From b9a48b0626bbc4d235fb91897c78baf7c2498b79 Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Tue, 5 May 2020 06:21:58 -0400 Subject: [PATCH 1/6] add scripts/dump_db_fixtures.py from roslin-qc branch --- scripts/dump_db_fixtures.py | 123 +++++++++++++++++++++++++++++++----- 1 file changed, 106 insertions(+), 17 deletions(-) diff --git a/scripts/dump_db_fixtures.py b/scripts/dump_db_fixtures.py index daffab62a..79b7e88d9 100755 --- a/scripts/dump_db_fixtures.py +++ b/scripts/dump_db_fixtures.py @@ -17,6 +17,8 @@ $ dump_db_fixtures.py port_files fd41534c-71eb-4b1b-b3af-e3b1ec3aecde +$ dump_db_fixtures.py run --onefile ca18b090-03ad-4bef-acd3-52600f8e62eb + Output ------ @@ -34,7 +36,7 @@ import json import argparse import django -from django.db.models import Prefetch +from django.db.models import Prefetch, Max from django.core import serializers from pprint import pprint @@ -44,9 +46,20 @@ os.environ.setdefault("DJANGO_SETTINGS_MODULE", "beagle.settings") django.setup() from file_system.models import File, FileMetadata, FileGroup, FileType -from runner.models import Run, RunStatus, Port, PortType, Pipeline +from runner.models import Run, RunStatus, Port, PortType, Pipeline, OperatorRun sys.path.pop(0) +def get_file_filemetadata_from_port(port_instance): + """ + Get the queryset of all File and FileMetadata entries for a given Port entry + returns a tuple of type (files_queryset, filemetadata_queryset) + """ + files_queryset = port_instance.files.all() + # filemetadata_queryset = FileMetadata.objects.filter(file__in = [i for i in files_queryset]) + filemetata_instances = [] + for file in files_queryset: + filemetata_instances.append(FileMetadata.objects.filter(file = file).order_by('-version').first()) + return(files_queryset, filemetata_instances) def dump_request(**kwargs): """ @@ -73,22 +86,75 @@ def dump_run(**kwargs): Dump re-loadable Django database fixtures for a Run entry and its associated input and output Port entries """ runID = kwargs.pop('runID') + onefile = kwargs.pop('onefile') output_run_file = "{}.run.json".format(runID) - output_port_input_file = "{}.port.input.json".format(runID) - output_port_output_file = "{}.port.output.json".format(runID) + output_port_input_file = "{}.run.port.input.json".format(runID) + output_port_output_file = "{}.run.port.output.json".format(runID) + output_port_file_input_file = "{}.run.port_file.input.json".format(runID) + output_port_filemetadata_input_file = "{}.run.port_filemetadata.input.json".format(runID) + output_port_file_output_file = "{}.run.port_file.output.json".format(runID) + output_port_filemetadata_output_file = "{}.run.port_filemetadata.output.json".format(runID) + output_operator_run_file = "{}.run.operator_run.json".format(runID) + + all_data = [] + input_files = [] + input_filemetadatas = [] + output_files = [] + output_filemetadatas = [] # get the parent Run instance run_instance = Run.objects.get(id = runID) - print(json.dumps(json.loads(serializers.serialize('json', [run_instance])), indent=4), file = open(output_run_file, "w")) - # get the Run input and output Port instances - input_queryset = run_instance.port_set.filter(port_type=PortType.INPUT) - print(json.dumps(json.loads(serializers.serialize('json', input_queryset.all())), indent=4), file = open(output_port_input_file, "w")) + operator_run_instance = run_instance.operator_run - output_queryset = run_instance.port_set.filter(port_type=PortType.OUTPUT) - print(json.dumps(json.loads(serializers.serialize('json', output_queryset.all())), indent=4), file = open(output_port_output_file, "w")) - for item in output_queryset: - pprint((item, item.files.all())) + # get the Run input and output Port instances + input_port_queryset = run_instance.port_set.filter(port_type=PortType.INPUT) + output_port_queryset = run_instance.port_set.filter(port_type=PortType.OUTPUT) + + for item in input_port_queryset: + files_queryset, filemetata_instances = get_file_filemetadata_from_port(item) + for file in files_queryset: + input_files.append(file) + for filemetadata in filemetata_instances: + input_filemetadatas.append(filemetadata) + + for item in output_port_queryset: + files_queryset, filemetata_instances = get_file_filemetadata_from_port(item) + for file in files_queryset: + output_files.append(file) + for filemetadata in filemetata_instances: + output_filemetadatas.append(filemetadata) + + # save each set of items to individual files by default + if onefile == False: + print(json.dumps(json.loads(serializers.serialize('json', [run_instance])), indent=4), file = open(output_run_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', [operator_run_instance])), indent=4), file = open(output_operator_run_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', input_port_queryset.all())), indent=4), file = open(output_port_input_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', output_port_queryset.all())), indent=4), file = open(output_port_output_file, "w")) + + print(json.dumps(json.loads(serializers.serialize('json', input_files)), indent=4), file = open(output_port_file_input_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', input_filemetadatas)), indent=4), file = open(output_port_filemetadata_input_file, "w")) + + print(json.dumps(json.loads(serializers.serialize('json', output_files)), indent=4), file = open(output_port_file_output_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', output_filemetadatas)), indent=4), file = open(output_port_filemetadata_output_file, "w")) + + # save all items to a single file + if onefile == True: + all_data.append(run_instance) + all_data.append(operator_run_instance) + for item in input_port_queryset: + all_data.append(item) + for item in output_port_queryset: + all_data.append(item) + for item in input_files: + all_data.append(item) + for item in input_filemetadatas: + all_data.append(item) + for item in output_files: + all_data.append(item) + for item in output_filemetadatas: + all_data.append(item) + print(json.dumps(json.loads(serializers.serialize('json', all_data)), indent=4), file = open(output_run_file, "w")) def dump_port_files(**kwargs): @@ -113,13 +179,23 @@ def dump_pipeline(**kwargs): Dump re-loadable Django database fixtures for Pipeline entries and related table fixtures """ pipelineName = kwargs.pop('pipelineName') - output_pipeline_file = "{}.pipeline.json".format(pipelineName) - output_pipeline_filegroup_file = "{}.pipeline.output_file_group.json".format(pipelineName) + if pipelineName == "all": + output_pipeline_file = "all_pipeline.json".format(pipelineName) + output_pipeline_filegroup_file = "all_pipeline.output_file_group.json".format(pipelineName) + + pipelines = Pipeline.objects.all() + print(json.dumps(json.loads(serializers.serialize('json', pipelines)), indent=4), file = open(output_pipeline_file, "w")) + + file_groups = FileGroup.objects.all() + print(json.dumps(json.loads(serializers.serialize('json', file_groups)), indent=4), file = open(output_pipeline_filegroup_file, "w")) + else: + output_pipeline_file = "{}.pipeline.json".format(pipelineName) + output_pipeline_filegroup_file = "{}.pipeline.output_file_group.json".format(pipelineName) - pipeline_instance = Pipeline.objects.get(name = pipelineName) - print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance])), indent=4), file = open(output_pipeline_file, "w")) + pipeline_instance = Pipeline.objects.get(name = pipelineName) + print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance])), indent=4), file = open(output_pipeline_file, "w")) - print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance.output_file_group])), indent=4), file = open(output_pipeline_filegroup_file, "w")) + print(json.dumps(json.loads(serializers.serialize('json', [pipeline_instance.output_file_group])), indent=4), file = open(output_pipeline_filegroup_file, "w")) def get_files(value, type): """ @@ -178,6 +254,14 @@ def dump_file(**kwargs): output_file = "all.file_filemetadata.json" print(json.dumps(all_data, indent=4), file = open(output_file, "w")) +def dump_file_group(**kwargs): + """ + Dump the FileGroup fixtures + """ + fileGroupId = kwargs.pop('fileGroupID') + output_file_group_file = "{}.file_group.json".format(fileGroupId) + filegroup_instance = FileGroup.objects.get(id = fileGroupId) + print(json.dumps(json.loads(serializers.serialize('json', [filegroup_instance])), indent=4), file = open(output_file_group_file, "w")) def parse(): """ @@ -193,6 +277,7 @@ def parse(): run = subparsers.add_parser('run', help = 'Dump output