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Merged
merged 11 commits into from
Oct 8, 2015
Merged

Ebi: ability to extend a submission #1489

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eb89f3b
Writing XML files conditionally
josenavas Oct 6, 2015
b5b5f57
Fixing ReadOnly tests
josenavas Oct 7, 2015
0022009
Partially fixing read-write errors
josenavas Oct 7, 2015
2facea1
Solving merge conflicts
josenavas Oct 7, 2015
670231e
All EBI tests passing again
josenavas Oct 7, 2015
96128d8
Fixing XML generation and adding a few more tests
josenavas Oct 7, 2015
b1732f6
Fixing commands.py
josenavas Oct 7, 2015
6651167
Merge branch 'ebi-improvements' of https://github.com/biocore/qiita i…
josenavas Oct 7, 2015
51b038e
pep8ing
josenavas Oct 7, 2015
1d80ea3
Addressing comments
josenavas Oct 7, 2015
ea328ce
Adding test
josenavas Oct 7, 2015
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23 changes: 9 additions & 14 deletions qiita_ware/commands.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,16 +60,7 @@ def submit_EBI(preprocessed_data_id, action, send, fastq_dir_fp=None):
raise

# step 3: generate and write xml files
ebi_submission.write_xml_file(ebi_submission.generate_study_xml(),
ebi_submission.study_xml_fp)
ebi_submission.write_xml_file(ebi_submission.generate_sample_xml(),
ebi_submission.sample_xml_fp)
ebi_submission.write_xml_file(ebi_submission.generate_experiment_xml(),
ebi_submission.experiment_xml_fp)
ebi_submission.write_xml_file(ebi_submission.generate_run_xml(),
ebi_submission.run_xml_fp)
ebi_submission.write_xml_file(ebi_submission.generate_submission_xml(),
ebi_submission.submission_xml_fp)
ebi_submission.generate_xml_files()

if send:
# step 4: sending sequences
Expand Down Expand Up @@ -121,10 +112,14 @@ def submit_EBI(preprocessed_data_id, action, send, fastq_dir_fp=None):
raise ComputeError("EBI Submission failed! Log id: %d" % le.id)

ebi_submission.study.ebi_submission_status = 'submitted'
ebi_submission.study.ebi_study_accession = st_acc
ebi_submission.sample_template.ebi_sample_accessions = sa_acc
ebi_submission.sample_template.biosample_accessions = bio_acc
ebi_submission.prep_template.ebi_experiment_accessions = ex_acc
if st_acc:
ebi_submission.study.ebi_study_accession = st_acc
if sa_acc:
ebi_submission.sample_template.ebi_sample_accessions = sa_acc
if bio_acc:
ebi_submission.sample_template.biosample_accessions = bio_acc
if ex_acc:
ebi_submission.prep_template.ebi_experiment_accessions = ex_acc
ebi_submission.preprocessed_data.ebi_run_accessions = run_acc
else:
st_acc, sa_acc, bio_acc, ex_acc, run_acc = None, None, None, None, None
Expand Down
177 changes: 129 additions & 48 deletions qiita_ware/ebi.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from gzip import GzipFile
from functools import partial

from future.utils import viewitems
from future.utils import viewitems, viewkeys
from skbio.util import safe_md5, create_dir

from qiita_core.qiita_settings import qiita_config
Expand Down Expand Up @@ -160,13 +160,13 @@ def __init__(self, preprocessed_data_id, action):

self.ebi_dir = join(qiita_config.working_dir,
'ebi_submission_%d' % preprocessed_data_id)
get_output_fp = partial(join, self.ebi_dir, 'xml_dir')
self.xml_dir = get_output_fp()
self.study_xml_fp = get_output_fp('study.xml')
self.sample_xml_fp = get_output_fp('sample.xml')
self.experiment_xml_fp = get_output_fp('experiment.xml')
self.run_xml_fp = get_output_fp('run.xml')
self.submission_xml_fp = get_output_fp('submission.xml')
self.xml_dir = join(self.ebi_dir, 'xml_dir')
self.study_xml_fp = None
self.sample_xml_fp = None
self.experiment_xml_fp = None
self.run_xml_fp = None
self.submission_xml_fp = None

self.pmids = self.study.pmids

# getting the restrictions
Expand Down Expand Up @@ -234,6 +234,11 @@ def __init__(self, preprocessed_data_id, action):
self._experiment_aliases = {}
self._run_aliases = {}

self._ebi_sample_accessions = \
self.sample_template.ebi_sample_accessions
self._ebi_experiment_accessions = \
self.prep_template.ebi_experiment_accessions

def _get_study_alias(self):
"""Format alias using ``self.preprocessed_data_id``"""
study_alias_format = '%s_sid_%s'
Expand Down Expand Up @@ -350,9 +355,15 @@ def generate_study_xml(self):

return study_set

def generate_sample_xml(self):
def generate_sample_xml(self, samples=None):
"""Generates the sample XML file

