def submit_VAMPS(artifact_id):
"""Submit artifact to VAMPS
Parameters
----------
artifact_id : int
The artifact id
Raises
------
ComputeError
- If the artifact cannot be submitted to VAMPS
- If the artifact is associated with more than one prep template
"""
artifact = Artifact(artifact_id)
if not artifact.can_be_submitted_to_vamps:
raise ComputeError("Artifact %d cannot be submitted to VAMPS" %
artifact_id)
study = artifact.study
sample_template = study.sample_template
prep_templates = artifact.prep_templates
if len(prep_templates) > 1:
raise ComputeError(
"Multiple prep templates associated with the artifact: %s" %
artifact_id)
prep_template = prep_templates[0]
# Also need to check that is not submitting (see item in #1523)
if artifact.is_submitted_to_vamps:
raise ValueError("Cannot resubmit artifact %s to VAMPS!" % artifact_id)
# Generating a tgz
targz_folder = mkdtemp(prefix=qiita_config.working_dir)
targz_fp = join(targz_folder,
'%d_%d_%d.tgz' % (study.id, prep_template.id, artifact_id))
targz = taropen(targz_fp, mode='w:gz')
# adding sample/prep
samp_fp = join(targz_folder, 'sample_metadata.txt')
sample_template.to_file(samp_fp)
targz.add(samp_fp, arcname='sample_metadata.txt')
prep_fp = join(targz_folder, 'prep_metadata.txt')
prep_template.to_file(prep_fp)
targz.add(prep_fp, arcname='prep_metadata.txt')
# adding preprocessed data
for _, fp, fp_type in artifact.filepaths:
if fp_type == 'preprocessed_fasta':
targz.add(fp, arcname='preprocessed_fasta.fna')
targz.close()
# submitting
cmd = ("curl -F user=%s -F pass='******' -F uploadFile=@%s -F "
"press=UploadFile %s" %
(qiita_config.vamps_user, qiita_config.vamps_pass, targz_fp,
qiita_config.vamps_url))
obs, stderr, rv = system_call(cmd)
if rv != 0:
error_msg = ("Error:\nStd output:%s\nStd error:%s" % (obs, stderr))
raise ComputeError(error_msg)
exp = ("<html>\n<head>\n<title>Process Uploaded File</title>\n</head>\n"
"<body>\n</body>\n</html>")
if obs != exp:
return False
else:
artifact.is_submitted_to_vamps = True
return True
def submit_VAMPS(artifact_id):
"""Submit artifact to VAMPS
Parameters
----------
artifact_id : int
The artifact id
Raises
------
ComputeError
- If the artifact cannot be submitted to VAMPS
- If the artifact is associated with more than one prep template
"""
artifact = Artifact(artifact_id)
if not artifact.can_be_submitted_to_vamps:
raise ComputeError("Artifact %d cannot be submitted to VAMPS"
% artifact_id)
study = artifact.study
sample_template = study.sample_template
prep_templates = artifact.prep_templates
if len(prep_templates) > 1:
raise ComputeError(
"Multiple prep templates associated with the artifact: %s"
% artifact_id)
prep_template = prep_templates[0]
# Also need to check that is not submitting (see item in #1523)
if artifact.is_submitted_to_vamps:
raise ValueError("Cannot resubmit artifact %s to VAMPS!" % artifact_id)
# Generating a tgz
targz_folder = mkdtemp(prefix=qiita_config.working_dir)
targz_fp = join(targz_folder, '%d_%d_%d.tgz' % (study.id,
prep_template.id,
artifact_id))
targz = taropen(targz_fp, mode='w:gz')
# adding sample/prep
samp_fp = join(targz_folder, 'sample_metadata.txt')
sample_template.to_file(samp_fp)
targz.add(samp_fp, arcname='sample_metadata.txt')
prep_fp = join(targz_folder, 'prep_metadata.txt')
prep_template.to_file(prep_fp)
targz.add(prep_fp, arcname='prep_metadata.txt')
# adding preprocessed data
for _, fp, fp_type in artifact.filepaths:
if fp_type == 'preprocessed_fasta':
targz.add(fp, arcname='preprocessed_fasta.fna')
targz.close()
# submitting
cmd = ("curl -F user=%s -F pass='******' -F uploadFile=@%s -F "
"press=UploadFile %s" % (qiita_config.vamps_user,
qiita_config.vamps_pass,
targz_fp,
qiita_config.vamps_url))
obs, stderr, rv = system_call(cmd)
if rv != 0:
error_msg = ("Error:\nStd output:%s\nStd error:%s" % (obs, stderr))
raise ComputeError(error_msg)
exp = ("<html>\n<head>\n<title>Process Uploaded File</title>\n</head>\n"
"<body>\n</body>\n</html>")
if obs != exp:
return False
else:
artifact.is_submitted_to_vamps = True
return True
