Merge pull request #59 from elixir-cloud-aai/update-alpine

Update filer and taskmaster

Author: jemaltahir

.github/workflows/tox.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3

README.md

@@ -14,11 +14,36 @@ Since the code is meant to be in kubernetes pods, the code needs to be packaged
 Their descriptions can be found in `containers/`.
 The root folder assumed to build the containers is the root of this package.
 
+To build the taskmaster container, run:
+
+```
+docker build . -f containers/taskmaster.Dockerfile -t taskmaster:latest
+```
+
+The command is similar for the filer container:
+
+```
+docker build . -f containers/filer.Dockerfile -t filer:latest
+```
+
 ## Unit testing
 
 Unit testing needs the `tox` package.
+
+You can install the package using `uv`:
+
+```
+uv install tox
+```
+
+To install different python versions using `uv`, you can type:
+
+```
+uv python install 3.10 3.11 3.12
+```
+
 This software will take care of creating virtual environments and installing dependencies in them before running the actual tests and generating the coverage reports.
 
 ```
-$ tox
+$ uv run tox
 ```

containers/filer.Dockerfile

@@ -1,19 +1,19 @@
 # Builder: produce wheels
 
-FROM alpine:3.19 as builder
+FROM alpine:3.23 AS builder
 
 RUN apk add --no-cache python3 py3-pip
 RUN apk add --no-cache git
-RUN python3 -m pip install --upgrade setuptools pip wheel --break-system-packages
+RUN python3 -m pip install --upgrade setuptools pip wheel build --break-system-packages
 
 WORKDIR /app/
 COPY . .
 
-RUN python3 setup.py bdist_wheel
+RUN python3 -m build --wheel && rm -rf dist/*.tar.gz
 
 # Install: copy tesk-core*.whl and install it with dependencies
 
-FROM alpine:3.19
+FROM alpine:3.23
 
 RUN apk add --no-cache python3 py3-pip
 

containers/taskmaster.Dockerfile

@@ -1,19 +1,19 @@
 # Builder: produce wheels
 
-FROM alpine:3.19 as builder
+FROM alpine:3.23 AS builder
 
 RUN apk add --no-cache python3 py3-pip
 RUN apk add --no-cache git
-RUN python3 -m pip install --upgrade setuptools pip wheel --break-system-packages
+RUN python3 -m pip install --upgrade setuptools pip wheel build --break-system-packages
 
 WORKDIR /app/
 COPY . .
 
-RUN python3 setup.py bdist_wheel
+RUN python3 -m build --wheel && rm -rf dist/*.tar.gz
 
 # Install: copy tesk-core*.whl and install it with dependencies
 
-FROM alpine:3.19
+FROM alpine:3.23
 
 RUN apk add --no-cache python3 py3-pip
 

setup.cfg

@@ -1,4 +1,4 @@
 [metadata]
-description-file=README.md
+description_file=README.md
 [aliases]
 test=pytest

setup.py

@@ -8,15 +8,11 @@
 with codecs.open(path.join(HERE, 'README.md'), encoding='utf-8') as f:
     LONG_DESC = f.read()
 
-INSTALL_DEPS = ['kubernetes==9.0.0',
+INSTALL_DEPS = ['kubernetes==35.0.0',
                 'requests>=2.20.0',
 
-                # urllib3 constraint
-                'urllib3>=1.26,<2.0 ; python_version < "3.10"',
-                'urllib3>=2.0,<3.0 ; python_version >= "3.10"',
+                'urllib3>=2.6.0,<3.0 ; python_version >= "3.10"',
 
-                # boto3 constraint
-                'boto3<=1.28 ; python_version == "3.8"',
                 'boto3>=1.28,<2.0 ; python_version >= "3.9"',
                 ]
 TEST_DEPS = [ 'pytest',
@@ -56,10 +52,8 @@
 
         'Intended Audience :: System Administrators',
 
-        'License :: OSI Approved :: Apache Software License',
-
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.7'
+        'Programming Language :: Python :: >=3.10'
     ],
 
     # What does your project relate to?
@@ -74,7 +68,6 @@
             'taskmaster = tesk_core.taskmaster:main'
         ]
     },
-    test_suite='tests',
 
