diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/authentication/group.py | 49 | ||||
| -rw-r--r-- | scripts/authentication/resource.py | 8 | ||||
| -rw-r--r-- | scripts/convert_dol_genotypes.py | 74 |
3 files changed, 110 insertions, 21 deletions
diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py index 76c7fb4f..c8c2caad 100644 --- a/scripts/authentication/group.py +++ b/scripts/authentication/group.py @@ -29,8 +29,10 @@ import argparse import datetime import redis import json +import uuid + +from typing import Dict, Optional, Set -from typing import Dict, List, Optional, Set def create_group_data(users: Dict, target_group: str, members: Optional[str] = None, @@ -39,6 +41,9 @@ def create_group_data(users: Dict, target_group: str, "field", and "value" that can be used in a redis hash as follows: HSET key field value + The "field" return value is a unique-id that is used to + distinguish the groups. + Parameters: - `users`: a list of users for example: @@ -71,26 +76,31 @@ def create_group_data(users: Dict, target_group: str, me@test2.com, me@test3.com" """ + # Emails + _members: Set = set("".join(members.split()).split(",") + if members else []) + _admins: Set = set("".join(admins.split()).split(",") + if admins else []) - _members: List = "".join(members.split()).split(",") if members else [] - _admins: List = "".join(admins.split()).split(",") if admins else [] + # Unique IDs + member_ids: Set = set() + admin_ids: Set = set() - user_ids: Dict = dict() for user_id, user_details in users.items(): _details = json.loads(user_details) - if _details.get("email_address"): - user_ids[_details.get("email_address")] = user_id - print(user_ids) + if _details.get("email_address") in _members: + member_ids.add(user_id) + if _details.get("email_address") in _admins: + admin_ids.add(user_id) + + timestamp: str = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') return {"key": "groups", - "field": target_group, + "field": str(uuid.uuid4()), "value": json.dumps({ - "id": target_group, "name": target_group, - "admins": [user_ids[admin] for admin in _admins - if admin in user_ids], - "members": [user_ids[member] for member in _members - if member in user_ids], - "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + "admins": list(admin_ids), + "members": list(member_ids), + "changed_timestamp": timestamp, })} @@ -124,17 +134,18 @@ if __name__ == "__main__": members=members, admins=admins) - if not REDIS_CONN.hget("groups", data.get("field", "")): - updated_data = json.loads(data["value"]) - updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - data["value"] = json.dumps(updated_data) + if not REDIS_CONN.hget("groups", data.get("field")): + updated_data = json.loads(data["value"]) + timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_data["created_timestamp"] = timestamp + data["value"] = json.dumps(updated_data) created_p = REDIS_CONN.hset(data.get("key", ""), data.get("field", ""), data.get("value", "")) groups = json.loads(REDIS_CONN.hget("groups", - args.group_name)) # type: ignore + data.get("field"))) # type: ignore if created_p: exit(f"\nSuccessfully created the group: '{args.group_name}'\n" f"`HGETALL groups {args.group_name}`: {groups}\n") diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py index 8fcf09d7..4996f34c 100644 --- a/scripts/authentication/resource.py +++ b/scripts/authentication/resource.py @@ -63,12 +63,16 @@ def recover_hash(name: str, file_path: str, set_function) -> bool: if __name__ == "__main__": # Initialising the parser CLI arguments parser = argparse.ArgumentParser() + parser.add_argument("--group-id", + help="Add the group id to all resources") parser.add_argument("--restore", help="Restore from a given backup") parser.add_argument("--enable-backup", action="store_true", help="Create a back up before edits") args = parser.parse_args() + if not args.group_id: + exit("Please specify the group-id!\n") if args.restore: if recover_hash(name="resources", file_path=args.back_up, @@ -92,8 +96,8 @@ if __name__ == "__main__": for resource_id, resource in RESOURCES.items(): _resource = json.loads(resource) # str -> dict conversion - _resource["group_masks"] = {"editors": {"metadata": "edit", - "data": "edit"}} + _resource["group_masks"] = {args.group_id: {"metadata": "edit", + "data": "edit"}} REDIS_CONN.hset("resources", resource_id, json.dumps(_resource)) diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py new file mode 100644 index 00000000..81b3bd6d --- /dev/null +++ b/scripts/convert_dol_genotypes.py @@ -0,0 +1,74 @@ +# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file +# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly + +import os + +geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/" +markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt" +gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno" + +# Iterate through the SNP_Map.txt file to get marker positions +marker_data = {} +with open(markers_file, "r") as markers_fh: + for i, line in enumerate(markers_fh): + if i == 0: + continue + else: + line_items = line.split("\t") + this_marker = {} + this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M" + this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}' + marker_data[line_items[1]] = this_marker + +# Iterate through R/qtl2 format genotype files and pull out the samplelist and genotypes for each marker +sample_names = [] +for filename in os.listdir(geno_dir): + if "gm4qtl2_geno" in filename: + with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh: + for i, line in enumerate(rqtl_geno_fh): + line_items = line.split(",") + if i < 3: + continue + elif not len(sample_names) and i == 3: + sample_names = [item.replace("TLB", "TB") for item in line_items[1:]] + elif i > 3: + marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]] + +# Generate list of marker obs to iterate through when writing to .geno file +marker_list = [] +for key, value in marker_data.items(): + if 'genotypes' in value: + this_marker = { + 'chr': value['chr'], + 'locus': key, + 'pos': value['pos'], + 'genotypes': value['genotypes'] + } + marker_list.append(this_marker) + +def sort_func(e): + """For ensuring that X/Y chromosomes/mitochondria are sorted to the end correctly""" + try: + return float((e['chr']))*1000 + float(e['pos']) + except: + if e['chr'] == "X": + return 20000 + float(e['pos']) + elif e['chr'] == "Y": + return 21000 + float(e['pos']) + elif e['chr'] == "M": + return 22000 + float(e['pos']) + +# Sort markers by chromosome +marker_list.sort(key=sort_func) + +# Write lines to .geno file +with open(gn_geno_path, "w") as gn_geno_fh: + gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names))) + for marker in marker_list: + row_contents = [ + marker['chr'], + marker['locus'], + marker['pos'], + marker['pos'] + ] + marker['genotypes'] + gn_geno_fh.write("\t".join(row_contents) + "\n") |