diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 43a9a953..200fbbd3 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,14 @@ foursight Change Log ---------- +4.4.3 +===== +* Add helper to convert user input str to list for select queries in higlass_checks.py +* Adjust output of check_validation_errors check to list affected items by type in full_output if not too many +* update lock file to use foursight-core with bug fix for local-check-execution script + +`PR 564: Improved handling of user query for higlass items `_ + 4.4.2 ===== * Added 'input_bed' to attr_keys in wfr_utils.py's start_missing_run for ATAC-seq pipeline diff --git a/chalicelib_fourfront/checks/audit_checks.py b/chalicelib_fourfront/checks/audit_checks.py index 26e2b799..715e7e47 100644 --- a/chalicelib_fourfront/checks/audit_checks.py +++ b/chalicelib_fourfront/checks/audit_checks.py @@ -781,17 +781,24 @@ def check_validation_errors(connection, **kwargs): returns link to search if found. ''' check = CheckResult(connection, 'check_validation_errors') - + search_url = 'search/?validation_errors.name!=No+value&type=Item' results = ff_utils.search_metadata(search_url + '&field=@id', key=connection.ff_keys) if results: - types = {item for result in results for item in result['@type'] if item != 'Item'} + ids_by_type = {} + for result in results: + ids_by_type.setdefault(result.get('@type')[0], []).append(result.get('@id')) check.status = 'WARN' check.summary = 'Validation errors found' check.description = ('{} items found with validation errors, comprising the following ' 'item types: {}. \nFor search results see link below.'.format( - len(results), ', '.join(list(types)))) + len(results), ', '.join(ids_by_type.keys()))) check.ff_link = connection.ff_server + search_url + # too many items of a type suggests a possibly general issue for that type + for ty, item_ids in ids_by_type.items(): + if len(item_ids) > 100: + ids_by_type[ty] = 'Many items of this type have validation errors' + check.full_output = ids_by_type else: check.status = 'PASS' check.summary = 'No validation errors' diff --git a/chalicelib_fourfront/checks/higlass_checks.py b/chalicelib_fourfront/checks/higlass_checks.py index c05d5211..1d69561e 100644 --- a/chalicelib_fourfront/checks/higlass_checks.py +++ b/chalicelib_fourfront/checks/higlass_checks.py @@ -354,12 +354,7 @@ def find_files_requiring_higlass_items(connection, check_name, action_name, sear check.queries = [] check.action = action_name - # If no search query was provided, fail - if not search_queries: - check.summary = check.description = "No search query provided, nothing to update." - check.status = 'PASS' - check.allow_action = False - return check + search_queries = verify_queries(check, search_queries) # Add the fields we want to return. fields_to_include = '&field=' + '&field='.join(( @@ -385,7 +380,7 @@ def find_files_requiring_higlass_items(connection, check_name, action_name, sear file_search_query = "/search/?type=File&higlass_uid!=No+value&genome_assembly!=No+value" + query + fields_to_include # Query the files - search_res = ff_utils.search_metadata(file_search_query, key=connection.ff_keys) + search_res = get_search_results(connection, check, file_search_query) # Collate the results into a dict of ExpSets, ordered by accession for found_file in search_res: @@ -430,11 +425,20 @@ def find_files_requiring_higlass_items(connection, check_name, action_name, sear check.full_output[full_output_key] = {} check.full_output[full_output_key][ga] = target_files_by_ga[ga] + if check.full_output.get('search_problems'): + check.summary = "Please check input query for typo or formatting error" + check.description = check.summary + ". See full_output for details." + check.allow_action = False + check.status = 'FAIL' + return check + if not target_files_by_ga: # nothing new to generate check.summary = check.description = "No new Higlass Items to generate" check.allow_action = False check.status = 'PASS' + return check + else: all_files = sum([len(x) for x in check.full_output["ready"].values()]) check.summary = "Ready to generate %s Higlass Items" % all_files @@ -827,12 +831,7 @@ def find_expsets_processedfiles_requiring_higlass_items(connection, check_name, "static_content", ]) - # If no search query was provided, fail - if not search_queries: - check.summary = check.description = "No search query provided, nothing to update." - check.status = 'PASS' - check.allow_action = False - return check + search_queries = verify_queries(check, search_queries) expsets_by_accession = {} # Use all of the search queries to make a list of the ExpSets we will work on. @@ -844,7 +843,7 @@ def find_expsets_processedfiles_requiring_higlass_items(connection, check_name, processed_expsets_query = "/search/?type=ExperimentSetReplicate" + query + fields_to_include # Query the Experiment Sets - search_res = ff_utils.search_metadata(processed_expsets_query, key=connection.ff_keys) + search_res = get_search_results(connection, check, processed_expsets_query) # Collate the results into a dict of ExpSets, ordered by accession for expset