     # List run-time dependencies here.  These will be installed by pip when
     # your project is installed. For an analysis of "install_requires" vs pip's
@@ -84,9 +77,7 @@
 
     setup_requires=['setuptools_scm'],
 
-    tests_require=TEST_DEPS,
-
-    python_requires='>=3.5, <4.0',
+    python_requires='>=3.10, <4.0',
 
     # List additional groups of dependencies here (e.g. development
     # dependencies). You can install these using the following syntax,

src/tesk_core/filer.py

@@ -7,7 +7,6 @@
 import json
 import re
 import os
-import distutils.dir_util
 import logging
 import netrc
 import requests
@@ -112,7 +111,7 @@ def copyFile(src, dst):
     '''
 
     # If there is any * in 'dst', use only the dirname (base path)
-    p = re.compile('.*\*.*')
+    p = re.compile(r'.*\*.*')
     if p.match(dst):
         dst=os.path.dirname(dst)
 
@@ -229,7 +228,8 @@ def download_file(self):
         logging.debug('Downloading ftp file: "%s" Target: %s', self.url,
                       self.path)
         basedir = os.path.dirname(self.path)
-        distutils.dir_util.mkpath(basedir)
+        if basedir and not os.path.exists(basedir):
+            os.makedirs(basedir, exist_ok=True)
 
         return ftp_download_file(self.ftp_connection, self.url_path, self.path)
 

src/tesk_core/filer_s3.py

@@ -4,6 +4,7 @@
 import re
 import botocore
 import boto3
+import mimetypes
 from tesk_core.transput import Transput, Type
 
 class S3Transput(Transput):
@@ -50,10 +51,24 @@ def download_file(self):
         os.makedirs(basedir, exist_ok=True)
         return self.get_s3_file(self.path, self.file_path)
 
+    def get_content_type(self):
+        # Guess content type based on filename; fallback to binary stream
+        mime, encoding = mimetypes.guess_type(self.path)
+        if mime is None:
+            return 'application/octet-stream'
+        elif mime.startswith('text/') or mime in ('application/json', 'application/xml', 'application/javascript'):
+            mime = f'{mime}; charset=utf-8'
+        return mime
+
+
     def upload_file(self):
         logging.debug('Uploading s3 object: "%s" Target: %s', self.path,  self.bucket + "/" + self.file_path)
+        content_type = self.get_content_type()
+        logging.debug('Guessed Content-Type: %s for file: %s', content_type, self.path)
         try:
-            self.bucket_obj.upload_file(Filename=self.path, Key=self.file_path)
+            # Pass ContentType via ExtraArgs so the object is uploaded with the right MIME type
+            self.bucket_obj.upload_file(Filename=self.path, Key=self.file_path,
+                                       ExtraArgs={'ContentType': content_type})
         except (botocore.exceptions.ClientError,  OSError) as err:
             logging.error("File upload failed for '%s'", self.bucket + "/" + self.file_path)
             logging.error(err)
@@ -100,7 +115,8 @@ def download_dir(self):
         for obj in objects["Contents"]:
             file_name = os.path.basename(obj["Key"])
             dir_name = os.path.dirname(obj["Key"])
-            path_to_create = re.sub(r'^' + self.file_path.strip('/').replace('/', '\/') + '', "", dir_name).strip('/')
+            prefix = re.escape(self.file_path.strip('/'))  
+            path_to_create = re.sub(r'^' + prefix, '', dir_name).strip('/')  
             path_to_create = os.path.join(self.path, path_to_create)
             os.makedirs(path_to_create, exist_ok=True)
             if self.get_s3_file(os.path.join(path_to_create, file_name), obj["Key"]):

tests/FilerClassTest.py

@@ -31,15 +31,15 @@ def test_env_vars(self):
 
         pprint(f.spec)
 
