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‎raisinbread/RB_files/CNV.sql‎

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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE CNV;
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LOCK TABLE CNV WRITE;
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LOAD DATA LOCAL INFILE 'CNV.tsv' INTO TABLE CNV
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IGNORE 1 LINES;
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SET FOREIGN_KEY_CHECKS=1;

‎raisinbread/RB_files/CNV.tsv‎

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CNVID CandidateID Description Type EventName Common_CNV Characteristics CopyNumChange Inheritance ArrayReport Markers ArrayReportDetail ValidationMethod PlatformID Chromosome Strand EndLoc StartLoc Symbol Name NCBIID OfficialSymbol OfficialName
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1 326 \N gain \N Y Unknown \N unknown Normal \N \N \N 1 chr1 + 11007 11008 \N \N \N \N \N
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2 326 \N unknown \N Y Unknown \N unknown Normal \N \N \N 1 chr1 - 11009 11010 \N \N \N \N \N
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3 302 \N unknown \N Y Unknown \N unknown Normal \N \N \N 1 chr1 + 11007 11008 \N \N \N \N \N
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4 323 \N unknown \N Y Unknown \N unknown Normal \N \N \N 1 chr1 + 11007 11008 \N \N \N \N \N

‎raisinbread/RB_files/Config.sql‎

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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE Config;
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LOCK TABLE Config WRITE;
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LOAD DATA LOCAL INFILE 'Config.tsv' INTO TABLE Config
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IGNORE 1 LINES;
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SET FOREIGN_KEY_CHECKS=1;

‎raisinbread/RB_files/Config.tsv‎

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ID ConfigID Value
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1 2 1
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2 3 LORIS Demonstration Database
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3 42 <h3>Example Study Description</h3>
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<p>This is a sample description for this study, because it is a new LORIS install that has not yet customized this text.</p>
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<p>A LORIS administrator can customize this text in the configuration module, under the configuration option labeled "Study Description"</p>
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<h3>Useful Links</h3>
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<ul>
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<li><a href="https://github.com/aces/Loris" >LORIS GitHub Repository</a></li>
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<li><a href="https://github.com/aces/Loris/wiki/Setup" >LORIS Setup Guide</a></li>
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<li><a href="https://www.youtube.com/watch?v=2Syd_BUbl5A" >A video of a loris on YouTube</a></li>
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</ul>
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4 4 images/LORIS_logo.png
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5 5 false
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6 6 5
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7 7 99
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9 9 false
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10 10 2016
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11 11 2028
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12 13 false
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13 14 false
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15 16 false
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16 20 false
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17 21 true
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18 22 true
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19 23 0
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20 24 Customize this text with your citation policy (via Configuration module)
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22 12 Ymd
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23 27 /data-raisinbread/
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24 28 /home/driusan/Code/Loris/
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26 30 /PATH/TO/EXTERNAL/LIBRARY/
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29 33 tools/logs/
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30 34 /data/incoming/
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31 35 /data/demo/bin/mri/
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32 36 /data/incoming/
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33 37 /PATH/TO/Genomic-Data/
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34 38 /data/uploads/
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37 44 localhost
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39 48 This database provides an on-line mechanism to store both imaging and behavioural data collected from various locations. Within this framework, there are several tools that will make this process as efficient and simple as possible. For more detailed information regarding any aspect of the database, please click on the Help icon at the top right. Otherwise, feel free to contact us at the DCC. We strive to make data collection almost fun.
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40 51 [a-zA-Z]{3}[0-9]{4}_[0-9]{6}_[vV][0-9]+
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41 52 (?i).
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42 53 (?i)phantom
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43 54 (?i)phantom
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44 55 true
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45 56 t1
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46 56 t2
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47 58 radiology_review
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48 58 mri_parameter_form
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49 60 [email protected]
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50 61 [email protected]
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51 62 Produced by LorisDB
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52 66 S3cret
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53 71 demo
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54 72 [email protected]
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55 73 /data/demo/bin/mri/dicom-archive/get_dicom_info.pl
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56 74 1
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57 75 1
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58 76 dcm2mnc
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59 77 /data-raisinbread/tarchive/
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60 78 PatientName
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61 79 1
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62 80 1
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63 81 0
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64 82 65
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65 83 t1
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66 84 19
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67 85 /opt/niak-0.6.4.1/
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68 86 INTERLACE_outputDWIFileNameSuffix
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75 87 /issue_tracker
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76 88 localizer
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77 88 scout
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78 89 true
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79 90 0
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80 91 mri_parameter_form
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82 92 prod
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83 94 t1
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84 95 flair
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85 95 t1
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86 95 t2
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87 95 pd
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88 96 flair
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89 96 t1
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90 96 t2
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91 96 pd
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92 97 /data/publication_uploads/
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93 98 /data/publication_uploads/to_be_deleted/
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94 99 true
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95 49 1000
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96 100 environment
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97 70 /data-raisinbread/
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98 93 V1
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102 19 false
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103 102 /data/document_repository_uploads/
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104 103 /data/data_release_uploads/
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105 104 Ymd
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106 105 Y-m-d H:i:s
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107 106 /data/issue_tracker/
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108 107
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113 112 warning
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114 113 warning
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115 114 none
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116 116
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117 117
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118 118
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119 119
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120 120 database_config.py
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121 125 false
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122 126 0
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126 129 365
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127 130 /var/www/loris/
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128 131 /data/EEGUploadIncomingPath/
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129 132 false
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130 133 EEGS3DataPath
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131 134 false

