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| from django.apps import AppConfig | ||
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| class GenericConfig(AppConfig): | ||
| name = 'samplesheets.assayapps.generic' |
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| """Assay app plugin for samplesheets""" | ||
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| import re | ||
| from django.conf import settings | ||
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| from altamisa.constants import table_headers as th | ||
| from samplesheets.plugins import SampleSheetAssayPluginPoint | ||
| from samplesheets.rendering import SIMPLE_LINK_TEMPLATE | ||
| from samplesheets.utils import get_top_header | ||
| from samplesheets.views import MISC_FILES_COLL, RESULTS_COLL | ||
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| # Local constants | ||
| APP_NAME = 'samplesheets.assayapps.generic' | ||
| RESULTS_COMMENT = 'SODAR Assay Link Results' | ||
| MISC_FILES_COMMENT = 'SODAR Assay Link MiscFiles' | ||
| DATA_COMMENT_PREFIX = 'SODAR Assay Row Path' | ||
| DATA_LINK_COMMENT = 'SODAR Assay Link Row' | ||
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| class SampleSheetAssayPlugin(SampleSheetAssayPluginPoint): | ||
| """Plugin for generic data linking in sample sheets""" | ||
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| #: Name (used in code and as unique idenfitier) | ||
| name = 'samplesheets_assay_generic' | ||
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| #: Title | ||
| title = 'Generic Assay Plugin' | ||
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| #: App name for dynamic reference to app in e.g. caching | ||
| app_name = APP_NAME | ||
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| #: Identifying assay fields (used to identify plugin by assay) | ||
| # NOTE: This assay plugin is accessed by the "SODAR Assay Plugin" override | ||
| assay_fields = [] | ||
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| #: Description string | ||
| description = 'Creates data links from comments in ISA investigation file' | ||
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| #: Template for assay addition (Assay object as "assay" in context) | ||
| assay_template = None | ||
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| #: Required permission for accessing the plugin | ||
| # TODO: TBD: Do we need this? | ||
| permission = None | ||
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| #: Toggle displaying of row-based iRODS links in the assay table | ||
| display_row_links = True | ||
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| @staticmethod | ||
| def _link_from_comment(cell, header, top_header, target_cols, url): | ||
| """ | ||
| Creates collection links for targeted columns. | ||
| :param cell: Dict (obtained by iterating over a row) | ||
| :param header: Column header | ||
| :param top_header: Column top header | ||
| :param target_cols: List of column names. | ||
| :param url: Base URL for link target. | ||
| """ | ||
| # Do nothing if not string or link | ||
| if not isinstance(cell['value'], str) or re.search( | ||
| '.+ <.*>', cell['value'] | ||
| ): | ||
| return True | ||
| # Special case for Material Names | ||
| if ( | ||
| top_header['value'] | ||
| in th.DATA_FILE_HEADERS + th.MATERIAL_NAME_HEADERS | ||
| ) and (header['value'] == 'Name'): | ||
| cell['link'] = f"{url}/{cell['value']}" | ||
| return True | ||
| # Handle everything else | ||
| if header['value'].lower() in target_cols: | ||
| cell['value'] = SIMPLE_LINK_TEMPLATE.format( | ||
| label=cell['value'], | ||
| url=f"{url}/{cell['value']}", | ||
| ) | ||
| return True | ||
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| @classmethod | ||
| def _get_col_value(cls, target_col, row, table): | ||
| """ | ||
| Return value of last matched column. | ||
| :param target_col: Column name to look for | ||
| :param row: List of dicts (a row returned by SampleSheetTableBuilder) | ||
| :param table: Full table with headers (dict returned by | ||
| SampleSheetTableBuilder) | ||
| :return: String with cell value of last matched column | ||
| """ | ||
| # Returns last match of row | ||
| value = None | ||
| if target_col: | ||
| for i in range(len(row)): | ||
