I
found your Blast project on GitHub. Furthermore, I was able to get it running with Docker as described below. Unfortunately, it crashed always when I try to upload a FASTA file with this error `
ImproperlyConfigured: Error finding Upload-Folder. Maybe it does not exist?`.
2. `$ cat requirements.txt` in this files the below dependencies had to be updated:
- psycopg2==2.8.6
I have the following Dockerfile:
```
FROM python:2
ENV PYTHONUNBUFFERED=1
RUN apt-get update && apt-get install -y postgresql-client
WORKDIR /code
COPY requirements.txt /code/
RUN pip install -r requirements.txt
COPY . /code/
RUN mkdir -p /var/log/django
RUN mkdir -p /var/log/i5k
```
For `docker-compose.yml` I use:
```
version: "3"
services:
db:
image: postgres
volumes:
- ./data/db:/var/lib/postgresql/data
- ./scripts/install-extensions.sql:/docker-entrypoint-initdb.d/install-extensions.sql
environment:
- POSTGRES_DB=postgres
- POSTGRES_USER=postgres
- POSTGRES_PASSWORD=postgres
web:
build: .
volumes:
- .:/code
ports:
- "8000:8000"
depends_on:
- db
links:
- db
```
```
$ cat scripts/install-extensions.sql
CREATE EXTENSION hstore;
```
I had to change:
```
$ vim i5k/settings.py
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.postgresql_psycopg2',
'NAME': 'postgres',
'USER': 'postgres',
'PASSWORD': 'postgres',
'HOST': 'db',
'PORT': '5432',
}
}
```
```
...
FILEBROWSER_SUIT_TEMPLATE = True
FILEBROWSER_DIRECTORY = ''
FILEBROWSER_VERSIONS_BASEDIR = '_versions/'
FILEBROWSER_MAX_UPLOAD_SIZE = 10737418240 # 10GB
FILEBROWSER_EXTENSIONS = {
'Folder': [''],
#'Image': ['.jpg', '.jpeg', '.gif', '.png', '.tif', '.tiff'],
'Document': ['.pdf', '.doc', '.rtf', '.txt', '.xls', '.csv', '.docx'],
#'Video': ['.mov', '.wmv', '.mpeg', '.mpg', '.avi', '.rm'],
#'Audio': ['.mp3', '.mp4', '.wav', '.aiff', '.midi', '.m4p'],
'FASTA': ['.fa', '.faa', '.fna', '.fasta', '.cds', '.pep'],
'FASTQ': ['.fq', '.fastq'],
'SAM': ['.sam', '.bam'],
'WIG': ['.wig', '.bw', '.bigwig'],
'JSON': ['.json'],
'GFF': ['.gff', '.gff3']
}
FILEBROWSER_SELECT_FORMATS = {
'file': ['Folder', 'Image', 'Document', 'Video', 'Audio', 'FASTA', 'FASTQ', 'SAM', 'WIG', 'JSON', 'GFF'],
#'image': ['Image'],
'document': ['Document'],
#'media': ['Video','Audio'],
'FASTA': ['FASTA'],
'FASTQ': ['FASTQ'],
'SAM': ['SAM'],
'WIG': ['WIG'],
'JSON': ['JSON'],
'GFF': ['GFF'],
}
FILEBROWSER_VERSIONS = {
'admin_thumbnail': {'verbose_name': 'Admin Thumbnail', 'width': 60, 'height': 60, 'opts': 'crop'},
'thumbnail': {'verbose_name': 'Thumbnail (1 col)', 'width': 60, 'height': 60, 'opts': 'crop'},
'small': {'verbose_name': 'Small (2 col)', 'width': 140, 'height': '', 'opts': ''},
'medium': {'verbose_name': 'Medium (4col )', 'width': 300, 'height': '', 'opts': ''},
'big': {'verbose_name': 'Big (6 col)', 'width': 460, 'height': '', 'opts': ''},
'large': {'verbose_name': 'Large (8 col)', 'width': 680, 'height': '', 'opts': ''},
}
...
```
Next, I ran:
- `docker-compose up --build`
- `docker-compose run web python manage.py`
- `docker-compose run web python manage.py migrate`
- `docker-compose run web python manage.py createsuperuser`
```
web_1 | [24/May/2021 18:04:53] "POST /admin/blast/sequencetype/add/?_to_field=id&_popup=1 HTTP/1.1" 200 237
web_1 | [24/May/2021 18:04:58] "GET /admin/blast/blastdb/add/ HTTP/1.1" 200 15281
web_1 | [24/May/2021 18:04:58] "GET /admin/jsi18n/ HTTP/1.1" 200 2372
web_1 | django.request ERROR 2021-05-24 18:05:05,381 10 [Internal Server Error: /admin/filebrowser/browse/]
web_1 | Traceback (most recent call last):
web_1 | File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 132, in get_response
web_1 | response = wrapped_callback(request, *callback_args, **callback_kwargs)
web_1 | File "/usr/local/lib/python2.7/site-packages/django/contrib/auth/decorators.py", line 22, in _wrapped_view
web_1 | return view_func(request, *args, **kwargs)
web_1 | File "/usr/local/lib/python2.7/site-packages/django/views/decorators/cache.py", line 57, in _wrapped_view_func
web_1 | response = view_func(request, *args, **kwargs)
web_1 | File "/code/filebrowser/views.py", line 89, in browse
web_1 | raise ImproperlyConfigured, _("Error finding Upload-Folder. Maybe it does not exist?")
web_1 | ImproperlyConfigured: Error finding Upload-Folder. Maybe it does not exist?
web_1
| [24/May/2021 18:05:05] "GET
/admin/filebrowser/browse/?pop=1&dir=blast/db/&type=FASTA&filter_type=FASTA
HTTP/1.1" 500 101471
```
I tried to create the missing `blast/db` folder in the following way but it still does not work:
```
$ docker-compose exec web /bin/bash
# pwd
/code
# mkdir -p blast/db
# mkdir -p i5k/blast/db
```
Where do I have to create blast/db folder?
Thank you in advance