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+elasticsearch = "7.10.0" gdcdictionary = "1.2.0" gen3datamodel = "3.0.2" hdfs = "2.7.0" psycopg2-binary="2.9.3" psqlgraph = "3.0.1" pyspark = "3.3.0" -urllib3 = "1.25.10" +urllib3 = "1.26.16" requests = "^2.28.1" setuptools = "65.3.0" six = "1.16.0" diff --git a/run_etl.py b/run_etl.py index 6ca53e24..d1e0761d 100644 --- a/run_etl.py +++ b/run_etl.py @@ -86,8 +86,8 @@ def main(): args = config_by_args() es_hosts = config.ES["es.nodes"] - es_port = config.ES["es.port"] - es = Elasticsearch([{"host": es_hosts, "port": es_port}]) + es_port = int(config.ES["es.port"]) + es = Elasticsearch([{"host": es_hosts, "port": es_port, "schema": "http"}]) index_names = interpreter.get_index_names(config) if args.force or check_to_run_etl(es, index_names): diff --git a/tests/integrated_tests/test_es/test_es.py b/tests/integrated_tests/test_es/test_es.py index 37841dad..023f4421 100644 --- a/tests/integrated_tests/test_es/test_es.py +++ b/tests/integrated_tests/test_es/test_es.py @@ -1,7 +1,6 @@ import pytest from elasticsearch import Elasticsearch from elasticsearch import client -from elasticsearch_dsl import Search import tube.settings as config from tube.etl.indexers.interpreter import create_translators @@ -22,14 +21,23 @@ def test_auth_resource_path_exist(doc_type): Check that the field "auth_resource_path" exist """ parser = dict_translators[doc_type].parser - es = Elasticsearch([{"host": config.ES["es.nodes"], "port": config.ES["es.port"]}]) - s = Search(using=es, index=parser.name, doc_type=doc_type) - response = s.execute() + es = Elasticsearch( + [ + { + "host": config.ES["es.nodes"], + "port": int(config.ES["es.port"]), + "scheme": "http", + } + ] + ) + response = es.search( + index=parser.name, body={"query": {"match_all": {}}}, size=9999 + ) + hit_response = response["hits"]["hits"] auth_resource_path = "/programs/jnkns/projects/jenkins" - - for hit in response: - assert hit.auth_resource_path == auth_resource_path + for hit in hit_response: + assert hit.get("_source").get("auth_resource_path") == auth_resource_path @pytest.mark.parametrize("doc_type", doc_types) @@ -38,7 +46,15 @@ def test_es_types(doc_type): Check that no field have "text" type """ parser = dict_translators[doc_type].parser - es = Elasticsearch([{"host": config.ES["es.nodes"], "port": config.ES["es.port"]}]) + es = Elasticsearch( + [ + { + "host": config.ES["es.nodes"], + "port": int(config.ES["es.port"]), + "scheme": "http", + } + ] + ) indices = client.IndicesClient(es) index_name = list(indices.get_alias(name=parser.name).keys())[0] @@ -47,7 +63,7 @@ def test_es_types(doc_type): # assert "_None_id" not in mapping[index_name]["mappings"][doc_type]["properties"] list_errors = [] - for k, t in list(mapping[index_name]["mappings"][doc_type]["properties"].items()): + for k, t in list(mapping[index_name]["mappings"]["properties"].items()): try: assert t["type"] != "text", f"field {k} has type as text" except AssertionError as ex: diff --git a/tests/integrated_tests/utils_es.py b/tests/integrated_tests/utils_es.py index caae8ed8..02cf7cd9 100644 --- a/tests/integrated_tests/utils_es.py +++ b/tests/integrated_tests/utils_es.py @@ -1,20 +1,30 @@ from itertools import chain from elasticsearch import Elasticsearch -from elasticsearch_dsl import Search import tube.settings as config def get_item_from_elasticsearch(index, doc_type, item): - es = Elasticsearch([{"host": config.ES["es.nodes"], "port": config.ES["es.port"]}]) - s = Search(using=es, index=index, doc_type=doc_type).query( - "match", submitter_id=item + es = Elasticsearch( + [ + { + "host": config.ES["es.nodes"], + "port": int(config.ES["es.port"]), + "scheme": "http", + } + ] ) - total = s.count() - s = s[0:total] - results = s.execute() - return results + search_results = es.search( + index=index, body={"query": {"match": {"submitter_id": item}}}, size=9999 + ) + print("Response:") + print(search_results) + result = search_results["hits"]["hits"] + total = len(result) + hits = result[0:total] + # results = s.execute() + return [h.get("_source") for h in hits] def get_names(p): diff --git a/tests/integrated_tests/value/es_value.py b/tests/integrated_tests/value/es_value.py index 3c558eac..971a0e40 100644 --- a/tests/integrated_tests/value/es_value.py +++ b/tests/integrated_tests/value/es_value.py @@ -12,7 +12,7 @@ def __init__(self, parser, submitter_id, doc_type, names): self.val, self.length = self.value() def __getattr__(self, item): - return self.val.__getattr__(item) if self.val and item in self.val else None + return self.val.get(item) if self.val and item in self.val else None def value(self): results = get_item_from_elasticsearch( diff --git a/tests/integrated_tests/value/value.py b/tests/integrated_tests/value/value.py index ae72ed5a..9ed11aff 100644 --- a/tests/integrated_tests/value/value.py +++ b/tests/integrated_tests/value/value.py @@ -27,7 +27,9 @@ def value_diff(left, right): diffs = ["attr: left != right"] for name in left.names: - left_val = left.__getattr__(name) + print(left) + print(left.__dict__) + left_val = left.val.get(name) right_val = right.__getattr__(name) if isinstance(right_val, list) and left_val is not None: diff --git a/tube/etl/indexers/base/translator.py b/tube/etl/indexers/base/translator.py index 56798a7a..185c7585 100644 --- a/tube/etl/indexers/base/translator.py +++ b/tube/etl/indexers/base/translator.py @@ -26,6 +26,7 @@ from tube.utils.spark import save_rdd_of_dataframe, get_all_files, save_rdds from tube.utils.general import get_node_id_name + def json_export_with_no_key(x, doc_type, root_name): x[1][get_node_id_name(doc_type)] = x[0] if root_name is not None and doc_type != root_name: @@ -33,12 +34,15 @@ def json_export_with_no_key(x, doc_type, root_name): x[1]["node_id"] = x[0] # redundant field for backward compatibility with arranger return json.dumps(x[1]) + cached_dataframe = {} + class Translator(object): """ The main entry point into the index export process for the mutation indices """ + def __init__(self, sc, hdfs_path, writer, parser: Parser): self.sc = sc if sc is not None: @@ -164,6 +168,7 @@ def translate_table_to_dataframe( props = props if props is not None else node.props try: print(f"Create scheme for node: {node.name}") + print(f"With props: {node.props}") schema = self.parser.create_schema(node) df, is_empty = self.read_text_files_of_table( node_tbl_name, self.get_empty_dataframe_with_name @@ -180,7 +185,7 @@ def translate_table_to_dataframe( new_df = new_df.select(*cols) return self.return_dataframe( new_df, - f"{Translator.translate_table_to_dataframe.__qualname__}__{node.name}" + f"{Translator.translate_table_to_dataframe.__qualname__}__{node.name}", ) except Exception as ex: print("HAPPEN WITH NODE: {}".format(node_tbl_name)) @@ -331,7 +336,9 @@ def save_dataframe_to_hadoop(self, df): def return_dataframe(self, df, dataframe_name): if config.RUNNING_MODE.lower() == enums.RUNNING_MODE_PRE_TEST.lower(): step_name = f"{self.current_step}_{dataframe_name}" - save_rdd_of_dataframe(df, self.get_path_to_save_dataframe(step_name), self.sc) + save_rdd_of_dataframe( + df, self.get_path_to_save_dataframe(step_name), self.sc + ) return df def get_path_to_save_dataframe(self, step): @@ -342,9 +349,7 @@ def