missing_cols))
ebi_disabled_msg = "<br/>".join(msg_list)
else:
ebi_disabled_msg = None
self.render('ebi_submission.html',
study_title=study.title, stats=stats.items(), message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=artifact_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
ebi_disabled_msg=ebi_disabled_msg)
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(
404, "Artifact %d does not exist!" % preprocessed_data_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(
403, "No permissions of admin, "
"get/VAMPSSubmitHandler: %s!" % user.id)
prep_templates = preprocessed_data.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = preprocessed_data.study
sample_template = study.sample_template
stats = [('Number of samples', len(prep_template)),
('Number of metadata headers',
len(sample_template.categories()))]
demux = [
path for _, path, ftype in preprocessed_data.filepaths
if ftype == 'preprocessed_demux'
]
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
# In EBI here we check that we have the required field for submission,
# however for VAMPS we don't need that
if not allow_submission:
disabled_msg = "<br/>".join(msg_list)
else:
disabled_msg = None
self.render('vamps_submission.html',
study_title=study.title,
stats=stats,
message=msg,
study_id=study.id,
level=msg_level,
preprocessed_data_id=preprocessed_data_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
disabled_msg=disabled_msg)
def display_template(self, artifact_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
artifact_id = int(artifact_id)
try:
artifact = Artifact(artifact_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
artifact_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/EBISubmitHandler: %s!" % user.id)
prep_templates = artifact.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = artifact.study
sample_template = study.sample_template
stats = {
'Number of samples': len(prep_template),
'Number of metadata headers': len(sample_template.categories()),
'Number of sequences': 'N/A',
'Total forward': 'N/A',
'Total reverse': 'N/A'
}
artifact_type = artifact.artifact_type
if artifact_type not in VALID_SUBMISSION_TYPES:
msg = "You can only submit: '%s' and this artifact is '%s'" % (
', '.join(VALID_SUBMISSION_TYPES), artifact_type)
msg_level = 'danger'
elif artifact_type == 'Demultiplexed':
demux = [path for _, path, ftype in artifact.filepaths
if ftype == 'preprocessed_demux']
demux_length = len(demux)
if demux_length > 1:
msg = "Study appears to have multiple demultiplexed files!"
msg_level = 'danger'
else:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats['Number of sequences'] = demux_file_stats.n
msg_level = 'success'
elif artifact_type == 'per_sample_FASTQ':
raw_forward_seqs = []
raw_reverse_seqs = []
for _, path, ftype in artifact.filepaths:
if ftype == 'raw_forward_seqs':
raw_forward_seqs.append(path)
elif ftype == 'raw_reverse_seqs':
raw_reverse_seqs.append(path)
stats['Total forward'] = len(raw_forward_seqs)
stats['Total reverse'] = len(raw_reverse_seqs)
msg_level = 'success'
# Check if the templates have all the required columns for EBI
pt_missing_cols = prep_template.check_restrictions(
[PREP_TEMPLATE_COLUMNS['EBI']])
st_missing_cols = sample_template.check_restrictions(
[SAMPLE_TEMPLATE_COLUMNS['EBI']])
allow_submission = (len(pt_missing_cols) == 0 and
len(st_missing_cols) == 0 and allow_submission)
if not allow_submission:
if len(pt_missing_cols) > 0:
msg_list.append("Columns missing in prep template: %s"
% ', '.join(pt_missing_cols))
if len(st_missing_cols) > 0:
msg_list.append("Columns missing in sample template: %s"
% ', '.join(st_missing_cols))
ebi_disabled_msg = "<br/>".join(msg_list)
else:
ebi_disabled_msg = None
self.render('ebi_submission.html',
study_title=study.title, stats=stats.items(), message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=artifact_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
ebi_disabled_msg=ebi_disabled_msg)
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
preprocessed_data_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/EBISubmitHandler: %s!" % user.id)
prep_templates = preprocessed_data.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = preprocessed_data.study
sample_template = study.sample_template
stats = [('Number of samples', len(prep_template)),
('Number of metadata headers',
len(sample_template.categories()))]
demux = [path for _, path, ftype in preprocessed_data.filepaths
if ftype == 'preprocessed_demux']
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
# Check if the templates have all the required columns for EBI
pt_missing_cols = prep_template.check_restrictions(
[PREP_TEMPLATE_COLUMNS['EBI']])
st_missing_cols = sample_template.check_restrictions(
[SAMPLE_TEMPLATE_COLUMNS['EBI']])
allow_submission = (len(pt_missing_cols) == 0 and
len(st_missing_cols) == 0 and allow_submission)
if not allow_submission:
