<commit_before>from ontobio.rdfgen.gocamgen.gocamgen import AssocGoCamModel
from ontobio.rdfgen.gocamgen.filter_rule import AssocFilter, FilterRule, get_filter_rule
from ontobio.rdfgen.gocamgen.collapsed_assoc import extract_properties
from ontobio.rdfgen.gocamgen.errors import GocamgenException, GeneErrorSet
from ontobio.io import gpadparser
from ontobio.io.assocparser import AssocParserConfig
from ontobio.io.entityparser import GpiParser
from ontobio.model.association import GoAssociation
from ontobio.ontol_factory import OntologyFactory
from ontobio.util.go_utils import GoAspector
import argparse
import logging
import requests
from requests.exceptions import ConnectionError
import gzip
import time
import click
from os import path
from typing import List
# from abc import ABC, abstractmethod
from rdflib.graph import ConjunctiveGraph
from rdflib.store import Store
from rdflib import plugin

logging.basicConfig()
logger = logging.getLogger(__name__)
logger.setLevel("DEBUG")

parser = argparse.ArgumentParser()
parser.add_argument('-g', '--gpad_file', help="Filepath of GPAD source with annotations to model", required=True)
parser.add_argument('-s', '--specific_gene', help="If specified, will only translate model for annotations "
                                                  "to this specific gene")
parser.add_argument('-o', '--ontology', help="Path to GO-LEGO ontology file")
parser.add_argument('-n', '--max_model_limit', help="Only translate specified number of models. Mainly for testing.")
parser.add_argument('-m', '--mod', help="MOD rules to follow for filtering and translating.")
parser.add_argument('-d', '--output_directory', help="Directory to output model ttl files to")
parser.add_argument('-r', '--report', help="Generate report", action="store_const", const=True)
parser.add_argument('-N', '--nquads', help="Filepath to write model file in N-Quads format")

# GoCamInputHandler


class GoCamBuilder:
    def __init__(self, parser_config: AssocParserConfig):
        self.config = parser_config
        self.aspector = GoAspector(self.config.ontology)
        self.store = plugin.get('IOMemory', Store)()
        self.errors = GeneErrorSet()  # Errors by gene ID
        self.gpi_entities = self.parse_gpi(parser_config.gpi_authority_path)

    def translate_to_model(self, gene, assocs: List[GoAssociation]):
        model_id = gene.replace(":", "_")
        model = AssocGoCamModel(gene, assocs, config=self.config, store=self.store, gpi_entities=self.gpi_entities, model_id=model_id)
        model.go_aspector = self.aspector  # TODO: Grab aspect from ontology node
        model.translate()

        return model

    def make_model(self, gene, annotations: List[GoAssociation], output_directory=None, nquads=False):
        # All these retry shenanigans are to prevent mid-run crashes due to an external resource simply blipping
        # out for a second.
        retry_count = 0
        retry_limit = 5
        while True:
            try:
                start_time = time.time()
                model = self.translate_to_model(gene, annotations)
                # add_to_conjunctive_graph(model, conjunctive_graph)
                if nquads:
                    logger.info(
                        "Model for {} added to graphstore in {} sec".format(gene, (time.time() - start_time)))
                else:
                    out_filename = "{}.ttl".format(gene.replace(":", "_"))
                    if output_directory is not None:
                        out_filename = path.join(output_directory, out_filename)
                    model.write(out_filename)
                    logger.info("Model for {} written to {} in {} sec".format(gene, out_filename,
                                                                              (time.time() - start_time)))
                for err in model.errors:
                    self.errors.add_error(gene, err)
                return model
            except GocamgenException as ex:
                self.errors.add_error(gene, ex)
            except (TimeoutError, ConnectionError) as ex:
                # This has been happening randomly and breaking full runs
                self.errors.add_error(gene, ex)
                if retry_count < retry_limit:
                    retry_count += 1
                    continue  # retry
                self.errors.add_error(gene,
                                 GocamgenException(f"Bailing on model for {gene} after {retry_count} retries"))
            break  # Done with this model. Move on to the next one.

    def make_model_and_add_to_store(self, gene, annotations):
        return self.make_model(gene, annotations, nquads=True)

    def make_model_and_write_out(self, gene, annotations, output_directory=None):
        return self.make_model(gene, annotations, output_directory=output_directory, nquads=False)

    def write_out_store_to_nquads(self, filepath):
        cg = ConjunctiveGraph(self.store)
        cg.serialize(destination=filepath, format="nquads")
        logger.info(f"Full model graphstore written out in N-Quads format to {filepath}")

    def write_report(self, report_filepath):
        with open(report_filepath, "w+") as reportf:
            for gene, errs in self.errors.errors.items():
                for ex in errs:
                    reportf.write(f"{type(ex).__name__} - {gene}: {ex}\n")

