1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
"""Procedures used to work with the various bio-informatics cli
commands"""
import sys
import json
import pickle
import tempfile
import subprocess
from datetime import datetime
from typing import Dict
from typing import List
from typing import Optional
from typing import Tuple
from typing import Union
from typing import Sequence
from uuid import uuid4
from redis.client import Redis # Used only in type hinting
from gn3.random import random_string
from gn3.exceptions import RedisConnectionError
def compose_gemma_cmd(gemma_wrapper_cmd: str = "gemma-wrapper",
gemma_wrapper_kwargs: Optional[Dict] = None,
gemma_kwargs: Optional[Dict] = None,
gemma_args: Optional[List] = None) -> str:
"""Compose a valid GEMMA command given the correct values"""
cmd = f"{gemma_wrapper_cmd} --json"
if gemma_wrapper_kwargs:
cmd += " " # Add extra space between commands
cmd += " ".join(
[f"--{key} {val}" for key, val in gemma_wrapper_kwargs.items()])
cmd += " -- "
if gemma_kwargs:
cmd += " ".join([f"-{key} {val}" for key, val in gemma_kwargs.items()])
if gemma_args:
cmd += " "
cmd += " ".join([f"{arg}" for arg in gemma_args])
return cmd
def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
rqtl_wrapper_kwargs: Dict,
rqtl_wrapper_bool_kwargs: list) -> str:
"""Compose a valid R/qtl command given the correct input"""
# Add kwargs with values
cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join(
[f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
# Add boolean kwargs (kwargs that are either on or off, like --interval)
if rqtl_wrapper_bool_kwargs:
cmd += " "
cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
return cmd
def compose_pcorrs_command_for_selected_traits(
prefix_cmd: Tuple[str, ...], target_traits: Tuple[str, ...]) -> Tuple[
str, ...]:
"""Build command for partial correlations against selected traits."""
return prefix_cmd + ("against-traits", ",".join(target_traits))
def compose_pcorrs_command_for_database(
prefix_cmd: Tuple[str, ...], target_database: str,
criteria: int = 500) -> Tuple[str, ...]:
"""Build command for partial correlations against an entire dataset."""
return prefix_cmd + (
"against-db", f"{target_database}", f"--criteria={criteria}")
def compose_pcorrs_command(
primary_trait: str, control_traits: Tuple[str, ...], method: str,
**kwargs):
"""Compose the command to run partias correlations"""
def __parse_method__(method):
mthd = method.lower().replace("'", "")
if "pearsons" in mthd:
return "pearsons"
if "spearmans" in mthd:
return "spearmans"
raise Exception(f"Invalid method '{method}'")
prefix_cmd = (
f"{sys.executable}", "-m", "scripts.partial_correlations",
primary_trait, ",".join(control_traits), __parse_method__(method))
if (
kwargs.get("target_database") is not None
and kwargs.get("target_traits") is None):
return compose_pcorrs_command_for_database(prefix_cmd, **kwargs)
if (
kwargs.get("target_database") is None
and kwargs.get("target_traits") is not None):
return compose_pcorrs_command_for_selected_traits(prefix_cmd, **kwargs)
raise Exception("Invalid state: I don't know what command to generate!")
def queue_cmd(conn: Redis,
job_queue: str,
cmd: Union[str, Sequence[str]],
email: Optional[str] = None,
env: Optional[dict] = None) -> str:
"""Given a command CMD; (optional) EMAIL; and a redis connection CONN, queue
it in Redis with an initial status of 'queued'. The following status codes
are supported:
queued: Unprocessed; Still in the queue
running: Still running
success: Successful completion
error: Erroneous completion
Returns the name of the specific redis hash for the specific task.
"""
if not conn.ping():
raise RedisConnectionError
unique_id = ("cmd::"
f"{datetime.now().strftime('%Y-%m-%d%H-%M%S-%M%S-')}"
f"{str(uuid4())}")
conn.rpush(job_queue, unique_id)
for key, value in {
"cmd": json.dumps(cmd), "result": "", "status": "queued"}.items():
conn.hset(name=unique_id, key=key, value=value)
if email:
conn.hset(name=unique_id, key="email", value=email)
if env:
conn.hset(name=unique_id, key="env", value=json.dumps(env))
return unique_id
def run_sample_corr_cmd(method, this_trait_data, target_dataset_data):
"Run the sample correlations in an external process, returning the results."
with tempfile.TemporaryDirectory() as tempdir:
traitfile = f"{tempdir}/traitfile_{random_string(10)}"
targetfile = f"{tempdir}/targetdb_{random_string(10)}"
destfile = f"{tempdir}/corrs_{random_string(10)}"
with open(traitfile, "wb") as trtfl:
pickle.dump(this_trait_data, trtfl)
with open(targetfile, "wb") as targfl:
pickle.dump(target_dataset_data, targfl)
subprocess.run(
["python3", "-m", "scripts.sample_correlations", method,
traitfile, targetfile, destfile],
check=True)
with open(destfile, "rb") as dstfl:
correlation_results = pickle.load(dstfl)
return correlation_results
def run_cmd(cmd: str, success_codes: Tuple = (0,), env: str = None) -> Dict:
"""Run CMD and return the CMD's status code and output as a dict"""
parsed_cmd = json.loads(cmd)
parsed_env = (json.loads(env) if env is not None else None)
results = subprocess.run(
parsed_cmd, capture_output=True, shell=isinstance(parsed_cmd, str),
check=False, env=parsed_env)
out = str(results.stdout, 'utf-8')
if results.returncode not in success_codes: # Error!
out = str(results.stderr, 'utf-8')
return {"code": results.returncode, "output": out}
def run_async_cmd(
conn: Redis, job_queue: str, cmd: Union[str, Sequence[str]],
email: Optional[str] = None, env: Optional[dict] = None) -> str:
"""A utility function to call `gn3.commands.queue_cmd` function and run the
worker in the `one-shot` mode."""
cmd_id = queue_cmd(conn, job_queue, cmd, email, env)
subprocess.Popen([f"{sys.executable}", "-m", "sheepdog.worker"]) # pylint: disable=[consider-using-with]
return cmd_id
|
