Merge pull request #36 from exnehilo7/master

Update version

Author: Tianhao-Gu

.github/workflows/action.yaml

@@ -0,0 +1,67 @@
+# 24-JAN-2025: Disable GitHub test action for now
+
+# name: KBase SDK Tests
+
+# on:
+#   push:
+#     branches:
+#     - master
+#     - main
+#   pull_request:
+#     branches:
+#     - master
+#     - main
+#     - develop
+#   schedule:
+#   # Run quarterly on the 15th
+#     - cron:  '0 0 15 1,4,7,10 *'
+
+# jobs:
+
+#   sdk_tests:
+#     runs-on: ubuntu-latest
+#     steps:
+
+#     - name: Check out GitHub repo
+#       if: "!contains(github.event.head_commit.message, 'skip ci')"
+#       uses: actions/checkout@v2
+
+#     - name: Check out Actions CI files
+#       if: "!contains(github.event.head_commit.message, 'skip ci')"
+#       uses: actions/checkout@v2
+#       with:
+#         repository: 'kbaseapps/kb_sdk_actions'
+#         path: 'kb_sdk_actions'
+
+
+#     - name: Set up test environment
+#       if: "!contains(github.event.head_commit.message, 'skip ci')"
+#       shell: bash
+#       env:
+#         KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+#       run: |
+#         # Verify kb_sdk_actions clone worked
+#         test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned"
+#         # Pull kb-sdk & create startup script
+#         docker pull kbase/kb-sdk
+       
+#         sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local"
+#         test -f "test_local/test.cfg" && echo "Confirmed config exists"
+
+#     - name: Configure authentication
+#       if: "!contains(github.event.head_commit.message, 'skip ci')"
+#       shell: bash
+#       env:
+#         KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+#       run: |
+#         # Add token to config
+#         sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg
+
+#     - name: Run tests
+#       if: "!contains(github.event.head_commit.message, 'skip ci')"
+#       shell: bash
+#       env:
+#         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+#       run: |
+#         sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
+#         bash <(curl -s https://codecov.io/bash)

Dockerfile

@@ -1,5 +1,5 @@
 FROM kbase/kbase:sdkbase2.latest
-MAINTAINER KBase Developer
+LABEL maintainer="KBase Developer"
 # -----------------------------------------
 # In this section, you can install any system dependencies required
 # to run your App.  For instance, you could place an apt-get update or
@@ -13,27 +13,21 @@ MAINTAINER KBase Developer
 
 RUN pip install coverage
 
-# update security libraries in the base image
-RUN pip install cffi --upgrade \
-    && pip install pyopenssl --upgrade \
-    && pip install ndg-httpsclient --upgrade \
-    && pip install pyasn1 --upgrade \
-    && pip install requests --upgrade \
-    && pip install 'requests[security]' --upgrade
-
 # -----------------------------------------
 
+# WORKDIR and Trimmomatic installation should be before COPY kb/module
+WORKDIR /kb/module
+
+# Install Trimmomatic
+RUN curl -L https://github.com/usadellab/Trimmomatic/files/5854859/Trimmomatic-0.39.zip -o Trimmomatic-0.39.zip && \
+    unzip Trimmomatic-0.39.zip
+
 COPY ./ /kb/module
 RUN mkdir -p /kb/module/work
 RUN chmod -R a+rw /kb/module
 
-WORKDIR /kb/module
-
 RUN make all
 
-# Install Trimmomatic
-RUN curl http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip -o Trimmomatic-0.36.zip && \
-    unzip Trimmomatic-0.36.zip
 
 ENTRYPOINT [ "./scripts/entrypoint.sh" ]
 

RELEASE_NOTES.md

@@ -1,3 +1,9 @@
+### Version 1.2.15
+__Changes__
+- replaced AbstractHandle with DataFileUtil
+- updated github curl
+- upgrade to Trimmomatic version 0.39
+
 ### Version 1.2.14
 __Changes__
 - improve docs

kbase.yml

@@ -11,4 +11,4 @@ module-version:
     1.2.15
 
 owners:
-    [psdehal, dylan, wjriehl, umaganapathyswork, tgu2]
+    [psdehal, dylan, wjriehl, umaganapathyswork, tgu2, dan_hopp]

lib/installed_clients/DataFileUtilClient.py

@@ -0,0 +1,94 @@
+'''
+Created on Aug 1, 2016
+
+A very basic KBase auth client for the Python server.
+
+@author: gaprice@lbl.gov
+'''
+import time as _time
+import requests as _requests
+import threading as _threading
+import hashlib
+
+
+class TokenCache(object):
+    ''' A basic cache for tokens. '''
+
+    _MAX_TIME_SEC = 5 * 60  # 5 min
+
+    _lock = _threading.RLock()
+
+    def __init__(self, maxsize=2000):
+        self._cache = {}
+        self._maxsize = maxsize
+        self._halfmax = maxsize / 2  # int division to round down
+
+    def get_user(self, token):
+        token = hashlib.sha256(token.encode('utf-8')).hexdigest()
+        with self._lock:
+            usertime = self._cache.get(token)
+        if not usertime:
+            return None
+
+        user, intime = usertime
+        if _time.time() - intime > self._MAX_TIME_SEC:
+            return None
+        return user
+
+    def add_valid_token(self, token, user):
+        if not token:
+            raise ValueError('Must supply token')
+        if not user:
+            raise ValueError('Must supply user')
+        token = hashlib.sha256(token.encode('utf-8')).hexdigest()
+        with self._lock:
+            self._cache[token] = [user, _time.time()]
+            if len(self._cache) > self._maxsize:
+                sorted_items = sorted(
+                    list(self._cache.items()),
+                    key=(lambda v: v[1][1])
+                )
+                for i, (t, _) in enumerate(sorted_items):
+                    if i <= self._halfmax:
+                        del self._cache[t]
+                    else:
+                        break
+
+
+class KBaseAuth(object):
+    '''
+    A very basic KBase auth client for the Python server.
+    '''
+
+    _LOGIN_URL = 'https://kbase.us/services/auth/api/legacy/KBase/Sessions/Login'
+
+    def __init__(self, auth_url=None):
+        '''
+        Constructor
+        '''
+        self._authurl = auth_url
+        if not self._authurl:
+            self._authurl = self._LOGIN_URL
+        self._cache = TokenCache()
+
+    def get_user(self, token):
+        if not token:
+            raise ValueError('Must supply token')
+        user = self._cache.get_user(token)
+        if user:
+            return user
+
+        d = {'token': token, 'fields': 'user_id'}
+        ret = _requests.post(self._authurl, data=d)
+        if not ret.ok:
+            try:
+                err = ret.json()
+            except Exception as e:
+                ret.raise_for_status()
+            raise ValueError('Error connecting to auth service: {} {}\n{}'
+                             .format(ret.status_code, ret.reason,
+                                     err['error']['message']))
+
+        user = ret.json()['user_id']
+        self._cache.add_valid_token(token, user)
+        return user