‎raisinbread/RB_files/ConfigI18n.sql‎

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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE ConfigI18n;
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LOCK TABLE ConfigI18n WRITE;
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LOAD DATA LOCAL INFILE 'ConfigI18n.tsv' INTO TABLE ConfigI18n
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IGNORE 1 LINES;
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SET FOREIGN_KEY_CHECKS=1;

‎raisinbread/RB_files/ConfigI18n.tsv‎

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‎raisinbread/RB_files/ConfigSettings.sql‎

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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE ConfigSettings;
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LOCK TABLE ConfigSettings WRITE;
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LOAD DATA LOCAL INFILE 'ConfigSettings.tsv' INTO TABLE ConfigSettings
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IGNORE 1 LINES;
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SET FOREIGN_KEY_CHECKS=1;

‎raisinbread/RB_files/ConfigSettings.tsv‎

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ID Name Description Visible AllowMultiple DataType Parent Label OrderNumber Multilingual
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1 study Settings related to details of the study 1 0 \N \N Study 1 0
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2 additional_user_info Display additional user profile fields on the User accounts page (e.g. Institution, Position, Country, Address) 1 0 boolean 1 Additional user information 15 0
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3 title Full descriptive title of the study 1 0 text 1 Study title 1 0
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4 studylogo Filename containing logo of the study. File should be located under the htdocs/images/ folder 1 0 text 1 Study logo 2 0
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5 useEDC Use EDC (Expected Date of Confinement) for birthdate estimations if the study involves neonatals 1 0 boolean 1 Use EDC 12 0
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6 ageMin Minimum candidate age in years (0+) 1 0 text 1 Minimum candidate age 7 0
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7 ageMax Maximum candidate age in years 1 0 text 1 Maximum candidate age 8 0
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9 useFamilyID Enable if family members are recruited for the study 1 0 boolean 1 Use family 11 0
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10 startYear Start year for study recruitment or data collection 1 0 text 1 Start year 5 0
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11 endYear End year for study recruitment or data collection 1 0 text 1 End year 6 0
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12 dobFormat Format of the Date of Birth 1 0 date_format 1 DOB Format 9 0
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13 useExternalID Enable if data is used for blind data distribution, or from external data sources 1 0 boolean 1 Use external ID 12 0
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14 useProband Enable for proband data collection 1 0 boolean 1 Use proband 11 0
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16 useScreening Enable if there is a Screening stage with its own distinct instruments, administered before the Visit stage 1 0 boolean 1 Use screening 14 0
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17 excluded_instruments Instruments to be excluded from the Data Dictionary and download via the Data Query Tool 1 1 instrument 1 Excluded instruments 16 0
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19 InstrumentResetting Allows resetting of instrument data 1 0 boolean 1 Instrument Resetting 18 0
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20 SupplementalSessionStatus Display supplemental session status information on Timepoint List page 1 0 boolean 1 Use Supplemental Session Status 19 0
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21 useScanDone Used for identifying timepoints that have (or should have) imaging data 1 0 boolean 1 Use Scan Done 20 0
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22 allowPrenatalTimepoints Determines whether creation of timepoints prior to Date of Birth is allowed 1 0 boolean 1 Allow Prenatal Timepoints 21 0
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23 ImagingUploaderAutoLaunch Allows running the ImagingUpload pre-processing scripts 1 0 boolean 1 ImagingUploader Auto Launch 22 0