Parameters
----------
samples : list of str, optional
The list of samples to be included in the sample xml. If not
provided or an empty list is provided, all the samples are used

Returns
-------
ET.Element
Expand All @@ -362,8 +373,11 @@ def generate_sample_xml(self):
'xmlns:xsi': self.xmlns_xsi,
"xsi:noNamespaceSchemaLocation": self.xsi_noNSL % "sample"})

for sample_name, sample_info in sorted(viewitems(self.samples)):
sample_info = dict(sample_info)
if not samples:
samples = viewkeys(self.samples)

for sample_name in sorted(samples):
sample_info = dict(self.samples[sample_name])
sample = ET.SubElement(sample_set, 'SAMPLE', {
'alias': self._get_sample_alias(sample_name),
'center_name': qiita_config.ebi_center_name}
Expand Down Expand Up @@ -418,22 +432,40 @@ def _generate_spot_descriptor(self, design, platform):
base_coord = ET.SubElement(read_spec, 'BASE_COORD')
base_coord.text = '1'

def generate_experiment_xml(self):
def generate_experiment_xml(self, samples=None):
"""Generates the experiment XML file

Parameters
----------
samples : list of str, optional
The list of samples to be included in the experiment xml

Returns
-------
ET.Element
Object with experiment XML values
"""
study_alias = self._get_study_alias()
study_accession = self.study.ebi_study_accession
if study_accession:
study_ref_dict = {'accession': study_accession}
else:
study_ref_dict = {'refname': self._get_study_alias()}

experiment_set = ET.Element('EXPERIMENT_SET', {
'xmlns:xsi': self.xmlns_xsi,
"xsi:noNamespaceSchemaLocation": self.xsi_noNSL % "experiment"})
for sample_name, sample_prep in sorted(self.samples_prep.items()):
sample_alias = self._get_sample_alias(sample_name)

samples = samples if samples is not None else viewkeys(self.samples)

for sample_name in sorted(samples):
experiment_alias = self._get_experiment_alias(sample_name)
sample_prep = dict(self.samples_prep[sample_name])
if self._ebi_sample_accessions[sample_name]:
sample_descriptor_dict = {
'accession': self._ebi_sample_accessions[sample_name]}
else:
sample_descriptor_dict = {
'refname': self._get_sample_alias(sample_name)}

platform = sample_prep.pop('platform')
experiment = ET.SubElement(experiment_set, 'EXPERIMENT', {
Expand All @@ -442,18 +474,14 @@ def generate_experiment_xml(self):
)
title = ET.SubElement(experiment, 'TITLE')
title.text = experiment_alias
ET.SubElement(experiment, 'STUDY_REF', {
'refname': study_alias}
)
ET.SubElement(experiment, 'STUDY_REF', study_ref_dict)

design = ET.SubElement(experiment, 'DESIGN')
design_description = ET.SubElement(design,
'DESIGN_DESCRIPTION')
edd = sample_prep.pop('experiment_design_description')
design_description.text = escape(clean_whitespace(edd))
ET.SubElement(
design, 'SAMPLE_DESCRIPTOR', {'refname': sample_alias}
)
ET.SubElement(design, 'SAMPLE_DESCRIPTOR', sample_descriptor_dict)

# this is the library contruction section. The only required fields
# is library_construction_protocol, the other are optional
Expand Down Expand Up @@ -513,10 +541,15 @@ def generate_run_xml(self):
run_set = ET.Element('RUN_SET', {
'xmlns:xsi': self.xmlns_xsi,
"xsi:noNamespaceSchemaLocation": self.xsi_noNSL % "run"})
for sample_name, sample_prep in viewitems(self.samples_prep):
for sample_name, sample_prep in sorted(viewitems(self.samples_prep)):
sample_prep = dict(sample_prep)

experiment_alias = self._get_experiment_alias(sample_name)
if self._ebi_experiment_accessions[sample_name]:
experiment_ref_dict = {
'accession': self._ebi_experiment_accessions[sample_name]}
else:
experiment_alias = self._get_experiment_alias(sample_name)
experiment_ref_dict = {'refname': experiment_alias}