get_path_to_save_dataframe(self, step): current_number = cached_dataframe.get(dataframe_name) + 1 dataframe_name = f"{dataframe_name}_{current_number}" cached_dataframe[dataframe_name] = current_number - return os.path.join( - self.hdfs_path, "output", dataframe_name - ) + return os.path.join(self.hdfs_path, "output", dataframe_name) def save_to_hadoop(self, df): save_rdds(df, self.get_path_from_step(self.current_step), self.sc) diff --git a/tube/etl/outputs/es/timestamp.py b/tube/etl/outputs/es/timestamp.py index 17983a6a..8f7a1058 100644 --- a/tube/etl/outputs/es/timestamp.py +++ b/tube/etl/outputs/es/timestamp.py @@ -79,13 +79,13 @@ def check_to_run_etl(es, index_names): def timestamp_from_transaction_time(dt): - return "time_{trans_time}".format(trans_time=dt.isoformat("T")) + return "time_{trans_time}".format(trans_time=dt.strftime("%Y-%m-%dT%H-%M-%S")) def get_timestamp_from_index(es, versioned_index): res = es.indices.get_alias(index=versioned_index, name="time_*") iso_str = list(res[versioned_index]["aliases"].keys())[0].replace("plus", "+")[5:] - return datetime.strptime(iso_str, "%Y-%m-%dT%H:%M:%S.%f") + return datetime.strptime(iso_str, "%Y-%m-%dT%H:%M:%S") def putting_timestamp(es, index_to_write): diff --git a/tube/etl/outputs/es/writer.py b/tube/etl/outputs/es/writer.py index 96e3d90b..1ee28beb 100644 --- a/tube/etl/outputs/es/writer.py +++ b/tube/etl/outputs/es/writer.py @@ -39,13 +39,13 @@ def get_es(self): :return: """ es_hosts = self.es_config["es.nodes"] - es_port = self.es_config["es.port"] - return Elasticsearch([{"host": es_hosts, "port": es_port}]) + es_port = int(self.es_config["es.port"]) + return Elasticsearch([{"host": es_hosts, "port": es_port, "scheme": "http"}]) def write_to_new_index(self, df, index, doc_type): df = df.map(lambda x: json_export(x, doc_type)) es_config = self.es_config - es_config["es.resource"] = index + "/{}".format(doc_type) + es_config["es.resource"] = index df.saveAsNewAPIHadoopFile( path="-", outputFormatClass="org.elasticsearch.hadoop.mr.EsOutputFormat", @@ -56,7 +56,7 @@ def write_to_new_index(self, df, index, doc_type): def write_df_to_new_index(self, df, index, doc_type): es_config = self.es_config - es_config["es.resource"] = index + "/{}".format(doc_type) + es_config["es.resource"] = index df.coalesce(1).write.format("org.elasticsearch.spark.sql").option( "es.nodes", es_config["es.nodes"] ).option("es.port", es_config["es.port"]).option( @@ -86,11 +86,9 @@ def create_guppy_array_config(self, parser): # etl_index_name, types, array_typ mapping = { "mappings": { - "_doc": { - "properties": { - "timestamp": {"type": "date"}, - "array": {"type": "keyword"}, - } + "properties": { + "timestamp": {"type": "date"}, + "array": {"type": "keyword"}, } } } @@ -107,7 +105,7 @@ def create_guppy_array_config(self, parser): # etl_index_name, types, array_typ index_to_write = self.versioning.create_new_index( mapping, self.versioning.get_next_index_version(index) ) - self.es.index(index_to_write, "_doc", id=etl_index_name, body=doc) + self.es.index(index_to_write, body=doc, id=etl_index_name) self.versioning.putting_new_version_tag(index_to_write, index) self.versioning.putting_new_version_tag(index_to_write, alias) putting_timestamp(self.es, index_to_write) @@ -124,7 +122,8 @@ def write_dataframe(self, df, index, doc_type, types): df = plugin(df) index_to_write = self.versioning.create_new_index( - {"mappings": types}, self.versioning.get_next_index_version(index) + {"mappings": types.get(doc_type)}, + self.versioning.get_next_index_version(index), ) self.write_to_es( df, index_to_write, index, doc_type, self.write_df_to_new_index