<commit_before><?xml version='1.0' encoding='UTF-8'?>
<dataset>
    <system_role description="A basic user in the system" name="ROLE_USER" />
    <system_role description="An administrator" name="ROLE_ADMIN" />
    <system_role description="A manager" name="ROLE_MANAGER" />
    <user id="1" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="Mr." lastName="Manager"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="mrtest" enabled="true" system_role="ROLE_ADMIN"
          credentialsNonExpired="true" />
    <user id="2" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="test" lastName="User"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="testUser" enabled="true" system_role="ROLE_USER"
          credentialsNonExpired="true" />
    <user id="3" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="project1Manager" lastName="Manager"
          password="<PASSWORD>BlF9ld.4v."
          phoneNumber="867-5309" username="project1Manager" enabled="true" system_role="ROLE_USER"
          credentialsNonExpired="true" />
    <user id="4" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="project1Manager" lastName="Manager"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="admin" enabled="true" system_role="ROLE_ADMIN"
          credentialsNonExpired="true" />
          
    <client_role name="ROLE_CLIENT" description="A client"/>
    <client_details id="1" clientId="testClient"
        clientSecret="testClientSecret" token_validity="100000" createdDate="2013-07-18 14:20:19.0" />
    <client_details_authorities
        client_details_id="1" authority_name="ROLE_CLIENT" />
    <client_details_grant_types
        client_details_id="1" grant_value="authorization_code" />
    <client_details_resource_ids
        client_details_id="1" resource_id="NmlIrida" />
    <client_details_scope client_details_id="1" scope="read" />

    <project id="1" createdDate="2013-07-12 14:20:19.0" name="project" modifiedDate="2013-07-18 14:20:19.0"
             organism="E. coli" projectDescription="This is an interesting project description." remoteURL="http://google.ca"/>
    <project id="2" createdDate="2013-07-18 14:20:19.0" name="project2" modifiedDate="2013-07-18 14:19:19.0" />
    <project id="3" createdDate="2013-07-18 14:20:19.0" name="project3" modifiedDate="2013-07-18 14:18:19.0" />
    <project id="4" createdDate="2013-07-18 14:21:19.0" name="project4" modifiedDate="2013-07-18 14:17:19.0" />
    <project id="5" createdDate="2013-07-18 14:21:19.0" name="project5" modifiedDate="2013-07-18 14:17:19.0" />

	<project_user id="1" project_id="1" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="2" project_id="2" user_id="1"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="3" project_id="3" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="4" project_id="4" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="6" project_id="1" user_id="2"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="7" project_id="1" user_id="3"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="8" project_id="2" user_id="3"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="9" project_id="2" user_id="2"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />

