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
|
#+STARTUP: inlineimages
#+TITLE: GeneNetwork Quality Control Application
** Project Goals
The project seeks to handle the checking of data files for correct syntax and
other errors before allowing the code to be uploaded.
The files are *"tab-separated"* values (TSV) files, and must conform to the
following criteria:
*** Line-Level Checks
- Must be tab-separated
-
*** Cell-Level Checks
- No empty data cells
- no data cells with spurious characters like `eeeee`, `5.555iloveguix`, etc.
- decimal numbers must conform to the following criteria:
- - when checking an average file decimal numbers must contain exactly three places to the right side of the dot.
- - when checking a standard error file decimal numbers must contain six or greater places to the right side of the dot.
- - there must be a number to the left side of the dot (e.g. 0.55555 is allowed but .55555 is not).
- check line endings to make sure they are Unix and not DOS
- check strain headers against a source of truth (see strains.csv)
** Development
For reproducibility, this project is developed using guix.
To launch a guix shell for development, do
#+BEGIN_SRC shell
guix shell --container --network --development --file=guix.scm --share=/some/host/directory=/the/upload/directory
#+END_SRC
which environment that is isolated from the rest of your system.
We share a host directory with the container (that is writeable by the user that
started the web application) to serve as the upload directory for the
application.
*** Run the CLI version
Run the CLI version of the application, with
#+BEGIN_SRC shell
python3 -m scripts.qc --help
#+END_SRC
*** Run the web version
You need to have a running Redis instance, and configure the application to
connect to it.
To run the web-version of the qc app in development mode, you need to set up a
few environment variables
#+BEGIN_SRC shell
export FLASK_APP=wsgi.py
export FLASK_ENV=development
export QCAPP_INSTANCE_PATH=/path/to/directory/with/config.py
#+END_SRC
then you can run the application with
#+BEGIN_SRC shell
flask run
#+END_SRC
*** Checks
Run tests with:
#+BEGIN_SRC shell
pytest
#+END_SRC
To run the linter over the code base, run:
#+BEGIN_SRC shell
pylint *.py tests quality_control qc_app scripts
#+END_SRC
To check for correct type usage in the application, run:
#+BEGIN_SRC shell
mypy --show-error-codes .
#+END_SRC
** Deploying/Installing QC
*** CLI: Docker
Generate the docker image file with
#+BEGIN_SRC shell
guix pack -f docker -S /bin=bin genenetwork-qc
#+END_SRC
That creates the image file with a path such as:
#+BEGIN_EXAMPLE
/gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
#+END_EXAMPLE
You can now load this file into docker withe
#+BEGIN_SRC shell
docker load < /gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
#+END_SRC
and from there, you can run the application as detailed in the
[[#run-cli-version][Running QC: CLI-Version]] section below
*** CLI: Guix
The application can be installed using guix by pointing to the [[./guix.scm][guix.scm]] file as
follows:
#+BEGIN_SRC shell
guix package [-p /path/to/qc/profile] -f guix.scm
#+END_SRC
*** Web-Version
**** TODO Document deployment details for the web version of GeneNetwork QC better
** Running QC
*** Command-Line Version
:PROPERTIES:
:CUSTOM_ID: run-cli-version
:END:
Install the application as shown in the [[Installing QC]] section above.
To run qc against a file, the syntax is:
#+BEGIN_SRC shell
qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>
#+END_SRC
where
- ~<filetype>~ is one of "*average*" or "*standard-error*"
- ~<filepath>~ is either an absolute path to the file, or a path relative to the
current working directory
- if the ~--strainsfile~ option is not provided, it will default to the one in
the root directory of this repository
- the ~--verbose~ option is a flag, defaulting to ~False~ that controls the
display of optional progress messages
To view the usage information for the application, run
#+BEGIN_SRC shell
qc --help
#+END_SRC
*** Web Version
**** TODO Document usage of the web-UI version of the application
*** Docker
Download the docker image file from [[https://git.genenetwork.org/fredmanglis/gnqc_py/releases][the releases page]] of the application and
load it to docker with something like:
#+BEGIN_SRC shell
docker load < genenetwork-qc-0.0.1-1-oxu472i-docker.tar.gz
#+END_SRC
replacing ~genenetwork-qc-0.0.1-1-oxu472i.tar.gz~ with the actual name of the
release you downloaded
Run the application with something like:
#+BEGIN_SRC shell
docker run -v /path/to/qnqc_py/tests/test_data:/data -ti \
genenetwork-qc:latest /bin/qc average /data/average_error_at_end_200MB.tsv
#+END_SRC
replacing ~/path/to/qnqc_py/tests/test_data~ with the path to the folder where
the file you want to check is in, and ~average_error_at_end_200MB.tsv~ with the
name of the file you want to check for errors.
|
