diff --git a/.gitignore b/.gitignore index e83fe2067..d8079ce60 100644 --- a/.gitignore +++ b/.gitignore @@ -75,3 +75,6 @@ notebooks/*/*.tsv.gz # jupyter notebooks input data notebooks/resource-allocation/data + +# ignore plugin SQL injection file +qiita_db/support_files/patches/test_db_sql/91.sql diff --git a/qiita_pet/handlers/study_handlers/prep_template.py b/qiita_pet/handlers/study_handlers/prep_template.py index e29d31d63..6afcde59c 100644 --- a/qiita_pet/handlers/study_handlers/prep_template.py +++ b/qiita_pet/handlers/study_handlers/prep_template.py @@ -77,18 +77,22 @@ def get(self): res['alert_message'] = url_escape(res['alert_message']) res['user_level'] = current_user.level if res['creation_job'] is not None: - fp = res['creation_job'].parameters.values['sample_sheet'] - res['creation_job_filename'] = fp['filename'] - res['creation_job_filename_body'] = fp['body'] + params = res['creation_job'].parameters.values summary = None - if res['creation_job'].status == 'success': - if res['creation_job'].outputs: - # [0] is the id, [1] is the filepath - _file = res['creation_job'].outputs[ - 'output'].html_summary_fp[1] - summary = relpath(_file, qiita_config.base_data_dir) + if 'sample_sheet' in params: + fp = params['sample_sheet'] + res['creation_job_filename'] = fp['filename'] + res['creation_job_filename_body'] = fp['body'] + if res['creation_job'].status == 'success': + if res['creation_job'].outputs: + # [0] is the id, [1] is the filepath + _file = res['creation_job'].outputs[ + 'output'].html_summary_fp[1] + summary = relpath(_file, qiita_config.base_data_dir) + else: + res['creation_job_filename'] = None + res['creation_job_filename_body'] = None res['creation_job_artifact_summary'] = summary - # res[''] res['human_reads_filter_method'] = None a = PrepTemplate(prep_id).artifact if a is not None: diff --git a/qiita_ware/ebi.py b/qiita_ware/ebi.py index 7c7861ec4..51e2bf762 100644 --- a/qiita_ware/ebi.py +++ b/qiita_ware/ebi.py @@ -33,6 +33,12 @@ from qiita_db.processing_job import _system_call as system_call +ENA_COLS_TO_FIX = { + 'country': 'geographic location (country and/or sea)', + 'collection_date': 'collection date' +} + + def clean_whitespace(text): """Standardizes whitespaces so there is only one space separating tokens @@ -406,9 +412,9 @@ def generate_sample_xml(self, samples=None, ignore_columns=None): for sample_name in sorted(samples): sample_info = dict(self.samples[sample_name]) - if 'country' in sample_info.keys(): - nname = 'geographic location (country and/or sea)' - sample_info[nname] = sample_info['country'] + for qname, ename in ENA_COLS_TO_FIX.items(): + if qname in sample_info.keys(): + sample_info[ename] = sample_info[qname] sample_accession = self._ebi_sample_accessions[sample_name] if self.action in ('ADD', 'VALIDATE'):