<commit_before>package ca.corefacility.bioinformatics.irida.ria.web.analysis;

import java.io.*;
import java.nio.file.Files;
import java.nio.file.NoSuchFileException;
import java.nio.file.Path;
import java.security.Principal;
import java.util.*;
import java.util.stream.Collectors;

import javax.servlet.http.HttpServletResponse;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.context.annotation.Scope;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.web.bind.annotation.*;

import ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig;
import ca.corefacility.bioinformatics.irida.exceptions.*;
import ca.corefacility.bioinformatics.irida.model.enums.AnalysisState;
import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectMetadataTemplateJoin;
import ca.corefacility.bioinformatics.irida.model.project.Project;
import ca.corefacility.bioinformatics.irida.model.project.ReferenceFile;
import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate;
import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField;
import ca.corefacility.bioinformatics.irida.model.sample.Sample;
import ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin;
import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile;
import ca.corefacility.bioinformatics.irida.model.user.Role;
import ca.corefacility.bioinformatics.irida.model.user.User;
import ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow;
import ca.corefacility.bioinformatics.irida.model.workflow.analysis.*;
import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes;
import ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission;
import ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin;
import ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor;
import ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities;
import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress;
import ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit;
import ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.*;
import ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager;
import ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData;
import ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails;
import ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities;
import ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission;
import ca.corefacility.bioinformatics.irida.service.*;
import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
import ca.corefacility.bioinformatics.irida.service.user.UserService;
import ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService;

import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.jsonldjava.shaded.com.google.common.base.Strings;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.ImmutableSet;<commit_msg>removed unused import statement import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.BuiltInAnalysisTypes from AnalysisAjaxController.java<commit_after>package ca.corefacility.bioinformatics.irida.ria.web.analysis;

import java.io.*;
import java.nio.file.Files;
import java.nio.file.NoSuchFileException;
import java.nio.file.Path;
import java.security.Principal;
import java.util.*;
import java.util.stream.Collectors;

import javax.servlet.http.HttpServletResponse;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.context.annotation.Scope;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.web.bind.annotation.*;

import ca.corefacility.bioinformatics.irida.config.analysis.ExecutionManagerConfig;
import ca.corefacility.bioinformatics.irida.exceptions.*;
import ca.corefacility.bioinformatics.irida.model.enums.AnalysisState;
import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectMetadataTemplateJoin;
import ca.corefacility.bioinformatics.irida.model.project.Project;
import ca.corefacility.bioinformatics.irida.model.project.ReferenceFile;
import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplate;
import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField;
import ca.corefacility.bioinformatics.irida.model.sample.Sample;
import ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin;
import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile;
import ca.corefacility.bioinformatics.irida.model.user.Role;
import ca.corefacility.bioinformatics.irida.model.user.User;
import ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow;
import ca.corefacility.bioinformatics.irida.model.workflow.analysis.*;
import ca.corefacility.bioinformatics.irida.model.workflow.analysis.type.AnalysisType;
import ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission;
import ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin;
import ca.corefacility.bioinformatics.irida.pipeline.results.AnalysisSubmissionSampleProcessor;
import ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities;
import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdatedAnalysisProgress;
import ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit;
import ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.*;
import ca.corefacility.bioinformatics.irida.ria.web.components.AnalysisOutputFileDownloadManager;
import ca.corefacility.bioinformatics.irida.ria.web.dto.ExcelData;
import ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails;
import ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities;
import ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission;
import ca.corefacility.bioinformatics.irida.service.*;
import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
import ca.corefacility.bioinformatics.irida.service.user.UserService;
import ca.corefacility.bioinformatics.irida.service.workflow.IridaWorkflowsService;

import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.jsonldjava.shaded.com.google.common.base.Strings;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.ImmutableSet;
{'fraction_non_alphanumeric': 0.09821640903686088, 'fraction_numerical': 0.0004756242568370987, 'mean_word_length': 7.863013698630137, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '264579', 'n_tokens_mistral': 2601, 'n_tokens_neox': 2424, 'n_words': 260}