-        self.assertEquals(f.getEnv(), [
+        self.assertEqual(f.getEnv(), [
 
             { 'name': 'JSON_INPUT'           , 'value': '{"a": 1}'                      }
            ,{ 'name': 'HOST_BASE_PATH'       , 'value': '/home/tfga/workspace/cwl-tes'  }
            ,{ 'name': 'CONTAINER_BASE_PATH'  , 'value': '/transfer'                     }
             ,{"name": "AWS_CONFIG_FILE", "value": "/aws/config"}
             ,{"name": "AWS_SHARED_CREDENTIALS_FILE", "value": "/aws/credentials"},
         ])
-        self.assertEquals(f.spec['spec']['backoffLimit'], 10)
+        self.assertEqual(f.spec['spec']['backoffLimit'], 10)
 
 
     def test_mounts(self):
@@ -69,15 +69,15 @@ def test_mounts(self):
 
         pprint(f.getVolumeMounts())
 
-        self.assertEquals(f.getVolumeMounts(), [
+        self.assertEqual(f.getVolumeMounts(), [
 
             { "name"        : 'transfer-volume'
             , 'mountPath'   : path.CONTAINER_BASE_PATH,
             },
             {'mountPath': '/aws', 'name': 's3-conf', 'readOnly': True}
         ])
 
-        self.assertEquals(f.getVolumes(), [
+        self.assertEqual(f.getVolumes(), [
 
             { "name"                  : 'transfer-volume'
             , 'persistentVolumeClaim' : { 'claimName' : 'transfer-pvc' }
@@ -112,10 +112,10 @@ def test_mounts_file_disabled(self):
 
         pprint(f.getVolumeMounts())
 
-        self.assertEquals(f.getVolumeMounts()   , [
+        self.assertEqual(f.getVolumeMounts()   , [
             {'mountPath': '/aws', 'name': 's3-conf', 'readOnly': True}
         ])
-        self.assertEquals(f.getVolumes()        , [
+        self.assertEqual(f.getVolumes()        , [
             {
                 "name": "s3-conf",
                 "secret": {
@@ -139,11 +139,10 @@ def test_mounts_file_disabled(self):
     def test_image_pull_policy(self):
 
         f = Filer('name', {'a': 1})
-        self.assertEquals(f.getImagePullPolicy()   , 'IfNotPresent')
+        self.assertEqual(f.getImagePullPolicy()   , 'IfNotPresent')
 
         f = Filer('name', {'a': 1}, pullPolicyAlways = True)
-        self.assertEquals(f.getImagePullPolicy()   , 'Always')
-
+        self.assertEqual(f.getImagePullPolicy()   , 'Always')
 
 
 

tests/TaskMasterTest.py

@@ -10,13 +10,15 @@
 
 
 
-def pvcCreateMock(self):    print '[mock] Creating PVC...'
-def pvcDeleteMock(self):    print '[mock] Deleting PVC...'
+def pvcCreateMock(self):
+    print('[mock] Creating PVC...')
+
+def pvcDeleteMock(self):
+    print('[mock] Deleting PVC...')
+
 
 def jobRunToCompletionMock(job, b, c):
-    
-    print "[mock] Creating job '{}'...".format(job.name)
-    
+    print('[mock] Creating job "{}"...'.format(job.name))
     return 'Complete'
 
 
@@ -31,7 +33,7 @@ def test_defaults(self):
 
         print(args)
 
-        self.assertEquals( args 
+        self.assertEqual( args 
                          , Namespace( debug=False, file=None, filer_version='v0.1.9', json='json', namespace='default', poll_interval=5, state_file='/tmp/.teskstate'
                                     , localKubeConfig=False
                                     , pull_policy_always=False
@@ -47,7 +49,7 @@ def test_localKubeConfig(self):
 
         print(args)
 
-        self.assertEquals( args 
+        self.assertEqual( args 
                          , Namespace( debug=False, file=None, filer_version='v0.1.9', json='json', namespace='default', poll_interval=5, state_file='/tmp/.teskstate'
                                     , localKubeConfig=True 
                                     , pull_policy_always=False
@@ -59,8 +61,8 @@ def test_pullPolicyAlways(self):
 
         parser = newParser()
 
-        self.assertEquals( parser.parse_args(['json'                        ]).pull_policy_always,       False )
-        self.assertEquals( parser.parse_args(['json', '--pull-policy-always']).pull_policy_always,       True  )
+        self.assertEqual( parser.parse_args(['json'                        ]).pull_policy_always,       False )
+        self.assertEqual( parser.parse_args(['json', '--pull-policy-always']).pull_policy_always,       True  )