    <related_project />

    <sample id="1" createdDate="2013-07-18 14:00:19.0" description="description1"
             sampleName="sample1" organism="E. coli" />
    <sample id="2" createdDate="2013-07-18 14:01:19.0" description="description2"
             sampleName="sample2" organism="E. coli" />
    <sample id="3" createdDate="2013-07-18 14:02:19.0" description="description3"
             sampleName="sample3" organism="E. coli" />
    <sample id="4" createdDate="2013-07-18 14:03:19.0" description="description4"
             sampleName="sample4" organism="Listeria" />
    <sample id="5" createdDate="2013-07-18 14:04:19.0" description="description5"
             sampleName="sample5" organism="Listeria" />
    <sample id="6" createdDate="2013-07-18 14:05:19.0" description="description5"
             sampleName="sample523423" />
    <sample id="7" createdDate="2013-07-18 14:06:19.0" description="description5"
             sampleName="sample534534" />
    <sample id="8" createdDate="2013-07-18 14:07:19.0" description="description5"
             sampleName="sample589789" />
    <sample id="9" createdDate="2013-07-18 14:08:19.0" description="description5"
             sampleName="sample52342" />
    <sample id="10" createdDate="2013-07-18 14:09:19.0" description="description5"
             sampleName="sample565" />
    <sample id="11" createdDate="2013-07-18 14:10:19.0" description="description5"
             sampleName="sample6735" />
    <sample id="12" createdDate="2013-07-18 14:11:19.0" description="description5"
             sampleName="sample3452345" />
    <sample id="13" createdDate="2013-07-18 14:12:19.0" description="description5"
             sampleName="sample3643225" />
    <sample id="14" createdDate="2013-07-18 14:13:19.0" description="description5"
             sampleName="sample64565" />
    <sample id="15" createdDate="2013-07-18 14:14:19.0" description="description5"
             sampleName="sample57567" />
    <sample id="16" createdDate="2013-07-18 14:15:19.0" description="description5"
             sampleName="sample55422r" />
    <sample id="17" createdDate="2013-07-18 14:16:19.0" description="description5"
             sampleName="sample5dt5" />
    <sample id="18" createdDate="2013-07-18 14:17:19.0" description="description5"
             sampleName="sample5ddfg4" />
    <sample id="19" createdDate="2013-07-18 14:18:19.0" description="description5"
             sampleName="sample554sg5" />
    <sample id="20" createdDate="2013-07-18 14:19:19.0" description="description5"
             sampleName="sample5fdgr" />
    <sample id="21" createdDate="2013-07-18 14:20:19.0" description="description5"
             sampleName="sample5fg44" />

    <project_sample id="1" project_id="1" sample_id="1" createdDate="2013-07-10 14:21:19.0" />
    <project_sample id="2" project_id="1" sample_id="2" createdDate="2013-07-12 14:22:19.0" />
    <project_sample id="3" project_id="1" sample_id="3" createdDate="2013-07-14 14:23:19.0" />
    <project_sample id="4" project_id="1" sample_id="4" createdDate="2013-07-16 14:24:19.0" />
    <project_sample id="5" project_id="1" sample_id="5" createdDate="2013-07-18 14:25:19.0" />
    <project_sample id="6" project_id="1" sample_id="6" createdDate="2013-07-18 14:26:19.0" />
    <project_sample id="7" project_id="1" sample_id="7" createdDate="2013-07-18 14:27:19.0" />
    <project_sample id="8" project_id="1" sample_id="8" createdDate="2013-07-18 14:28:19.0" />
    <project_sample id="9" project_id="1" sample_id="9" createdDate="2013-07-18 14:29:19.0" />
    <project_sample id="10" project_id="1" sample_id="10" createdDate="2013-07-18 14:31:19.0" />
    <project_sample id="11" project_id="1" sample_id="11" createdDate="2013-07-18 14:32:19.0" />
    <project_sample id="12" project_id="1" sample_id="12" createdDate="2013-07-18 14:33:19.0" />
    <project_sample id="13" project_id="1" sample_id="13" createdDate="2013-07-18 14:34:19.0" />
    <project_sample id="14" project_id="1" sample_id="14" createdDate="2013-07-18 14:35:19.0" />
    <project_sample id="15" project_id="1" sample_id="15" createdDate="2013-07-18 14:36:19.0" />
    <project_sample id="16" project_id="1" sample_id="16" createdDate="2013-07-18 14:37:19.0" />
    <project_sample id="17" project_id="1" sample_id="17" createdDate="2013-07-18 14:38:19.0" />
    <project_sample id="18" project_id="1" sample_id="18" createdDate="2013-07-18 14:39:19.0" />
    <project_sample id="19" project_id="2" sample_id="19" createdDate="2013-07-18 14:40:19.0" />
    <project_sample id="20" project_id="2" sample_id="20" createdDate="2013-07-18 14:41:19.0" />
    <project_sample id="21" project_id="2" sample_id="21" createdDate="2013-07-18 14:42:19.0" />


    <sequence_file id="1" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/01-1111_S1_L001_R1_001.fastq"/>
    <sequence_file id="2" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/02-2222_S1_L001_R2_001.fastq"/>
    <sequence_file id="3" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/03-3333_S1_L001_R1_001.fastq"/>

