Fix build and upgrade to 5.2.0

.github/workflows/kb_sdk_test.yaml

@@ -14,33 +14,20 @@ on:
 jobs:
 
   sdk_tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     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"
+        sh GHA_scripts/make_testdir && echo "Created test_local"
         test -f "test_local/test.cfg" && echo "Confirmed config exists"
 
     - name: Configure authentication
@@ -55,8 +42,12 @@ jobs:
     - 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)
+        sh GHA_scripts/kb-sdk test --verbose
+
+# TODO COVERAGE alter the Makefile to generate coverage info and uncomment
+#    - name: Upload coverage to Codecov
+#      uses: codecov/codecov-action@v3
+#      with:
+#        token: ${{ secrets.CODECOV_TOKEN }}
+#        fail_ci_if_error: true

.gitignore

@@ -1,2 +1,5 @@
 test_local
 sdk.cfg
+/.project
+/.pydevproject
+/.settings/

Dockerfile

@@ -1,35 +1,22 @@
-FROM kbase/sdkbase2:python
+FROM kbase/sdkpython:3.8.10
 MAINTAINER KBase Developer
 # -----------------------------------------
 
 # Insert apt-get instructions here to install
 # any required dependencies for your module.
 
-# RUN apt-get update
-
-
-RUN apt-get update \
-    && apt-get -y install libboost-all-dev \
-    && apt-get -y install wget \
-    && apt-get -y install g++
+RUN apt update && apt install -y  g++ nano tree
 
 RUN python -m pip install --upgrade pip \
-    && pip install psutil \
-    && pip install matplotlib
-
-# DO NOT use install_full - downloads the Silva database, which has a non open source license
-# As a result cannot use MetaQUAST
-# deletes genemark executables, also non open source license
-RUN cd /opt \
-    && wget https://github.com/ablab/quast/releases/download/quast_5.0.2/quast-5.0.2.tar.gz \
-    && tar -xzf quast-5.0.2.tar.gz \
-    && cd quast-5.0.2 \
-    && ./setup.py install \
-    && rm -r quast_libs/genemark\
-    && rm -r quast_libs/genemark-es
-
-RUN apt-get install nano \
-    && apt-get install tree
+    && pip install \
+            psutil==6.0.0 \
+            matplotlib==3.7.5 \
+            quast==5.2.0 \
+            biopython==1.83 \
+    && rm -r /opt/conda3/lib/python3.8/site-packages/quast_libs/genemark \
+    && rm -r /opt/conda3/lib/python3.8/site-packages/quast_libs/genemark-es
+
+# Genemark is not open source for non-academic use, and so can't be used in KBase
 
 # -----------------------------------------
 

GHA_scripts/kb-sdk

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# TODO may want to make the image an env var or argument
+
+# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/kb-sdk for source
+
+# Cache the group for the docker file
+if [ ! -e $HOME/.kbsdk.cache ] ; then
+  docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache
+fi
+
+exec docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 $@

GHA_scripts/make_testdir

@@ -0,0 +1,16 @@
+#!/bin/sh
+
+# TODO may want to make the image an env var or argument
+
+# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/make_testdir for source
+
+# Disable the default `return 1` when creating `test_local`
+set +e
+
+# Cache the group for the docker file
+if [ ! -e $HOME/.kbsdk.cache ] ; then
+  docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache
+fi
+
+exec docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock  -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 test
+exit

RELEASE_NOTES.md

@@ -1,3 +1,8 @@
+### 1.1.0
+
+- Updated base image to `kbase/sdkpython:3.8.10` to fix build
+- Updated QUAST to 5.2.0
+
 ### 1.0.0
 - Version bump to meet release requirements. No other changes.
 

kbase.yml

@@ -11,7 +11,7 @@ service-language:
     python
 
 module-version:
-    1.0.0
+    1.1.0
 
 owners:
     [gaprice]

lib/kb_quast/authclient.py

@@ -0,0 +1,94 @@
+'''
+Created on Aug 1, 2016
+
+A very basic KBase auth client for the Python server.
+
+@author: [email protected]
+'''
+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

lib/kb_quast/kb_quastImpl.py

@@ -53,9 +53,9 @@ class kb_quast:
     # state. A method could easily clobber the state set by another while
     # the latter method is running.
     ######################################### noqa
-    VERSION = "0.0.6"
-    GIT_URL = "https://github.com/kbaseapps/kb_quast.git"
-    GIT_COMMIT_HASH = "8d29af55af662fa41442c0134dd90c45decd8cf4"
+    VERSION = "1.1.0"
+    GIT_URL = "https://github.com/kbaseapps/kb_quast"
+    GIT_COMMIT_HASH = "f6be7c27bbf44a0d65b0250dbdb8079b5df9d7ae"
 