# We only submit fastq
file_type = 'fastq'
Expand All @@ -529,9 +562,7 @@ def generate_run_xml(self):
'alias': self._get_run_alias(sample_name),
'center_name': qiita_config.ebi_center_name}
)
ET.SubElement(run, 'EXPERIMENT_REF', {
'refname': experiment_alias}
)
ET.SubElement(run, 'EXPERIMENT_REF', experiment_ref_dict)
data_block = ET.SubElement(run, 'DATA_BLOCK')
files = ET.SubElement(data_block, 'FILES')
ET.SubElement(files, 'FILE', {
Expand Down Expand Up @@ -573,23 +604,26 @@ def generate_submission_xml(self, submission_date=None):

actions = ET.SubElement(submission, 'ACTIONS')

study_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(study_action, self.action, {
'schema': 'study',
'source': basename(self.study_xml_fp)}
)
if self.study_xml_fp:
study_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(study_action, self.action, {
'schema': 'study',
'source': basename(self.study_xml_fp)}
)

sample_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(sample_action, self.action, {
'schema': 'sample',
'source': basename(self.sample_xml_fp)}
)
if self.sample_xml_fp:
sample_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(sample_action, self.action, {
'schema': 'sample',
'source': basename(self.sample_xml_fp)}
)

experiment_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(experiment_action, self.action, {
'schema': 'experiment',
'source': basename(self.experiment_xml_fp)}
)
if self.experiment_xml_fp:
experiment_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(experiment_action, self.action, {
'schema': 'experiment',
'source': basename(self.experiment_xml_fp)}
)

run_action = ET.SubElement(actions, 'ACTION')
ET.SubElement(run_action, self.action, {
Expand Down Expand Up @@ -620,6 +654,51 @@ def write_xml_file(self, element, fp):
create_dir(self.xml_dir)
ET.ElementTree(element).write(fp, encoding='UTF-8')

def generate_xml_files(self):
"""Generate all the XML files"""
get_output_fp = partial(join, self.xml_dir)

# The study.xml file needs to be generated if and only if the study
# does NOT have an ebi_study_accession
if not self.study.ebi_study_accession:
self.study_xml_fp = get_output_fp('study.xml')
self.write_xml_file(self.generate_study_xml(), self.study_xml_fp)

# The sample.xml file needs to be generated if and only if there are
# samples in the current submission that do NOT have an
# ebi_sample_accession
new_samples = {
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Should this be the prep template and not the sample template?

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No, the ebi_sample_accessions are stored in the sample template.

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K, thanks!

sample for sample, accession in viewitems(
self.sample_template.ebi_sample_accessions)
if accession is None}
new_samples = new_samples.intersection(self.samples)
if new_samples:
self.sample_xml_fp = get_output_fp('sample.xml')
self.write_xml_file(self.generate_sample_xml(new_samples),
self.sample_xml_fp)

# The experiment.xml needs to be generated if and only if there are
# samples in the current submission that do NO have an
# ebi_experiment_accession
new_samples = {
sample for sample, accession in viewitems(
self.prep_template.ebi_experiment_accessions)
if accession is None}
new_samples = new_samples.intersection(self.samples)
if new_samples:
self.experiment_xml_fp = get_output_fp('experiment.xml')
self.write_xml_file(self.generate_experiment_xml(new_samples),
self.experiment_xml_fp)

# Generate the run.xml as it should always be generated
self.run_xml_fp = get_output_fp('run.xml')
self.write_xml_file(self.generate_run_xml(), self.run_xml_fp)

# The submission.xml is always generated
self.submission_xml_fp = get_output_fp('submission.xml')
self.write_xml_file(self.generate_submission_xml(),
self.submission_xml_fp)

def generate_curl_command(
self,
ebi_seq_xfer_user=qiita_config.ebi_seq_xfer_user,
Expand Down Expand Up @@ -743,13 +822,15 @@ def parse_EBI_reply(self, curl_result):
% curl_result)

study_elem = root.findall("STUDY")
if len(study_elem) > 1:
raise EBISubmissionError(
"Multiple study tags found in EBI reply: %d\n%s"
% (len(study_elem),
"".join([ET.tostring(s) for s in study_elem])))
study_elem = study_elem[0]
study_accession = study_elem.get('accession')
if study_elem:
if len(study_elem) > 1:
raise EBISubmissionError(
"Multiple study tags found in EBI reply: %d"
% len(study_elem))
study_elem = study_elem[0]
study_accession = study_elem.get('accession')
else:
study_accession = None

sample_accessions = {}
biosample_accessions = {}
Expand Down
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