    <sequencefile_sample id="1" createdDate="2013-07-18 14:20:19.0"
                         sample_id="18" sequencefile_id="1" />
    <sequencefile_sample id="2" createdDate="2013-07-18 14:20:19.0"
                         sample_id="18" sequencefile_id="2" />
    <sequencefile_sample id="3" createdDate="2013-07-18 14:20:19.0"
                         sample_id="18" sequencefile_id="3" />

    <sequence_file_pair id="1" created_date="2014-07-30 08:24:34" />

    <sequence_file_pair_files pair_id="1" files_id="1" />
    <sequence_file_pair_files pair_id="1" files_id="2" />

    <reference_file id="1" createdDate="2013-06-16 11:15:36.2" filePath="/tmp/path/to/nowhere/02-222.fastq" fileRevisionNumber="1" modifiedDate="2013-06-16 11:15:36.2" />
    <reference_file id="2" createdDate="2013-07-16 11:15:36.2" filePath="/tmp/path/to/nowhere/03-333.fastq" fileRevisionNumber="1" modifiedDate="2013-07-17 11:15:36.2" />

    <project_referencefile id="1" createdDate="2013-08-16 15:15:36.2" project_id="1" reference_file_id="1"/>
    <project_referencefile id="2" createdDate="2013-08-17 15:15:36.2" project_id="1" reference_file_id="2"/>
</dataset><commit_msg>fixed the majority of pipeline-phylo tests<commit_after><?xml version='1.0' encoding='UTF-8'?>
<dataset>
    <system_role description="A basic user in the system" name="ROLE_USER" />
    <system_role description="An administrator" name="ROLE_ADMIN" />
    <system_role description="A manager" name="ROLE_MANAGER" />
    <user id="1" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="Mr." lastName="Manager"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="mrtest" enabled="true" system_role="ROLE_ADMIN"
          credentialsNonExpired="true" />
    <user id="2" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="test" lastName="User"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="testUser" enabled="true" system_role="ROLE_USER"
          credentialsNonExpired="true" />
    <user id="3" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="project1Manager" lastName="Manager"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="project1Manager" enabled="true" system_role="ROLE_USER"
          credentialsNonExpired="true" />
    <user id="4" createdDate="2013-07-18 14:20:19.0" modifiedDate="2013-07-18 14:20:19.0"
          email="<EMAIL>" firstName="project1Manager" lastName="Manager"
          password="<PASSWORD>."
          phoneNumber="867-5309" username="admin" enabled="true" system_role="ROLE_ADMIN"
          credentialsNonExpired="true" />
          
    <client_role name="ROLE_CLIENT" description="A client"/>
    <client_details id="1" clientId="testClient"
        clientSecret="testClientSecret" token_validity="10<PASSWORD>0" createdDate="2013-07-18 14:20:19.0" />
    <client_details_authorities
        client_details_id="1" authority_name="ROLE_CLIENT" />
    <client_details_grant_types
        client_details_id="1" grant_value="authorization_code" />
    <client_details_resource_ids
        client_details_id="1" resource_id="NmlIrida" />
    <client_details_scope client_details_id="1" scope="read" />

    <project id="1" createdDate="2013-07-12 14:20:19.0" name="project" modifiedDate="2013-07-18 14:20:19.0"
             organism="E. coli" projectDescription="This is an interesting project description." remoteURL="http://google.ca"/>
    <project id="2" createdDate="2013-07-18 14:20:19.0" name="project2" modifiedDate="2013-07-18 14:19:19.0" />
    <project id="3" createdDate="2013-07-18 14:20:19.0" name="project3" modifiedDate="2013-07-18 14:18:19.0" />
    <project id="4" createdDate="2013-07-18 14:21:19.0" name="project4" modifiedDate="2013-07-18 14:17:19.0" />
    <project id="5" createdDate="2013-07-18 14:21:19.0" name="project5" modifiedDate="2013-07-18 14:17:19.0" />