if len(pt_missing_cols) > 0:
msg_list.append("Columns missing in prep template: %s"
% ', '.join(pt_missing_cols))
if len(st_missing_cols) > 0:
msg_list.append("Columns missing in sample template: %s"
% ', '.join(st_missing_cols))
ebi_disabled_msg = "<br/>".join(msg_list)
else:
ebi_disabled_msg = None
self.render('ebi_submission.html',
study_title=study.title, stats=stats, message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=preprocessed_data_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
ebi_disabled_msg=ebi_disabled_msg)
len(sample_template.categories()))]
demux = [path for _, path, ftype in preprocessed_data.get_filepaths()
if ftype == 'preprocessed_demux']
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
self.render('vamps_submission.html',
study_title=study.title, stats=stats, message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=preprocessed_data_id)
@authenticated
def get(self, preprocessed_data_id):
self.display_template(preprocessed_data_id, "", "")
@authenticated
@execute_as_transaction
def post(self, preprocessed_data_id):
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
preprocessed_data_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/VAMPSSubmitHandler: %s!" % user.id)
prep_templates = preprocessed_data.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did so it doesn't fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = preprocessed_data.study
sample_template = study.sample_template
stats = [('Number of samples', len(prep_template)),
('Number of metadata headers',
len(sample_template.categories()))]
demux = [x['fp'] for x in preprocessed_data.filepaths
if x['fp_type'] == 'preprocessed_demux']
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
# In EBI here we check that we have the required field for submission,
# however for VAMPS we don't need that
if not allow_submission:
disabled_msg = "<br/>".join(msg_list)
else:
disabled_msg = None
self.render('vamps_submission.html',
study_title=study.title, stats=stats, message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=preprocessed_data_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
disabled_msg=disabled_msg)
def display_template(self, preprocessed_data_id, msg, msg_level):
"""Simple function to avoid duplication of code"""
preprocessed_data_id = int(preprocessed_data_id)
try:
preprocessed_data = Artifact(preprocessed_data_id)
except QiitaDBUnknownIDError:
raise HTTPError(404, reason="Artifact %d does not exist!" %
preprocessed_data_id)
else:
user = self.current_user
if user.level != 'admin':
raise HTTPError(403, reason="No permissions of admin, "
"get/EBISubmitHandler: %s!" % user.id)
prep_templates = preprocessed_data.prep_templates
allow_submission = len(prep_templates) == 1
msg_list = ["Submission to EBI disabled:"]
if not allow_submission:
msg_list.append(
"Only artifacts with a single prep template can be submitted")
# If allow_submission is already false, we technically don't need to
# do the following work. However, there is no clean way to fix this
# using the current structure, so we perform the work as we
# did not fail.
# We currently support only one prep template for submission, so
# grabbing the first one
prep_template = prep_templates[0]
study = preprocessed_data.study
sample_template = study.sample_template
stats = [('Number of samples', len(prep_template)),
('Number of metadata headers',
len(sample_template.categories()))]
demux = [path for _, path, ftype in preprocessed_data.filepaths
if ftype == 'preprocessed_demux']
demux_length = len(demux)
if not demux_length:
msg = ("Study does not appear to have demultiplexed "
"sequences associated")
msg_level = 'danger'
elif demux_length > 1:
msg = ("Study appears to have multiple demultiplexed files!")
msg_level = 'danger'
elif demux_length == 1:
demux_file = demux[0]
demux_file_stats = demux_stats(demux_file)
stats.append(('Number of sequences', demux_file_stats.n))
msg_level = 'success'
# Check if the templates have all the required columns for EBI
pt_missing_cols = prep_template.check_restrictions(
[PREP_TEMPLATE_COLUMNS['EBI']])
st_missing_cols = sample_template.check_restrictions(
[SAMPLE_TEMPLATE_COLUMNS['EBI']])
allow_submission = (len(pt_missing_cols) == 0 and
len(st_missing_cols) == 0 and allow_submission)
if not allow_submission:
if len(pt_missing_cols) > 0:
msg_list.append("Columns missing in prep template: %s"
% ', '.join(pt_missing_cols))
if len(st_missing_cols) > 0:
msg_list.append("Columns missing in sample template: %s"
% ', '.join(st_missing_cols))
ebi_disabled_msg = "<br/>".join(msg_list)
else:
ebi_disabled_msg = None
self.render('ebi_submission.html',
study_title=study.title, stats=stats, message=msg,
study_id=study.id, level=msg_level,
preprocessed_data_id=preprocessed_data_id,
investigation_type=prep_template.investigation_type,
allow_submission=allow_submission,
ebi_disabled_msg=ebi_disabled_msg)