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24 citation_policy Citation Policy for Acknowledgements module 1 0 textarea 1 Citation Policy 23 0
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25 CSPAdditionalHeaders Extensions to the Content-security policy allow only for self-hosted content 1 0 text 1 Content-Security Extensions 24 0
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26 paths Specify directories where LORIS-related files are stored or created. Take care when editing these fields as changing them incorrectly can cause certain modules to lose functionality. 1 0 \N \N Paths 2 0
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27 imagePath Path to images for display in Imaging Browser (e.g. /data/$project/data/) 1 0 web_path 26 Images 9 0
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28 base The base filesystem path where LORIS is installed 1 0 web_path 26 Base 1 0
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33 log Path to logs (relative path starting from /var/www/$projectname) 1 0 path 26 Logs 2 0
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34 IncomingPath Path for imaging data transferred to the project server (e.g. /data/incoming/$project/) 1 0 web_path 26 Incoming data 7 0
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35 MRICodePath Path to directory where Loris-MRI (git) code is installed 1 0 path 69 LORIS-MRI code 6 0
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36 MRIUploadIncomingPath Path to the upload directory for incoming MRI studies 1 0 web_path 69 MRI Incoming Directory 7 0
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37 GenomicDataPath Path to Genomic data files 1 0 web_path 26 Genomic Data Path 8 0
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38 mediaPath Path to uploaded media files 1 0 web_path 26 Media 9 0
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39 gui Settings related to the overall display of LORIS 1 0 \N \N GUI 3 0
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42 StudyDescription Description of the Study 1 0 textarea 39 Study Description 2 0
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43 www Web address settings 1 0 \N \N WWW 4 0
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44 host Host 1 0 text 43 Host 1 0
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45 eeg_pipeline EEG Pipeline settings 1 0 \N \N EEG Pipeline 15 0
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46 mantis_url Bug tracker URL 0 0 text 43 Bug tracker URL 3 0
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47 dashboard Settings that affect the appearance of the dashboard and its charts 1 0 \N \N Dashboard 5 0
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48 projectDescription Description of the study displayed in main dashboard panel 1 0 textarea 47 Project Description 1 1
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49 recruitmentTarget Target number of participants for the study 1 0 text 47 Target number of participants 2 0
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50 imaging_modules DICOM Archive and Imaging Browser settings 1 0 \N \N Imaging Modules 6 0
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51 patientIDRegex Regex for masking the Patient ID header field 1 0 text 50 Patient ID regex 1 0
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52 patientNameRegex Regex for masking the Patient Name header field 1 0 text 50 Patient name regex 2 0
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53 LegoPhantomRegex Regex for identifying a Lego Phantom scan header 1 0 text 50 Lego phantom regex 3 0
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54 LivingPhantomRegex Regex to be used on Living Phantom scan header 1 0 text 50 Living phantom regex 4 0
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55 showTransferStatus Show transfer status in the DICOM Archive table 1 0 boolean 50 Show transfer status 5 0
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56 tblScanTypes Scan types from the mri_scan_type table that the project wants to see displayed in Imaging Browser table 1 1 scan_type 50 Imaging Browser Tabulated Scan Types 6 0
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57 statistics Statistics module settings 1 0 \N \N Statistics 7 0
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58 excludedMeasures Instruments to be excluded from Statistics calculations 1 1 instrument 57 Excluded instruments 1 0
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59 mail LORIS email settings for notifications sent to users 1 0 \N \N Email 8 0
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60 From Sender email address header (e.g. [email protected]) 1 0 email 59 From 1 0