	<project_user id="1" project_id="1" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="2" project_id="2" user_id="1"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="3" project_id="3" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="4" project_id="4" user_id="1"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="6" project_id="1" user_id="2"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="7" project_id="1" user_id="3"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="8" project_id="2" user_id="3"
		projectRole="PROJECT_OWNER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />
	<project_user id="9" project_id="2" user_id="2"
		projectRole="PROJECT_USER" createdDate="2013-07-18 14:20:19.0"
		email_subscription="false" />

    <related_project />

    <sample id="1" createdDate="2013-07-18 14:00:19.0" description="description1"
             sampleName="sample1" organism="E. coli" />
    <sample id="2" createdDate="2013-07-18 14:01:19.0" description="description2"
             sampleName="sample2" organism="E. coli" />
    <sample id="3" createdDate="2013-07-18 14:02:19.0" description="description3"
             sampleName="sample3" organism="E. coli" />
    <sample id="4" createdDate="2013-07-18 14:03:19.0" description="description4"
             sampleName="sample4" organism="Listeria" />
    <sample id="5" createdDate="2013-07-18 14:04:19.0" description="description5"
             sampleName="sample5" organism="Listeria" />
    <sample id="6" createdDate="2013-07-18 14:05:19.0" description="description5"
             sampleName="sample523423" />
    <sample id="7" createdDate="2013-07-18 14:06:19.0" description="description5"
             sampleName="sample534534" />
    <sample id="8" createdDate="2013-07-18 14:07:19.0" description="description5"
             sampleName="sample589789" />
    <sample id="9" createdDate="2013-07-18 14:08:19.0" description="description5"
             sampleName="sample52342" />
    <sample id="10" createdDate="2013-07-18 14:09:19.0" description="description5"
             sampleName="sample565" />
    <sample id="11" createdDate="2013-07-18 14:10:19.0" description="description5"
             sampleName="sample6735" />
    <sample id="12" createdDate="2013-07-18 14:11:19.0" description="description5"
             sampleName="sample3452345" />
    <sample id="13" createdDate="2013-07-18 14:12:19.0" description="description5"
             sampleName="sample3643225" />
    <sample id="14" createdDate="2013-07-18 14:13:19.0" description="description5"
             sampleName="sample64565" />
    <sample id="15" createdDate="2013-07-18 14:14:19.0" description="description5"
             sampleName="sample57567" />
    <sample id="16" createdDate="2013-07-18 14:15:19.0" description="description5"
             sampleName="sample55422r" />
    <sample id="17" createdDate="2013-07-18 14:16:19.0" description="description5"
             sampleName="sample5dt5" />
    <sample id="18" createdDate="2013-07-18 14:17:19.0" description="description5"
             sampleName="sample5ddfg4" />
    <sample id="19" createdDate="2013-07-18 14:18:19.0" description="description5"
             sampleName="sample554sg5" />
    <sample id="20" createdDate="2013-07-18 14:19:19.0" description="description5"
             sampleName="sample5fdgr" />
    <sample id="21" createdDate="2013-07-18 14:20:19.0" description="description5"
             sampleName="sample5fg44" />