    @staticmethod
    def extract_relations_ontology(ontology_graph):
        # TODO: This is probably all wrong - trying to reconstruct RO from broader ontology_graph
        # According to Ontobee RO top-level terms are RO:0002410 (causally related to)
        #  and RO:0002222 (temporally related to) - try reconstructing RO with these<commit_msg>Model title in 'GeneSymbol (GeneID)' format; for geneontology/gocamgen#90<commit_after>from ontobio.rdfgen.gocamgen.gocamgen import AssocGoCamModel
from ontobio.rdfgen.gocamgen.filter_rule import AssocFilter, FilterRule, get_filter_rule
from ontobio.rdfgen.gocamgen.collapsed_assoc import extract_properties
from ontobio.rdfgen.gocamgen.errors import GocamgenException, GeneErrorSet
from ontobio.io import gpadparser
from ontobio.io.assocparser import AssocParserConfig
from ontobio.io.entityparser import GpiParser
from ontobio.model.association import GoAssociation
from ontobio.ontol_factory import OntologyFactory
from ontobio.util.go_utils import GoAspector
import argparse
import logging
import requests
from requests.exceptions import ConnectionError
import gzip
import time
import click
from os import path
from typing import List
# from abc import ABC, abstractmethod
from rdflib.graph import ConjunctiveGraph
from rdflib.store import Store
from rdflib import plugin

logging.basicConfig()
logger = logging.getLogger(__name__)
logger.setLevel("DEBUG")

parser = argparse.ArgumentParser()
parser.add_argument('-g', '--gpad_file', help="Filepath of GPAD source with annotations to model", required=True)
parser.add_argument('-s', '--specific_gene', help="If specified, will only translate model for annotations "
                                                  "to this specific gene")
parser.add_argument('-o', '--ontology', help="Path to GO-LEGO ontology file")
parser.add_argument('-n', '--max_model_limit', help="Only translate specified number of models. Mainly for testing.")
parser.add_argument('-m', '--mod', help="MOD rules to follow for filtering and translating.")
parser.add_argument('-d', '--output_directory', help="Directory to output model ttl files to")
parser.add_argument('-r', '--report', help="Generate report", action="store_const", const=True)
parser.add_argument('-N', '--nquads', help="Filepath to write model file in N-Quads format")

# GoCamInputHandler


class GoCamBuilder:
    def __init__(self, parser_config: AssocParserConfig):
        self.config = parser_config
        self.aspector = GoAspector(self.config.ontology)
        self.store = plugin.get('IOMemory', Store)()
        self.errors = GeneErrorSet()  # Errors by gene ID
        self.gpi_entities = self.parse_gpi(parser_config.gpi_authority_path)

    def translate_to_model(self, gene, assocs: List[GoAssociation]):
        model_id = gene.replace(":", "_")
        model_title = self.model_title(gene)
        model = AssocGoCamModel(model_title, assocs, config=self.config, store=self.store, gpi_entities=self.gpi_entities, model_id=model_id)
        model.go_aspector = self.aspector  # TODO: Grab aspect from ontology node
        model.translate()

        return model

    def make_model(self, gene, annotations: List[GoAssociation], output_directory=None, nquads=False):
        # All these retry shenanigans are to prevent mid-run crashes due to an external resource simply blipping
        # out for a second.
        retry_count = 0
        retry_limit = 5
        while True:
            try:
                start_time = time.time()
                model = self.translate_to_model(gene, annotations)
                # add_to_conjunctive_graph(model, conjunctive_graph)
                if nquads:
                    logger.info(
                        "Model for {} added to graphstore in {} sec".format(gene, (time.time() - start_time)))
                else:
                    out_filename = "{}.ttl".format(gene.replace(":", "_"))
                    if output_directory is not None:
                        out_filename = path.join(output_directory, out_filename)
                    model.write(out_filename)
                    logger.info("Model for {} written to {} in {} sec".format(gene, out_filename,
                                                                              (time.time() - start_time)))
                for err in model.errors:
                    self.errors.add_error(gene, err)
                return model
            except GocamgenException as ex:
                self.errors.add_error(gene, ex)
            except (TimeoutError, ConnectionError) as ex:
                # This has been happening randomly and breaking full runs
                self.errors.add_error(gene, ex)
                if retry_count < retry_limit:
                    retry_count += 1
                    continue  # retry
                self.errors.add_error(gene,
                                 GocamgenException(f"Bailing on model for {gene} after {retry_count} retries"))
            break  # Done with this model. Move on to the next one.

    def make_model_and_add_to_store(self, gene, annotations):
        return self.make_model(gene, annotations, nquads=True)

    def make_model_and_write_out(self, gene, annotations, output_directory=None):
        return self.make_model(gene, annotations, output_directory=output_directory, nquads=False)

    def write_out_store_to_nquads(self, filepath):
        cg = ConjunctiveGraph(self.store)
        cg.serialize(destination=filepath, format="nquads")
        logger.info(f"Full model graphstore written out in N-Quads format to {filepath}")

    def write_report(self, report_filepath):
        with open(report_filepath, "w+") as reportf:
            for gene, errs in self.errors.errors.items():
                for ex in errs:
                    reportf.write(f"{type(ex).__name__} - {gene}: {ex}\n")

    def model_title(self, gene_id: str) -> str:
        entity = self.gpi_entities.get(gene_id)
        model_title = "{} ({})".format(entity["label"], gene_id)
        return model_title

    @staticmethod
    def extract_relations_ontology(ontology_graph):
        # TODO: This is probably all wrong - trying to reconstruct RO from broader ontology_graph
        # According to Ontobee RO top-level terms are RO:0002410 (causally related to)
        #  and RO:0002222 (temporally related to) - try reconstructing RO with these
{'fraction_non_alphanumeric': 0.09056089879989786, 'fraction_numerical': 0.0030640905608988, 'mean_word_length': 2.797672915319974, 'pattern_counts': {'":': 4, '<': 5, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 12, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1546995', 'n_tokens_mistral': 3404, 'n_tokens_neox': 3245, 'n_words': 896}