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61 Reply-to Reply-to email address header (e.g. [email protected]) 1 0 email 59 Reply-to 2 0
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62 X-MimeOLE X-MimeOLE 1 0 text 59 X-MimeOLE 3 0
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63 uploads Settings related to file uploading 1 0 \N \N Uploads 9 0
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64 FileGroup Determines the group permission for new subdirectories created for uploaded files 1 0 text 63 File Group for Uploads 1 0
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65 APIKeys Specify any API keys required for LORIS 1 0 \N \N API Keys 10 0
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66 JWTKey Secret key for signing JWT tokens on this server. This should be unique and never shared with anyone. 1 0 text 65 JWT Secret Key 1 0
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67 reCAPTCHAPrivate Private Key for Google reCAPTCHA 1 0 text 65 reCAPTCHA Private Key 2 0
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68 reCAPTCHAPublic Public Key for Google reCaptcha 1 0 text 65 reCAPTCHA Public Key 3 0
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69 imaging_pipeline Imaging Pipeline settings 1 0 \N \N Imaging Pipeline 14 0
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70 dataDirBasepath Base Path to the data directory of Loris-MRI 1 0 web_path 69 Loris-MRI Data Directory 1 0
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71 prefix Study prefix or study name 1 0 text 69 Study Name 2 0
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72 mail_user User to be notified during imaging pipeline execution 1 0 text 69 User to notify when executing the pipeline 3 0
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73 get_dicom_info Full path to get_dicom_info.pl 1 0 path 69 Full path to get_dicom_info.pl script 4 0
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74 horizontalPics Enable generation of horizontal pictures 1 0 boolean 69 Horizontal pictures creation 5 0
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75 create_nii Enable creation of NIfTI files 1 0 boolean 69 NIfTI file creation 6 0
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76 converter If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the converter, you will have to specify what it is called and the uploader will try to invoke it 1 0 text 69 DICOM converter tool to use (dcm2mnc or dcm2niix) 7 0
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77 tarchiveLibraryDir Location of storing the library of used tarchives. If this is not set, they will not be moved 1 0 path 69 Path to Tarchives 8 0
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78 lookupCenterNameUsing DICOM field (either PatientName or PatientID) to use to get the patient identifiers and the center name of the DICOM study 1 0 lookup_center 69 Patient identifiers and center name lookup variable 9 0
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79 createCandidates Enable candidate creation in the imaging pipeline 1 0 boolean 69 Enable candidate creation 10 0
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80 is_qsub Enable use of batch management in the imaging pipeline 1 0 boolean 69 Project batch management used 15 0
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81 use_legacy_dicom_study_importer Use the legacy DICOM study importer instead of the new one 1 0 boolean 69 Use legacy DICOM study importer 15 0
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82 DTI_volumes Number of volumes in native DTI acquisitions 1 0 text 69 Number of volumes in native DTI acquisitions 16 0
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83 t1_scan_type Scan type of native T1 acquisition (as in the mri_scan_type table) 1 0 text 69 Scan type of native T1 acquisition 17 0
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84 reject_thresh Max number of directions that can be rejected to PASS QC 1 0 text 69 Max number of DTI rejected directions for passing QC 18 0
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85 niak_path Path to niak quarantine to use if mincdiffusion will be run (option -runMincdiffusion set when calling DTIPrep_pipeline.pl) 1 0 path 69 NIAK Path 19 0
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86 QCed2_step DTIPrep protocol step at which a secondary QCed dataset is produced (for example one without motion correction and eddy current correction would be saved at INTERLACE_outputDWIFileNameSuffix step of DTIPrep) 1 0 text 69 Secondary QCed dataset 20 0
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87 issue_tracker_url URL of the preferred issue tracker for this study 1 0 text 43 Issue Tracker URL 3 0
