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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,66 @@ | ||
| import os | ||
| import logging | ||
| import pandas as pd | ||
| from airflow.models import Variable | ||
| from igf_airflow.logging.upload_log_msg import send_log_to_channels | ||
| from igf_data.utils.epmc_utils import search_epmc_for_keyword | ||
| from igf_data.utils.confluence_utils import update_confluence_page | ||
| # import os | ||
| # import logging | ||
| # import pandas as pd | ||
| # from airflow.models import Variable | ||
| # from igf_airflow.logging.upload_log_msg import send_log_to_channels | ||
| # from igf_data.utils.epmc_utils import search_epmc_for_keyword | ||
| # from igf_data.utils.confluence_utils import update_confluence_page | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
| # logger = logging.getLogger(__name__) | ||
|
|
||
| CONFLUENCE_CONFIG_FILE = Variable.get('confluence_config', default_var=None) | ||
| SLACK_CONF = Variable.get('slack_conf', default_var=None) | ||
| MS_TEAMS_CONF = Variable.get('ms_teams_conf', default_var=None) | ||
| WIKI_PUBLICATION_PAGE_ID = Variable.get('wiki_publication_page_id', default_var=None) | ||
| WIKI_PUBLICATION_PAGE_TITLE = Variable.get('wiki_publication_page_title', default_var=None) | ||
| # CONFLUENCE_CONFIG_FILE = Variable.get('confluence_config', default_var=None) | ||
| # SLACK_CONF = Variable.get('slack_conf', default_var=None) | ||
| # MS_TEAMS_CONF = Variable.get('ms_teams_conf', default_var=None) | ||
| # WIKI_PUBLICATION_PAGE_ID = Variable.get('wiki_publication_page_id', default_var=None) | ||
| # WIKI_PUBLICATION_PAGE_TITLE = Variable.get('wiki_publication_page_title', default_var=None) | ||
|
|
||
| def update_wiki_publication_page_func(**context): | ||
| try: | ||
| ti = context.get('ti') | ||
| all_data = \ | ||
| search_epmc_for_keyword( | ||
| search_term="\"Imperial BRC Genomics Facility\"") | ||
| columns = [ | ||
| 'title', | ||
| 'authorString', | ||
| 'journalTitle', | ||
| 'firstPublicationDate', | ||
| 'firstIndexDate', | ||
| 'doi'] | ||
| all_df = \ | ||
| pd.DataFrame(all_data)[columns] | ||
| all_df['doi'] = \ | ||
| all_df['doi'].\ | ||
| map(lambda x: 'https://doi.org/{0}'.format(x)) | ||
| html_data = \ | ||
| all_df.\ | ||
| to_html(index=False) | ||
| update_confluence_page( | ||
| confluence_conf_file=CONFLUENCE_CONFIG_FILE, | ||
| page_id=WIKI_PUBLICATION_PAGE_ID, | ||
| page_title=WIKI_PUBLICATION_PAGE_TITLE, | ||
| html_data=html_data) | ||
| message = \ | ||
| 'Updated wiki page {0}'.\ | ||
| format(WIKI_PUBLICATION_PAGE_TITLE) | ||
| send_log_to_channels( | ||
| slack_conf=SLACK_CONF, | ||
| ms_teams_conf=MS_TEAMS_CONF, | ||
| task_id=context['task'].task_id, | ||
| dag_id=context['task'].dag_id, | ||
| comment=message, | ||
| reaction='pass') | ||
| except Exception as e: | ||
| logger.error(e) | ||
| message = \ | ||
| f'Wiki update error: {e}' | ||
| message = \ | ||
| f'{message}, Log: {os.environ.get("AIRFLOW__LOGGING__BASE_LOG_FOLDER")}/dag_id={ti.dag_id}/run_id={ti.run_id}/task_id={ti.task_id}/attempt={ti.try_number}.log' | ||
| send_log_to_channels( | ||
| slack_conf=SLACK_CONF, | ||
| ms_teams_conf=MS_TEAMS_CONF, | ||
| task_id=context['task'].task_id, | ||
| dag_id=context['task'].dag_id, | ||
| comment=message, | ||
| reaction='fail') | ||
| raise | ||
| # def update_wiki_publication_page_func(**context): | ||
| # try: | ||
| # ti = context.get('ti') | ||
| # all_data = \ | ||
| # search_epmc_for_keyword( | ||
| # search_term="\"Imperial BRC Genomics Facility\"") | ||
| # columns = [ | ||
| # 'title', | ||
| # 'authorString', | ||
| # 'journalTitle', | ||
| # 'firstPublicationDate', | ||
| # 'firstIndexDate', | ||
| # 'doi'] | ||
| # all_df = \ | ||
| # pd.DataFrame(all_data)[columns] | ||
| # all_df['doi'] = \ | ||
| # all_df['doi'].\ | ||
| # map(lambda x: 'https://doi.org/{0}'.format(x)) | ||
| # html_data = \ | ||
| # all_df.\ | ||
| # to_html(index=False) | ||
| # update_confluence_page( | ||
| # confluence_conf_file=CONFLUENCE_CONFIG_FILE, | ||
| # page_id=WIKI_PUBLICATION_PAGE_ID, | ||
| # page_title=WIKI_PUBLICATION_PAGE_TITLE, | ||
| # html_data=html_data) | ||
| # message = \ | ||
| # 'Updated wiki page {0}'.\ | ||
| # format(WIKI_PUBLICATION_PAGE_TITLE) | ||
| # send_log_to_channels( | ||
| # slack_conf=SLACK_CONF, | ||
| # ms_teams_conf=MS_TEAMS_CONF, | ||
| # task_id=context['task'].task_id, | ||
| # dag_id=context['task'].dag_id, | ||
| # comment=message, | ||
| # reaction='pass') | ||
| # except Exception as e: | ||
| # logger.error(e) | ||
| # message = \ | ||
| # f'Wiki update error: {e}' | ||
| # message = \ | ||
| # f'{message}, Log: {os.environ.get("AIRFLOW__LOGGING__BASE_LOG_FOLDER")}/dag_id={ti.dag_id}/run_id={ti.run_id}/task_id={ti.task_id}/attempt={ti.try_number}.log' | ||
| # send_log_to_channels( | ||
| # slack_conf=SLACK_CONF, | ||
| # ms_teams_conf=MS_TEAMS_CONF, | ||
| # task_id=context['task'].task_id, | ||
| # dag_id=context['task'].dag_id, | ||
| # comment=message, | ||
| # reaction='fail') | ||
| # raise |