Fix build, add coverage, ignore google download tests

Google download doesn't seem to work currently.

Also
* Updated service auth client. There's something strange here - the
authclient didn't get updated on a compile, so I did it manually.
* Deleted the unused baseclient in lib
* Just fetched the one jar from `jars` rather than cloning the whole
thing
* Got rid of `six`

.github/workflows/kb_sdk_test.yaml

@@ -52,3 +52,8 @@ jobs:
       shell: bash
       run: |
         sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: true

.gitignore

@@ -1,2 +1,7 @@
 test_local
 sdk.cfg
+/bin/
+/.classpath
+/.project
+/.pydevproject
+*.py.bak-*

Dockerfile

@@ -1,25 +1,19 @@
-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 mkdir -p /opt/lib
+
 RUN apt-get update \
-    && apt-get install -y g++ \
-    && apt-get install libz-dev\
-    && apt-get install nano \
-    && apt-get install tree
+    && apt-get install -y g++ libz-dev wget nano tree
 
-# Debug tools = all below six
-RUN pip install six \
-    && pip install ipython==5.3.0 \
-    && pip install pyftpdlib==1.5.6
+RUN wget -O /opt/lib/FastaValidator-1.0.jar https://github.com/kbase/jars/raw/master/lib/jars/FastaValidator/FastaValidator-1.0.jar
+
+RUN pip install ipython==5.3.0 pyftpdlib==1.5.6
 
-RUN cd /opt \
-    && git clone https://github.com/kbase/jars \
-    && mkdir lib \
-    && cp jars/lib/jars/FastaValidator/FastaValidator-1.0.jar lib
 
 RUN cd /opt \
     && git clone https://github.com/statgen/libStatGen.git \

lib/ReadsUtils/ReadsUtilsImpl.py

@@ -36,9 +36,9 @@ class ReadsUtils:
     # state. A method could easily clobber the state set by another while
     # the latter method is running.
     ######################################### noqa
-    VERSION = "0.3.13"
-    GIT_URL = "https://github.com/Tianhao-Gu/ReadsUtils.git"
-    GIT_COMMIT_HASH = "6882a74364922dbdacea2714f225fa57fd4b3b2f"
+    VERSION = "1.0.0"
+    GIT_URL = "https://github.com/kbaseapps/ReadsUtils.git"
+    GIT_COMMIT_HASH = "e921d1fa303c14bd0298353cdf73087fdeb6f884"
 
     #BEGIN_CLASS_HEADER
 
@@ -97,7 +97,7 @@ def _proc_upload_reads_params(self, params):
         dfu = DataFileUtil(self.callback_url)
         if wsname:
             self.log('Translating workspace name to id')
-            if not isinstance(wsname, six.string_types):
+            if not isinstance(wsname, str):
                 raise ValueError('wsname must be a string')
             wsid = dfu.ws_name_to_id(wsname)
             self.log('translation done')

lib/ReadsUtils/authclient.py

@@ -24,7 +24,7 @@ def __init__(self, maxsize=2000):
         self._halfmax = maxsize / 2  # int division to round down
 
     def get_user(self, token):
-        token = hashlib.sha256(token).hexdigest()
+        token = hashlib.sha256(token.encode('utf-8')).hexdigest()
         with self._lock:
             usertime = self._cache.get(token)
         if not usertime:
@@ -40,12 +40,15 @@ def add_valid_token(self, token, user):
             raise ValueError('Must supply token')
         if not user:
             raise ValueError('Must supply user')
-        token = hashlib.sha256(token).hexdigest()
+        token = hashlib.sha256(token.encode('utf-8')).hexdigest()
         with self._lock:
             self._cache[token] = [user, _time.time()]
             if len(self._cache) > self._maxsize:
-                for i, (t, _) in enumerate(sorted(self._cache.items(),
-                                                  key=lambda (_, v): v[1])):
+                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:
@@ -57,7 +60,7 @@ class KBaseAuth(object):
     A very basic KBase auth client for the Python server.
     '''
 
-    _LOGIN_URL = 'https://kbase.us/services/authorization/Sessions/Login'
+    _LOGIN_URL = 'https://kbase.us/services/auth/api/legacy/KBase/Sessions/Login'
 
     def __init__(self, auth_url=None):
         '''
@@ -80,11 +83,11 @@ def get_user(self, token):
         if not ret.ok:
             try:
                 err = ret.json()
-            except:
+            except Exception as e:
                 ret.raise_for_status()
             raise ValueError('Error connecting to auth service: {} {}\n{}'
                              .format(ret.status_code, ret.reason,
-                                     err['error_msg']))
+                                     err['error']['message']))
 
         user = ret.json()['user_id']
         self._cache.add_valid_token(token, user)