| header = table['field_header'][i] | ||
| if header['value'].lower() == target_col.lower(): | ||
| value = row[i]['value'] | ||
| return value | ||
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| def get_row_path(self, row, table, assay, assay_path): | ||
| """ | ||
| Return iRODS path for an assay row in a sample sheet. If None, | ||
| display default path. Used if display_row_links = True. | ||
| :param row: List of dicts (a row returned by SampleSheetTableBuilder) | ||
| :param table: Full table with headers (dict returned by | ||
| SampleSheetTableBuilder) | ||
| :param assay: Assay object | ||
| :param assay_path: Root path for assay | ||
| :return: String with full iRODS path or None | ||
| """ | ||
| # Extract comments starting with DATA_COMMENT_PREFIX; sorted | ||
| data_columns = [ | ||
| value | ||
| for name, value in sorted(assay.comments.items()) | ||
| if name.startswith(DATA_COMMENT_PREFIX) | ||
| ] | ||
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| data_collections = [] | ||
| for column_name in data_columns: | ||
| col_value = self._get_col_value(column_name, row, table) | ||
| if col_value: | ||
| data_collections.append(col_value) | ||
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| # Build iRODS path from list and stop at first None value | ||
| if data_collections: | ||
| data_path = '/' + '/'.join(data_collections) | ||
| return assay_path + data_path | ||
| return None | ||
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| def update_row(self, row, table, assay, index): | ||
| """ | ||
| Update render table row with e.g. links. Return the modified row. | ||
| :param row: Original row (list of dicts) | ||
| :param table: Full table (dict) | ||
| :param assay: Assay object | ||
| :param index: Row index (int) | ||
| :return: List of dicts | ||
| """ | ||
| if not settings.IRODS_WEBDAV_ENABLED or not assay: | ||
| return row | ||
| assay_path = self.get_assay_path(assay) | ||
| if not assay_path: | ||
| return row | ||
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| base_url = settings.IRODS_WEBDAV_URL + assay_path | ||
| top_header = None | ||
| th_colspan = 0 | ||
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| results_cols = assay.comments.get(RESULTS_COMMENT) | ||
| if results_cols: | ||
| results_cols = results_cols.lower().split(';') | ||
| misc_cols = assay.comments.get(MISC_FILES_COMMENT) | ||
| if misc_cols: | ||
| misc_cols = misc_cols.lower().split(';') | ||
| data_cols = assay.comments.get(DATA_LINK_COMMENT) | ||
| if data_cols: | ||
| data_cols = data_cols.lower().split(';') | ||
| if table['irods_paths'][index]: | ||
| row_path = table['irods_paths'][index]['path'] | ||
| else: | ||
| row_path = self.get_row_path(row, table, assay, assay_path) | ||
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| for i in range(len(row)): | ||
| header = table['field_header'][i] | ||
| if not top_header or i >= th_colspan: | ||
| top_header = get_top_header(table, i) | ||
| th_colspan += top_header['colspan'] | ||
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| # TODO: Check if two comments reference the same column header? | ||
| # Create Results links | ||
| if results_cols: | ||
| if self._link_from_comment( | ||
| row[i], | ||
| header, | ||
| top_header, | ||
| results_cols, | ||
| f'{base_url}/{RESULTS_COLL}', | ||
| ): | ||
| continue | ||
| # Create MiscFiles links | ||
| if misc_cols: | ||
| if self._link_from_comment( | ||
| row[i], | ||
| header, | ||
| top_header, | ||
| misc_cols, | ||
| f'{base_url}/{MISC_FILES_COLL}', | ||
| ): | ||
| continue | ||
| # Create DataCollection links | ||
| if data_cols: | ||
| self._link_from_comment( | ||
| row[i], | ||
| header, | ||
| top_header, | ||
| data_cols, | ||
| f'{settings.IRODS_WEBDAV_URL}{row_path}', | ||
| ) | ||
| return row | ||
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| def update_cache(self, name=None, project=None, user=None): | ||
| """ | ||
| Update cached data for this app, limitable to item ID and/or project. | ||
| :param name: Item name to limit update to (string, optional) | ||
| :param project: Project object to limit update to (optional) | ||
| :param user: User object to denote user triggering the update (optional) | ||
| """ | ||
| self._update_cache_rows(APP_NAME, name, project, user) |