data for pipeline run') run.add_argument('runID', help = 'Run ID to dump items for') + run.add_argument('--onefile', action = "store_true", help = 'Put all the outputs into a single file ') run.set_defaults(func = dump_run) pipeline = subparsers.add_parser('pipeline', help = 'Dump pipeline fixture') @@ -210,6 +295,10 @@ def parse(): port_files.add_argument('portID', help = 'Port ID to dump files for') port_files.set_defaults(func = dump_port_files) + file_group = subparsers.add_parser('filegroup', help = 'Dump filegroup fixture') + file_group.add_argument('fileGroupID', help = 'FileGroup ID ID to dump items for') + file_group.set_defaults(func = dump_file_group) + args = parser.parse_args() args.func(**vars(args)) From 909b82d6bd8c3f9db0b8dce33d04f4d0b0fa0d2d Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Tue, 5 May 2020 06:23:07 -0400 Subject: [PATCH 2/6] add scripts/duplicate_fixtures.py from roslin-qc --- scripts/duplicate_fixtures.py | 198 ++++++++++++++++++++++++++++++++++ 1 file changed, 198 insertions(+) create mode 100755 scripts/duplicate_fixtures.py diff --git a/scripts/duplicate_fixtures.py b/scripts/duplicate_fixtures.py new file mode 100755 index 000000000..152098619 --- /dev/null +++ b/scripts/duplicate_fixtures.py @@ -0,0 +1,198 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +Script to use for creating a modified, non-conflicting duplicate of an existing database fixture +Use this after you have dumped some fixtures to a .json file using `dump_db_fixtures.py`, and now you +want another fixture set that has different UUIDs and identifiers so you can load both at once in a dev database +in order to get work done with them. + +Input: .json file produced by dump_db_fixtures.py + +Output: a new .json file with updated key values + +Usage +----- + ./duplicate_fixtures.py ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json + +Notes +----- +The input .json file must have been produced with 'indent = 4' or have equivalent indenting, or this script will probably not work +""" +import os +import sys +import json +import uuid +import copy +import re +import time +import argparse + +def get_unique_id(): + """ + Get a unique ID + maybe replace with with uuid4? + uuid1 has a lower chance of duplicate id's being generated + + TODO: see what Sinisa thinks about this later + """ + return(uuid.uuid1()) + +def replace_primary_keys(input_file, no_change_files): + """ + Replaces all primary keys in the file with new values + """ + # get all primary keys that need to be changed + all_pk = [] + with open(input_file) as f: + for item in json.load(f): + # do not change the pk's on 'File' objects because that causes unique constraint issues on file path + if item['model'] != 'file_system.file': + all_pk.append(item['pk']) + elif item['model'] == 'file_system.file': + if no_change_files == True: + pass + elif no_change_files == False: + all_pk.append(item['pk']) + + # sort unique based on descending length + # this makes sure we replace the longer pattern first in the next steps + all_pk = sorted(list(set(all_pk)), key = len, reverse=True) + + # load all lines of text from the file + lines = open(input_file).readlines() + + # make a copy for editing + output_lines = copy.deepcopy(lines) + + editted_lines = [] + + # search for every primary key in every line of text ... !! Yes, we are doing this + for old_pk in all_pk: + new_pk = str(get_unique_id()) + for i, old_line in enumerate(lines): + if old_pk in old_line: + # I think this only replaces first intance of the pattern? shouldnt matter for this if you printed JSON with indent = 4 + new_line = re.sub(old_pk, new_pk, output_lines[i]) + output_lines[i] = new_line + + # each line should only get editted one time doing this otherwise something is wrong + if i not in editted_lines: + editted_lines.append(i) + else: + print("ERROR: line {} is about to get editted twice; that is not supposed to happen something is wrong".format(i)) + raise + return(output_lines) + +def get_field_values(input_lines, field_name): + """ + Finds a list of all unique values for a given field in the file lines + + examples: + + "runId": "PITT_0390", + >>> ["PITT_0390"] + + "requestId": "09670_D_1581808018", + "sampleId": "09670_D_1", + "patientId": "C-K2902H", + "sampleName": "C-K2902H-P001-d", + "externalSampleId": "S16-68609", + "investigatorSampleId": "S16-68609", + """ + all_values = set() + search_pattern = '.