in search_res: @@ -897,6 +896,14 @@ def find_expsets_processedfiles_requiring_higlass_items(connection, check_name, ready_to_generate_count = sum([len(accessions) for x, accessions in check.full_output["ready_expsets"].items()]) check.summary = "" + + if check.full_output.get('search_problems'): + check.summary = "Please check input query for typo or formatting error" + check.description = check.summary + ". See full_output for details." + check.allow_action = False + check.status = 'FAIL' + return check + # If there are no files to act upon, we're done. if not target_files_by_ga: check.summary = check.description = "No new view configs to generate" @@ -1177,19 +1184,15 @@ def find_expsets_otherprocessedfiles_requiring_higlass_items(connection, check_n check.queries = [] check.action = action_name - # If no search query was provided and find_opfs_missing_higlass is False, pass with no results - if not (search_queries or find_opfs_missing_higlass): - check.summary = check.description = "No search query provided, nothing to update." - check.status = 'PASS' - check.allow_action = False - return check - if find_opfs_missing_higlass: search_queries = [ "&experiments_in_set.other_processed_files.files.higlass_uid%21=No+value", "&other_processed_files.files.higlass_uid%21=No+value" ] + else: + search_queries = verify_queries(check, search_queries) + # get the fields you need to include fields_to_include = "" for new_field in ( @@ -1216,7 +1219,7 @@ def find_expsets_otherprocessedfiles_requiring_higlass_items(connection, check_n expset_query = "/search/?type=ExperimentSetReplicate" + query + fields_to_include # Store results by accession - search_res = ff_utils.search_metadata(expset_query, key=connection.ff_keys) + search_res = get_search_results(connection, check, expset_query) for expset in search_res: expsets_by_accession[ expset["accession"] ] = expset @@ -1368,6 +1371,13 @@ def consider_filegroup(fg): all_filegroups_to_update[accession] = filegroups_to_update higlass_view_count += len(filegroups_to_update.keys()) + if check.full_output.get('search_problems'): + check.summary = "Please check input query for typo or formatting error" + check.description = check.summary + ". See full_output for details." + check.allow_action = False + check.status = 'FAIL' + return check + # check announces success check.full_output['filegroups_to_update'] = all_filegroups_to_update check.full_output['expsets_to_update'] = expsets_to_update @@ -1697,7 +1707,7 @@ def does_url_exist(path): continue # Query all possible files - possibly_reg = ff_utils.search_metadata(search_query, key=connection.ff_keys) + possibly_reg = get_search_results(connection, check, search_query) for procfile in possibly_reg: current_file_cat = file_cat @@ -2287,3 +2297,40 @@ def convert_es_timestamp_to_datetime(raw): "%Y-%m-%dT%H:%M:%S" ) return converted_date + +def verify_queries(check, search_queries): + """ + Helper to check that a search query if properly formatted and reformat if necessary + + Args: + check(CheckResult): Result of check, to be passed from check. + search_queries(list or string): A list of search queries. All Files found in at least one of the queries will be modified. + + Returns: + Formatted search_queries (list) + """ + # If no search query was provided, pass with no results + if not (search_queries): + check.summary = check.description = "No search query provided, nothing to update." + check.status = 'PASS' + check.allow_action = False + + if isinstance(search_queries, str): + # for case where (possibly multiple) query is passed in via kwargs + queries = search_queries.split(',') + search_queries = [q.strip() for q in queries] + check.brief_output = { + "corrected_query": "The query was not formatted as a list, please double check results" + } + + # add '&' when missing from str + search_queries = [q if q[0] == '&' else '&' + q for q in search_queries] + + return search_queries + +def get_search_results(connection, check, search_query): + try: + return ff_utils.search_metadata(search_query, key=connection.ff_keys) + except Exception as e: + check.full_output.setdefault('search_problems', []).append(str(e)) + return [] diff --git a/poetry.lock b/poetry.lock index 27d51b51..9db15e74 100644 --- a/poetry.lock +++ b/poetry.lock @@ -136,18 +136,18 @@ wcwidth = ">=0.1.4" [[package]] name = "boto3" -version = "1.34.57" +version = "1.34.64" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.8" files = [ - {file = "boto3-1.34.57-py3-none-any.whl", hash = "sha256:f8046e3e2d1186a49b49f7464c4811c265c86001f404dd1a96c4365c773a4245"}, - {file = "boto3-1.34.57.tar.gz", hash = "sha256:c26c31ceeeb2bc5d2bb96ba0fdc9a04d7b10e6e0b081c55b9cea9069a0be04dd"}, + {file = "boto3-1.34.64-py3-none-any.whl", hash = "sha256:8c6fbd3d45399a4e4685010117fb2dc52fc6afdab5a9460957d463ae0c2cc55d"}, + {file = "boto3-1.34.64.tar.gz", hash = "sha256:e5d681f443645e6953ed0727bf756bf16d85efefcb69cf051d04a070ce65e545"}, ] [package.dependencies] -botocore = ">=1.34.57,<1.35.0" +botocore = ">=1.34.64,<1.35.0" jmespath = 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