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88 excluded_series_description Series description to be excluded from insertion into the database (typically localizers and scouts) 1 1 text 69 Series description to exclude from imaging insertion 21 0
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89 useConsent Enable if the study uses the loris architecture for consent 1 0 boolean 1 Use consent 15 0
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90 ComputeDeepQC Determines whether a call is made from LORIS-MRI to the DeepQC app for automatic QC prediction 1 0 boolean 69 Compute automatic QC 22 0
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91 ImagingBrowserLinkedInstruments Instruments that the users want to see linked from Imaging Browser 1 1 instrument 50 Imaging Browser Links to Instruments 7 0
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92 MriConfigFile Name of the Perl MRI config file (stored in dicom-archive/.loris_mri/) 1 0 text 69 Name of the Perl MRI config file 23 0
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93 default_bids_vl Default visit label to use when no visit label set in the BIDS dataset 1 0 text 69 Default visit label for BIDS dataset 14 0
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94 reference_scan_type_for_defacing Scan type to use as a reference for registration when defacing anatomical images (typically a T1W image) 1 0 scan_type 69 Scan type to use as a reference for defacing (typically a T1W image) 26 0
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95 modalities_to_deface Modalities for which defacing should be run and defaced image inserted in the database 1 1 scan_type 69 Modalities on which to run the defacing pipeline 27 0
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96 compute_snr_modalities Modalities for which the SNR should be computed when running the insertion MRI scripts 1 1 scan_type 69 Modalities on which SNR should be calculated 25 0
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97 publication_uploads Path to uploaded publications 1 0 web_path 26 Publications 11 0
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98 publication_deletions Path to deleted publications 1 0 web_path 26 Deleted Publications 11 0
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99 usePwnedPasswordsAPI Whether to query the Have I Been Pwned password API on password changes to prevent the usage of common and breached passwords 1 0 boolean 1 Enable "Pwned Password" check 22 0
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100 EnvironmentFile Name of the environment file that need to be sourced for the imaging pipeline 1 0 text 69 Name of the environment file 24 0
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101 MINCToolsPath Path to the MINC tools 1 0 web_path 69 Path to the MINC tools 12 0
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102 documentRepositoryPath Path to uploaded document repository files 1 0 text 26 Document Repository Upload Path 13 0
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103 dataReleasePath Path to uploaded data release files 1 0 text 26 Data Release Upload Path 14 0
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104 dodFormat Format of the Date of Death 1 0 date_format 1 DOD Format 10 0
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105 dateDisplayFormat The date format to use throughout LORIS for displaying date information - formats for date inputs are browser- and locale-dependent. 1 0 text 1 Date display format 27 0
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106 IssueTrackerDataPath Path to Issue Tracker data files 1 0 web_path 26 Issue Tracker Data Path 8 0
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107 adminContactEmail An email address that users can write to in order to report issues or ask question 1 0 text 1 Administrator Email 28 0
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111 logs Settings related to logging 1 0 \N \N Log Settings 12 0
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112 database_log_level Verbosity of database logging 1 0 log_level 111 Database Log Level 3 0
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113 request_log_level Verbosity of HTTP request logs 1 0 log_level 111 HTTP Request Log Level 3 0
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114 exception_log_level Verbosity of PHP exception logging 1 0 log_level 111 HTTP Request Log Level 3 0
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115 minc2bids Settings related to converting MINC to BIDS LORIS-MRI tool script 1 0 \N \N MINC to BIDS Converter Tool Options 13 0