*"{field_name}": "(.*)"'.format(field_name = field_name) + for line in input_lines: + match = re.search(search_pattern, line) + if match != None: + value = match.group(1) + all_values.add(value) + + # return reverse sorted on length to ensure sub-patterns do not get replaced first later + all_values = sorted(list(set(all_values)), key = len, reverse=True) + return(all_values) + +def replace_field_value(input_lines, field_name, old_value, new_value): + """ + Replace the old value for a field with the new value in all file lines + """ + # make a copy for editing + output_lines = copy.deepcopy(input_lines) + + fieldname_search_pattern = '"{field_name}":'.format(field_name = field_name) + + # search for the field label in all lines and replace the value if found + for i, line in enumerate(input_lines): + # check that its a line with the desired field name in it + line_match = re.search(fieldname_search_pattern, line) + if line_match != None: + # check that the desired value to be changed is present + id_match = re.search(old_value, line) + if id_match != None: + # replace the old value with the new value + new_line = re.sub(old_value, new_value, output_lines[i]) + output_lines[i] = new_line + return(output_lines) + +def main(**kwargs): + """ + Main function for editing a fixtures file to replace all old primary keys with new keys + So that both old and new fixtures sets can be loaded into the database at the same time + """ + input_file = kwargs.pop('input_file') + output_file = kwargs.pop('output_file', None) + no_change_files = kwargs.pop('output_file', False) + + if output_file == None: + output_file_name = "{}.duplicated.json".format(input_file) + else: + output_file_name = output_file + + # generate a timestamp string to use for new unique identifiers + timestamp_str = str(int(time.time())) + + # replace all the primary keys with new values; need special handling for pk's because they do not always have a field label in the file + output_lines = replace_primary_keys(input_file, no_change_files) + + # replace the values for all of these other desired fields; these fields are always clearly labeled in the file so they are easy to find + fields_to_change = [ + 'runId', + 'requestId', + 'sampleId', + 'patientId', + 'sampleName', + 'externalSampleId', + 'investigatorSampleId', + 'file_name', + 'path' + ] + for field_name in fields_to_change: + all_values = get_field_values(input_lines = output_lines, field_name = field_name) + for old_value in all_values: + # make a new value by appending the timestamp + if field_name in ['file_name', 'path']: + # special handling for adding timestamp to file paths + name, ext = os.path.splitext(old_value) + new_value = name + '.' + timestamp_str + ext + else: + new_value = old_value + '_' + timestamp_str + output_lines = replace_field_value(input_lines = output_lines, field_name = field_name, old_value = old_value, new_value = new_value) + + # save the output files + with open(output_file_name, "w") as fout: + fout.writelines(output_lines) + +def parse(): + """ + Parses script args + Script arg parsing will go here as this script grows + """ + parser = argparse.ArgumentParser(description = 'Duplicate database fixtures that were previously dumped in json format with indentation') + parser.add_argument('input_file', help = "Input file containing fixtures") + parser.add_argument('--output-file', dest = "output_file", default = None, help = "Name of output file to write to") + parser.add_argument('--no-change-files', dest = "no_change_files", action = 'store_true', help = "Dont change the File items' primary keys and paths") + + args = parser.parse_args() + main(**vars(args)) + +if __name__ == '__main__': + parse() From 0506c952c4d2c41b1224285258aa2c4e7175bad9 Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Tue, 5 May 2020 07:04:20 -0400 Subject: [PATCH 3/6] add metadata sanitizer to fixture dump script --- scripts/dump_db_fixtures.py | 71 ++++++++++++++++++++++++++++++++++++- 1 file changed, 70 insertions(+), 1 deletion(-) diff --git a/scripts/dump_db_fixtures.py b/scripts/dump_db_fixtures.py