Restrict micromamba version < 2.0 (#201)

* directly download fixed micromamba version

* Update test_service.py

* Update service.py

---------

Co-authored-by: Volodymyr <[email protected]>

nb2workflow/galaxy.py

@@ -6,6 +6,7 @@
 from textwrap import dedent
 import argparse
 import logging
+import requests
 
 import yaml
 import json
@@ -16,7 +17,6 @@
 import nbformat
 from nbconvert.exporters import ScriptExporter
 
-from ensureconda.api import ensureconda
 import subprocess as sp
 
 import bibtexparser as bib
@@ -476,13 +476,25 @@ def _parse_requirements_txt(filepath):
         return reqs_str_list
 
     @staticmethod
-    def _get_micromamba_binary(): 
-        mamba_bin = ensureconda(no_install=False, 
-                                micromamba=True, 
-                                mamba=False, 
-                                conda=False, 
-                                conda_exe=False)
-        return mamba_bin
+    def _get_micromamba_binary():
+        micromamba_dir = os.path.join(
+            os.environ.get('HOME', os.getcwd()),
+            '.local',
+            'bin'
+            )
+        os.makedirs(micromamba_dir, exist_ok=True)
+        mambapath = os.path.join(micromamba_dir, 'micromamba')
+
+        if not os.path.isfile(mambapath):
+            release_url="https://github.com/mamba-org/micromamba-releases/releases/download/1.5.10-0/micromamba-linux-64"
+            res = requests.get(release_url, allow_redirects=True)
+            with open(mambapath, 'wb') as fd:
+                fd.write(res.content)
+
+        if not os.access(mambapath, os.X_OK):
+            os.chmod(mambapath, 0o744)
+
+        return mambapath
 
 def _split_bibfile(filepath):
     # parse bibfile and return only entries (no preamble/comments/strings) as list of strings

nb2workflow/service.py

@@ -26,6 +26,7 @@
 import tempfile
 import nbformat
 import yaml
+import traceback
 
 from io import BytesIO
 from bs4 import BeautifulSoup
@@ -153,7 +154,7 @@ def run(self):
         try:
             self._run()
         except Exception as e:
-            logger.error("run failed unexplicably: %s", repr(e))
+            logger.error("run failed inexplicably: %s\n%s", repr(e), traceback.format_exc())
             app.async_workflows[self.key] = dict(
                 output={}, 
                 exceptions=[serialize_workflow_exception(e)]

setup.py

@@ -69,7 +69,6 @@
             'Jinja2'
         ],
         'galaxy':[
-            'ensureconda',
             'bibtexparser >= 2.0.0b3',
             'pypandoc_binary',
             'black',

tests/test_service.py

@@ -172,5 +172,7 @@ def test_worker_run():
 
     test_worker_thread.join()
 
+    logger.info("output has keys: %s", list(r.json['data']['output']))
+
     open("output.png","wb").write(base64.b64decode(r.json['data']['output']['spectrum_png_content']))
-
+