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116 bids_dataset_authors Authors for the BIDS dataset 1 1 text 115 BIDS Dataset Authors 1 0
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117 bids_acknowledgments_text Acknowledgments to be added in the dataset_description.json file of the BIDS dataset created out of the MINC files 1 0 text 115 BIDS Dataset Acknowledgments 2 0
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118 bids_readme_text Content to be added to the README of the BIDS dataset generated out of the MINC files 1 0 textarea 115 BIDS Dataset README 3 0
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119 bids_validator_options_to_ignore Options to be ignored for BIDS validation 1 1 text 115 BIDS Validation options to ignore 4 0
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120 MriPythonConfigFile Name of the Python MRI config file (stored in dicom-archive/.loris_mri/) 1 0 text 69 Name of the Python MRI config file 28 0
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121 aws Settings related to AWS services 1 0 \N \N AWS Settings 13 0
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122 AWS_S3_Endpoint Endpoint to use for accessing files stored in S3. Endpoint or region are required for S3 support. 1 0 text 121 AWS S3 Endpoint 3 0
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123 AWS_S3_Region AWS Region to use for accessing files stored in S3. Endpoint or region are required for S3 support. 1 0 text 121 AWS S3 Region 3 0
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124 AWS_S3_Default_Bucket Default bucket for LORIS to use for accessing files in S3. 1 0 text 121 AWS S3 Default Bucket 3 0
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125 useEEGBrowserVisualizationComponents Whether to enable the visualization components on the EEG Browser module 1 0 boolean 39 Enable the EEG Browser components 4 0
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126 createVisit Enable visit creation in the imaging pipeline 1 0 boolean 69 Enable visit creation 11 0
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127 default_project Default project used when creating scan candidate or visit 1 0 text 69 Default project 12 0
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128 default_cohort Default cohort used when creating scan visit 1 0 text 69 Default cohort 13 0
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129 UserMaximumDaysInactive The maximum number of days since last login before making a user inactive. 1 0 text 1 Maximum Days Before Making User Inactive 30 0
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130 DownloadPath Where files are downloaded 1 0 text 26 Downloads 4 0
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131 EEGUploadIncomingPath Path to the upload directory for incoming EEG studies 1 0 text 45 EEG Incoming Directory 15 0
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132 useDoB Use DoB (Date of Birth) 1 0 boolean 1 Use DoB 12 0
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133 EEGS3DataPath EEG S3 data path for assembly data 1 0 text 45 EEG S3 data path 15 0
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134 useAdvancedPermissions Restricts access to data based on both sites and projects and require a special permission to access data not affiliated to a session (SessionID null). Keeping this setting to NO should ensure backwards compatibility (access to all data when module loads) 1 0 boolean 50 Use Advanced Permissions 5 0
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135 biobank Settings related to the biobank module 1 0 \N \N Biobank 14 0
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136 printEndpoint Endpoint address for label printing logic 1 0 text 135 Label Printing Endpoint 1 0

‎raisinbread/RB_files/ExternalLinkTypes.sql‎

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SET FOREIGN_KEY_CHECKS=0;
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TRUNCATE TABLE ExternalLinkTypes;
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LOCK TABLE ExternalLinkTypes WRITE;
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LOAD DATA LOCAL INFILE 'ExternalLinkTypes.tsv' INTO TABLE ExternalLinkTypes
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IGNORE 1 LINES;
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SET FOREIGN_KEY_CHECKS=1;

‎raisinbread/RB_files/ExternalLinkTypes.tsv‎

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LinkTypeID LinkType
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4 FooterLink
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5 StudyLinks
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6 dashboard

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