index 79b7e88d9..a90b1c4fa 100755 --- a/scripts/dump_db_fixtures.py +++ b/scripts/dump_db_fixtures.py @@ -49,6 +49,70 @@ from runner.models import Run, RunStatus, Port, PortType, Pipeline, OperatorRun sys.path.pop(0) +def sanitize_metadata(queryset_data_dicts): + """ + Strip personal data from the FileMetadata queryset instances that have been converted to dicts + + Parameters + ---------- + queryset_data_dicts: list + a list of dicts that represent the FileMetadata instances. + + Output + ------ + list + a list of modified dicts + + Notes + ----- + Modifies dicts in place; pass by reference + + Example of FileMetadata dict data structure: + + [{ + "model": "file_system.filemetadata", + "fields": { + "metadata": { + "patientId": "C-ABCD", + "sampleName": "C-ABCD-P001-d", + "labHeadName": "Roslyn Franklin", + "labHeadEmail": "username@internet.com", + "dataAnalystName": "", + "dataAnalystEmail": "", + "externalSampleId": "AB-123-XYZ", + "investigatorName": "Dr. Smith", + "investigatorEmail": "username@internet.com", + "projectManagerName": "Dr. Jones", + "investigatorSampleId": "AB-123-XYZ", + }, + } + }, ... ] + """ + for queryset_data_dict in queryset_data_dicts: + if 'metadata' in queryset_data_dict['fields']: + if 'labHeadName' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['labHeadName'] = 'Roslyn Franklin' + + if 'labHeadEmail' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['labHeadEmail'] = 'username@internet.com' + + if 'dataAnalystName' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['dataAnalystName'] = 'E Wilson' + + if 'dataAnalystEmail' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['dataAnalystEmail'] = 'username@internet.com' + + if 'investigatorName' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['investigatorName'] = 'Dr. Smith' + + if 'investigatorEmail' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['investigatorEmail'] = 'username@internet.com' + + if 'projectManagerName' in queryset_data_dict['fields']['metadata']: + queryset_data_dict['fields']['metadata']['projectManagerName'] = 'Dr. Jones' + + return(queryset_data_dicts) + def get_file_filemetadata_from_port(port_instance): """ Get the queryset of all File and FileMetadata entries for a given Port entry @@ -66,12 +130,16 @@ def dump_request(**kwargs): Dump re-loadable fixtures for File and FileMetadata items from a given request """ requestID = kwargs.pop('requestID') + sanitize = kwargs.pop('sanitize', False) output_file_file = "{}.file.json".format(requestID) output_filemetadata_file = "{}.filemetadata.json".format(requestID) # get FileMetadata entries that match the request ID file_instances = FileMetadata.objects.filter(metadata__requestId = requestID) - print(json.dumps(json.loads(serializers.serialize('json', file_instances)), indent=4), file = open(output_filemetadata_file, "w")) + data = json.loads(serializers.serialize('json', file_instances)) + if sanitize == True: + data = sanitize_metadata(queryset_data_dicts = data) + print(json.dumps(data, indent=4), file = open(output_filemetadata_file, "w")) # get the File entries that corresponds to the request ID queryset = File.objects.prefetch_related( @@ -273,6 +341,7 @@ def parse(): # subparser for dumping requests request = subparsers.add_parser('request', help = 'Dump File and FileMetadata based on a requestId') request.add_argument('requestID', help = 'requestID to dump items for') + request.add_argument('--sanitize', action = "store_true", help = 'Attempt to scrub personal data from the FileMetadata entries') request.set_defaults(func = dump_request) run = subparsers.add_parser('run', help = 'Dump output data for pipeline run') From 5591dcdc71a0a71af3dea546cd6a65ec54e5b8f7 Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Mon, 11 May 2020 17:00:26 -0400 Subject: [PATCH 4/6] add fixture sanitize scripts --- .gitignore | 1 + scripts/generate_cmo_id.py | 7 ++++++ scripts/get_fields_to_sanitize.sh | 9 ++++++++ scripts/sanitize.sh | 37 +++++++++++++++++++++++++++++++ 4 files changed, 54 insertions(+) create mode 100755 scripts/generate_cmo_id.py create mode 100755 scripts/get_fields_to_sanitize.sh create mode 100755 scripts/sanitize.sh diff --git a/.gitignore b/.gitignore index 32eea3fe3..43ed832e9 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ scripts/*.json conda* input.json *.swp +patterns.tsv diff --git a/scripts/generate_cmo_id.py b/scripts/generate_cmo_id.py new file mode 100755 index 000000000..8324e3a4d --- /dev/null +++ b/scripts/generate_cmo_id.py @@ -0,0 +1,7 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +""" +import uuid +cmo_id = "C-" + str(uuid.uuid4())[0:6].upper() +print(cmo_id) diff --git a/scripts/get_fields_to_sanitize.sh b/scripts/get_fields_to_sanitize.sh new file mode 100755 index 000000000..939aa52b6 --- /dev/null +++ b/scripts/get_fields_to_sanitize.