    <project_sample id="1" project_id="1" sample_id="1" createdDate="2013-07-10 14:21:19.0" />
    <project_sample id="2" project_id="1" sample_id="2" createdDate="2013-07-12 14:22:19.0" />
    <project_sample id="3" project_id="1" sample_id="3" createdDate="2013-07-14 14:23:19.0" />
    <project_sample id="4" project_id="1" sample_id="4" createdDate="2013-07-16 14:24:19.0" />
    <project_sample id="5" project_id="1" sample_id="5" createdDate="2013-07-18 14:25:19.0" />
    <project_sample id="6" project_id="1" sample_id="6" createdDate="2013-07-18 14:26:19.0" />
    <project_sample id="7" project_id="1" sample_id="7" createdDate="2013-07-18 14:27:19.0" />
    <project_sample id="8" project_id="1" sample_id="8" createdDate="2013-07-18 14:28:19.0" />
    <project_sample id="9" project_id="1" sample_id="9" createdDate="2013-07-18 14:29:19.0" />
    <project_sample id="10" project_id="1" sample_id="10" createdDate="2013-07-18 14:31:19.0" />
    <project_sample id="11" project_id="1" sample_id="11" createdDate="2013-07-18 14:32:19.0" />
    <project_sample id="12" project_id="1" sample_id="12" createdDate="2013-07-18 14:33:19.0" />
    <project_sample id="13" project_id="1" sample_id="13" createdDate="2013-07-18 14:34:19.0" />
    <project_sample id="14" project_id="1" sample_id="14" createdDate="2013-07-18 14:35:19.0" />
    <project_sample id="15" project_id="1" sample_id="15" createdDate="2013-07-18 14:36:19.0" />
    <project_sample id="16" project_id="1" sample_id="16" createdDate="2013-07-18 14:37:19.0" />
    <project_sample id="17" project_id="1" sample_id="17" createdDate="2013-07-18 14:38:19.0" />
    <project_sample id="18" project_id="1" sample_id="18" createdDate="2013-07-18 14:39:19.0" />
    <project_sample id="19" project_id="2" sample_id="19" createdDate="2013-07-18 14:40:19.0" />
    <project_sample id="20" project_id="2" sample_id="20" createdDate="2013-07-18 14:41:19.0" />
    <project_sample id="21" project_id="2" sample_id="21" createdDate="2013-07-18 14:42:19.0" />


    <sequence_file id="1" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/01-1111_S1_L001_R1_001.fastq"/>
    <sequence_file id="2" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/02-2222_S1_L001_R2_001.fastq"/>
    <sequence_file id="3" created_date="2013-07-18 14:20:19.0"
                   file_path="src/test/resources/files/sequence-files/03-3333_S1_L001_R1_001.fastq"/>

	<sequencing_object id="1" created_date="2014-07-30 08:24:34" />
	<sequencing_object id="2" created_date="2013-07-18 14:20:19.0" />

	<sequence_file_pair id="1" />
	<sequence_file_pair_files pair_id="1"
		files_id="1" />
	<sequence_file_pair_files pair_id="1"
		files_id="2" />

	<sequence_file_single_end id="2" file_id="3" />

	<sample_sequencingobject id="1"
		created_date="2013-07-18 14:20:19.0" sample_id="18"
		sequencingobject_id="1" />
	<sample_sequencingobject id="2"
		created_date="2013-07-18 14:20:19.0" sample_id="18"
		sequencingobject_id="2" />

    <reference_file id="1" createdDate="2013-06-16 11:15:36.2" filePath="/tmp/path/to/nowhere/02-222.fastq" fileRevisionNumber="1" modifiedDate="2013-06-16 11:15:36.2" />
    <reference_file id="2" createdDate="2013-07-16 11:15:36.2" filePath="/tmp/path/to/nowhere/03-333.fastq" fileRevisionNumber="1" modifiedDate="2013-07-17 11:15:36.2" />

    <project_referencefile id="1" createdDate="2013-08-16 15:15:36.2" project_id="1" reference_file_id="1"/>
    <project_referencefile id="2" createdDate="2013-08-17 15:15:36.2" project_id="1" reference_file_id="2"/>
</dataset>
{'fraction_non_alphanumeric': 0.17572115384615383, 'fraction_numerical': 0.15475961538461538, 'mean_word_length': 4.3597011079618655, 'pattern_counts': {'":': 0, '<': 192, '<?xml version=': 2, '>': 192, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '146069', 'n_tokens_mistral': 9298, 'n_tokens_neox': 7506, 'n_words': 1095}