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\n \n )\n found = True\nexcept ImportError:\n found = False\n \nif found is True:\n import allensdk\n vers = allensdk.__version__\n message = \"AllenSDK is installed. Version: \" + vers\n print(message)\nelse:\n print(\"AllenSDK is NOT installed\")\n

AllenSDK is installed. Version: 0.16.2
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Check If AllenSDK Is Installed (Python3)

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Colab supports both Python 2 and Python 3. This snippet checks if the AllenSDK is installed on Python 3. This will not work on Python 2.

\n
# Python3: Check If AllenSDK Is Installed\nimport importlib.util\nimport pkg_resources\nimport sys\n\n# See https://stackoverflow.com/a/41815890\npackage_name = \"allensdk\"\nspec = importlib.util.find_spec(package_name)\nif spec is None:\n    print(package_name +\" is NOT installed\")\nelse:\n    print(\"%s (version: %s) is installed.\" % (package_name, pkg_resources.get_distribution(\"allensdk\").version))
\n
allensdk is NOT installed
\n

Note that this can return a false result if AllenSDK classes were instantiated followed by a pip uninstall allensdk. In that case this test will still report that allensdk is installed, until the runtime is restarted.

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Note, if this Python3 code is run inside Python2 notebook, then the result will be ImportError: No module named util.

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TODO: Guess this should be enhanced to first check if the user is using the appropriate test version (python2 vs python3). Or maybe even combine both tests into one. That sounds more elegant and foolproof.

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Probe File System for AllenSDK Files

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From the output of the above pip install is seems packages are getting installed in /usr/local/lib/python3.6/dist-packages (or similar for python2) so might be interesting to see what allensdk related stuff shows up after a pip install allensdk. Two items usually show up, allensdk and an allensdk-0.xy.z.dist-info where x,y,z are digit charters corresponding to the version number installed.

\n
# Probe File System for AllenSDK Files\nimport os\nimport platform\nimport site\n\nallensdk_was_found = False\n\nsites = site.getsitepackages()\nfor a_site_dir_name in sites:\n    if os.path.isdir(a_site_dir_name):\n        maybe_allensdk_install_dir = os.path.join(a_site_dir_name, \"allensdk\")\n        if os.path.isdir(maybe_allensdk_install_dir):\n            allensdk_was_found = True\n\n            a_message = \"AllenSDK looks to be installed in:\\n  \" + maybe_allensdk_install_dir + \"\\n\"\n            print(a_message)\n      \n            import allensdk\n            vers = allensdk.__version__\n            vers_message = \"AllenSDK installed version seems to be:\\n  \" + vers + \"\\n\"\n            print(vers_message)\n\n            dist_info_dir_name = \"allensdk-\" + vers + \".dist-info\"\n            full_path_dist_info_dir_name = os.path.join(a_site_dir_name, dist_info_dir_name) \n            another_message = \"AllenSDK dist-info directory name:\\n  \" + full_path_dist_info_dir_name + \"\\n\\nContents of dist-info dir:\"\n            print(another_message)\n            !ls {full_path_dist_info_dir_name}/\nif allensdk_was_found == False:\n    failed_message = \"AllenSDK does not appear to be installed for Python \" + platform.python_version()[0]\n    print(failed_message)
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Test AllenSDK Install Sanity

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This is a trivial sanity checker to confirm that AllenSDK is installed and working within a machine. This can be quite useful on Colab (and the like) where VMs are getting tossed away on a regular, frequent schedule. Just run this cell and if fetched_data is an array with one more elements and there are no errors, one can assume AllenSDK is a happy camper.

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If this next cell throws ModuleNotFoundError that is an indication that AllenSDK is not installed.

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# Perform a simple test query against the Allen Institute public RESTful API\n#\n# TODO: Intentionally defeated cache? or complexing issues, are we here?\n#   Maybe a network test snippet would be good. With random string in the query criteria\n\nfrom allensdk.api.queries.rma_api import RmaApi\n\nrma = RmaApi()\n\nfetched_data = rma.model_query('Atlas', criteria=\"[name$il'*Human*']\")\nif len(fetched_data) > 0:\n  print( \"Length of fetched_data: \", (len(fetched_data)) )\nelse:\n  print( \"WARNING: Zero data records fetched. Probably a failure.\" )
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Length of fetched_data:  6
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