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -euo pipefail + +# script to get the fields from a FileMetadata JSON that need to be sanitized +# requires that the JSON is saved with 'indent = 4' or similar indentation + +input_file="${1}" + +grep -E 'sampleId|patientId|sampleName|externalSampleId|investigatorSampleId' "${input_file}" | tr -s ' ' | cut -d ':' -f2 | tr -d '"' | tr -d ',' | sed -e 's|^ ||g' | sort -u | awk '{print length($1), $0}' | sort -k 1,1nr | cut -d ' ' -f2- diff --git a/scripts/sanitize.sh b/scripts/sanitize.sh new file mode 100755 index 000000000..c8544b147 --- /dev/null +++ b/scripts/sanitize.sh @@ -0,0 +1,37 @@ +#!/bin/bash +set -euo pipefail + +# script for sanitizing the contents of a file to remove unwanted patterns (such as sample ID's) +# +# requires file "patterns.tsv" +# which should be in the format of: +# +# \t +# +# which can be generated by 1) using the included './get_fields_to_sanitize.sh' script to get the starting fields from the FileMetadata JSON +# 2) copy/paste those values into a new "patterns.tsv" file in this directory (can do this in nano from command line) +# 3) open the "patterns.tsv" in Excel and fill in the new patterns in the adjacent column (can use generate_cmo_id.py to make fake CMO id's quickly) +# 4) do not save the updated "patterns.tsv" file in Excel, but instead highlight & copy both columns, then open "patterns.tsv" in Atom and paste the full contents there, they will come out TSV formatted +# +# USAGE: +# ./sanitize.sh filemetadata.json + +input_file="${1}" +patterns_file="patterns.tsv" + +# make sure patterns file exists +[ ! -e "${patterns_file}" ] && echo "ERROR: file does not exist: ${patterns_file}" && exit 1 + +# make sure 'patterns' file doesnt have less than 1 line +[ "$(cat "${patterns_file}" | wc -l)" -lt "1" ] && echo "ERROR: Not enough lines in patterns file ${patterns_file}" && exit 1 + +# need to clean the 'patterns' file; remove Windows carriage returns, empty lines +perl -pi -e 's|\r\n$|\n|g' "${patterns_file}" +perl -pi -e 's|^[[:space:]]*$||g' "${patterns_file}" + +# create regex pattern for replacement +# need to sort patterns from longest to shortest +patterns_str="$(cat ${patterns_file} | awk '{ print length($1), $0 }' | sort -k1,1nr | cut -d ' ' -f2- | sed -e '/^$/d' -e 's|[[:space:]]|/|g' -e 's|^|s/|g' -e 's|$|/g;|g' | tr '\n' ' ')" + +# do the actual string replacement in the file +perl -pi -e "${patterns_str}" "${input_file}" From 7ec77bc7f0b23cd82eeb700b3085895eda50c3b3 Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Mon, 11 May 2020 17:01:45 -0400 Subject: [PATCH 5/6] add fixtures for 09603_I --- fixtures/requests/09603_I/09603_I.file.json | 522 +++ .../09603_I/09603_I.filemetadata.json | 3182 +++++++++++++++++ 2 files changed, 3704 insertions(+) create mode 100644 fixtures/requests/09603_I/09603_I.file.json create mode 100644 fixtures/requests/09603_I/09603_I.filemetadata.json diff --git a/fixtures/requests/09603_I/09603_I.file.json b/fixtures/requests/09603_I/09603_I.file.json new file mode 100644 index 000000000..33f7d1ebf --- /dev/null +++ b/fixtures/requests/09603_I/09603_I.file.json @@ -0,0 +1,522 @@ +[ + { + "model": "file_system.file", + "pk": "583cc81d-ed20-4360-89c5-1ca39d4c883c", + "fields": { + "created_date": "2020-01-18T17:14:42.344Z", + "modified_date": "2020-03-23T22:04:01.606Z", + "file_name": "ABCDEF22_IGO_Sample8_S145_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0408_AHG2WCBBXY/Project_09603_I/Sample_ABCDEF22_IGO_Sample8/ABCDEF22_IGO_Sample8_S145_R1_001.fastq.gz", + "file_type": 1, + "size": 