     #BEGIN_CLASS_HEADER
 
@@ -195,13 +195,15 @@ def run_QUAST_app(self, ctx, params):
            QUAST as a Narrative application. workspace_name - the name of the
            workspace where the KBaseReport object will be saved. assemblies -
            the list of assemblies upon which QUAST will be run. force_glimmer
-           - running '--glimmer' option regardless of assembly object size)
-           -> structure: parameter "workspace_name" of String, parameter
-           "assemblies" of list of type "assembly_ref" (An X/Y/Z style
-           reference to a workspace object containing an assembly, either a
-           KBaseGenomes.ContigSet or KBaseGenomeAnnotations.Assembly.),
-           parameter "force_glimmer" of type "boolean" (A boolean - 0 for
-           false, 1 for true. @range (0, 1))
+           - running '--glimmer' option regardless of assembly object size
+           min_contig_length - set the minimum size of contigs to process.
+           Defaults to 500, minimum allowed is 50.) -> structure: parameter
+           "workspace_name" of String, parameter "assemblies" of list of type
+           "assembly_ref" (An X/Y/Z style reference to a workspace object
+           containing an assembly, either a KBaseGenomes.ContigSet or
+           KBaseGenomeAnnotations.Assembly.), parameter "force_glimmer" of
+           type "boolean" (A boolean - 0 for false, 1 for true. @range (0,
+           1)), parameter "min_contig_length" of Long
         :returns: instance of type "QUASTAppOutput" (Output of the
            run_quast_app function. report_name - the name of the
            KBaseReport.Report workspace object. report_ref - the workspace
@@ -256,18 +258,20 @@ def run_QUAST(self, ctx, params):
            be run. -OR- files - the list of FASTA files upon which QUAST will
            be run. Optional arguments: make_handle - create a handle for the
            new shock node for the report. force_glimmer - running '--glimmer'
-           option regardless of file/assembly object size) -> structure:
-           parameter "assemblies" of list of type "assembly_ref" (An X/Y/Z
-           style reference to a workspace object containing an assembly,
-           either a KBaseGenomes.ContigSet or
-           KBaseGenomeAnnotations.Assembly.), parameter "files" of list of
-           type "FASTAFile" (A local FASTA file. path - the path to the FASTA
-           file. label - the label to use for the file in the QUAST output.
-           If missing, the file name will be used.) -> structure: parameter
-           "path" of String, parameter "label" of String, parameter
-           "make_handle" of type "boolean" (A boolean - 0 for false, 1 for
-           true. @range (0, 1)), parameter "force_glimmer" of type "boolean"
-           (A boolean - 0 for false, 1 for true. @range (0, 1))
+           option regardless of file/assembly object size min_contig_length -
+           set the minimum size of contigs to process. Defaults to 500,
+           minimum allowed is 50.) -> structure: parameter "assemblies" of
+           list of type "assembly_ref" (An X/Y/Z style reference to a
+           workspace object containing an assembly, either a
+           KBaseGenomes.ContigSet or KBaseGenomeAnnotations.Assembly.),
+           parameter "files" of list of type "FASTAFile" (A local FASTA file.
+           path - the path to the FASTA file. label - the label to use for
+           the file in the QUAST output. If missing, the file name will be
+           used.) -> structure: parameter "path" of String, parameter "label"
+           of String, parameter "make_handle" of type "boolean" (A boolean -
+           0 for false, 1 for true. @range (0, 1)), parameter "force_glimmer"
+           of type "boolean" (A boolean - 0 for false, 1 for true. @range (0,
+           1)), parameter "min_contig_length" of Long
         :returns: instance of type "QUASTOutput" (Ouput of the run_quast
            function. shock_id - the id of the shock node where the zipped
            QUAST output is stored. handle - the new handle for the shock