0, + "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" + } + }, + { + "model": "file_system.file", + "pk": "583cc81d-ed20-4360-89c5-1ca39d4c883c", + "fields": { + "created_date": "2020-01-18T17:14:42.344Z", + "modified_date": "2020-03-23T22:04:01.606Z", + "file_name": "ABCDEF22_IGO_Sample8_S145_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0408_AHG2WCBBXY/Project_09603_I/Sample_ABCDEF22_IGO_Sample8/ABCDEF22_IGO_Sample8_S145_R1_001.fastq.gz", + "file_type": 1, + "size": 0, + "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" + } + }, + { + "model": "file_system.file", + "pk": "bafa1e08-d712-4e80-a84a-9f77ef8b0389", + "fields": { + "created_date": "2020-01-18T17:14:42.363Z", + "modified_date": "2020-03-23T22:04:01.627Z", + "file_name": "ABCDEF22_IGO_Sample8_S145_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0408_AHG2WCBBXY/Project_09603_I/Sample_ABCDEF22_IGO_Sample8/ABCDEF22_IGO_Sample8_S145_R2_001.fastq.gz", + "file_type": 1, + "size": 0, + "file_group": 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scripts/README.md create mode 100644 scripts/example.patterns.tsv diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 000000000..4b60acefb --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,56 @@ +# Helper Scripts + +## Dumping Database Fixtures + +In order to dump JSON copies of database fixtures, you should first have loaded a copy of a production database backup into your Beagle PostgreSQL database instance. + +The included `dump_db_fixtures.py` script can be used to some types of fixtures. See `dump_db_fixtures.py -h` for the most up to date details. + +### Dump Requests + +A request can be dumped with `dump_db_fixtures.py request `. This will output a JSON for the File entries associated with the request, and a JSON for the FileMetadata entries. Use the `--santize` flag to replace personal information in the fixtures (e.g. people's names and email addresses) with fake ones. Currently, `--sanitize` + +Example: + +``` +$ ./dump_db_fixtures.py request 09603_I --sanitize + +$ ls +09603_I.file.json +09603_I.filemetadata.json +``` + +- NOTE: `dump_db_fixtures.py` should be run from your Beagle dev environment since it requires Python 3 + Django. If you installed with the `Makefile` in the `beagle` root directory, from there you can just use `make bash` to load your dev instance environment to run the script with. + +## Sanitize Fixtures + +Fixtures for use in the repo should be further sanitized to remove sample ID's and replace CMO ID's. + +Some easy helper scripts have been included for this purpose. + +Use the script `get_fields_to_sanitize.sh` to print out a list of all recognized CMO ID's and sample ID's in the JSON you generated with `dump_db_fixtures.py` + +``` +$ ./get_fields_to_sanitize.sh 09603_I.filemetadata.json +# a list of id's +``` + +Use the list of ID's that are printed out to create a `patterns.tsv` file in this same directory. This will be used for the `sanitize.sh` script later. The `patterns.tsv` file should be formatted like this: + +``` +old_pattern1 new_pattern1 +old_pattern2 new_pattern2 +``` + +A quick & easy way to do this is to utilize both Excel and a raw text editor (`nano`, Atom, Sublime, etc.). You can copy the terminal output from `get_fields_to_sanitize.sh` into Excel, then in the adjacent column fill in dummy identifiers such as `Sample1`, `Sample2`, etc.. For CMO ID's, you can generate fake ones with the included `generate_cmo_id.py` script. Once you have two columns, simple highlight them in Excel (just the two columns, not the entire sheet) and paste them into `nano`/Atom/Sublime/etc. and they should be entered as tab delimited text which you can save with the filename of `patterns.tsv` + +- TODO: write a script to do this instead + +Once `patterns.tsv` is present, you can run the `sanitize.sh` script on your JSON to replace all the old patterns with new ones. + + +``` +./sanitize.sh 09603_I.filemetadata.json +``` + +For good measure, double check the contents of the JSON to verify that it looks correct before commiting it. The JSON should be moved to the appropriate `fixtures` directory. diff --git a/scripts/example.patterns.tsv b/scripts/example.patterns.tsv new file mode 100644 index 000000000..849f4c1e5 --- /dev/null +++ b/scripts/example.patterns.tsv @@ -0,0 +1,2 @@ +C-ABCDEF-P001-d Sample1 +C-FB3D87 C-47D8BA