chore(superset): bump superset version to 2.* by luabida · Pull Request #195 · thegraphnetwork/EpiGraphHub

luabida · 2023-08-23T20:46:48Z

No description provided.

luabida · 2023-08-23T20:47:10Z

2023-08-23 20:47:18,936:WARNING:superset.db_engine_specs:Unable to load dialect <class 'sqlalchemy.dialects.mssql.pyodbc.MSDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
Unable to load dialect <class 'sqlalchemy.dialects.mssql.pyodbc.MSDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
2023-08-23 20:47:18,937:WARNING:superset.db_engine_specs:Unable to load dialect <class 'sqlalchemy.dialects.mssql.pyodbc.MSDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
Unable to load dialect <class 'sqlalchemy.dialects.mysql.pyodbc.MySQLDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
2023-08-23 20:47:18,940:WARNING:superset.db_engine_specs:Unable to load dialect <class 'sqlalchemy.dialects.mysql.pyodbc.MySQLDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
Unable to load dialect <class 'sqlalchemy.dialects.sybase.pyodbc.SybaseDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
2023-08-23 20:47:18,944:WARNING:superset.db_engine_specs:Unable to load dialect <class 'sqlalchemy.dialects.sybase.pyodbc.SybaseDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
Unable to load dialect <class 'sqlalchemy.dialects.sybase.pyodbc.SybaseDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
2023-08-23 20:47:18,944:WARNING:superset.db_engine_specs:Unable to load dialect <class 'sqlalchemy.dialects.sybase.pyodbc.SybaseDialect_pyodbc'>: libodbc.so.2: cannot open shared object file: No such file or directory
Unable to load SQLAlchemy dialect <class 'sqlalchemy.dialects.postgresql.psycopg2.PGDialect_psycopg2'>: The 'enum34' distribution was not found and is required by the application
2023-08-23 20:47:19,032:WARNING:superset.db_engine_specs:Unable to load SQLAlchemy dialect <class 'sqlalchemy.dialects.postgresql.psycopg2.PGDialect_psycopg2'>: The 'enum34' distribution was not found and is required by the application
Unable to load SQLAlchemy dialect <class 'shillelagh.backends.apsw.dialects.safe.APSWSafeDialect'>: libodbc.so.2: cannot open shared object file: No such file or directory
2023-08-23 20:47:19,040:WARNING:superset.db_engine_specs:Unable to load SQLAlchemy dialect <class 'shillelagh.backends.apsw.dialects.safe.APSWSafeDialect'>: libodbc.so.2: cannot open shared object file: No such file or directory

fixed libodbc.so.2: cannot open shared object file

http://0.0.0.0:8088/superset/welcome/:

2023-08-23 20:58:05,121:WARNING:superset.views.base:HTTPException
Traceback (most recent call last):
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask/app.py", line 1517, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask/app.py", line 1503, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask/scaffold.py", line 322, in send_static_file
    return send_from_directory(
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask/helpers.py", line 676, in send_from_directory
    return werkzeug.utils.send_from_directory(  # type: ignore
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/werkzeug/utils.py", line 586, in send_from_directory
    raise NotFound()
werkzeug.exceptions.NotFound: 404 Not Found: The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.
2023-08-23 20:58:05,123:INFO:werkzeug:172.21.0.1 - - [23/Aug/2023 20:58:05] "GET /static/appbuilder/css/font-awesome.min.css HTTP/1.1" 404 -

luabida · 2023-08-23T21:05:52Z

+DB_PASS = os.getenv("POSTGRES_PASSWORD")
+DB_DATABASE = os.getenv("POSTGRES_DB")
+SQLALCHEMY_DATABASE_URI = (
+    f"postgresql://{DB_HOST}:{DB_PASS}@{DB_HOST}:{DB_PORT}/{DB_DATABASE}"


is there any problem of using the postgres container database to store superset core data?

i don't think so

xmnlab

I would keep the superset dep from conda-forge, instead of the pypi, if possible.
normally the package from pypi is always bugged and we need to fix it on conda-forge.

xmnlab · 2023-08-23T22:10:23Z

  - jsonschema<5,>=3
-  # dependencies from superset 1.5.*
+  # dependencies from superset 2.*
  - cryptography<39.0.0


Suggested change

- cryptography<39.0.0

xmnlab · 2023-08-23T22:14:03Z

    - markupsafe==2.0.1
    - 'six>=1.16'
-    - 'apache-superset>=1.5.0,<2.0.0'
+    - 'apache-superset>=2.0.0,<3.0.0'


Suggested change

- 'apache-superset>=2.0.0,<3.0.0'

xmnlab · 2023-08-23T22:14:21Z

+    - enum34
    - packaging
    - webencodings
    - 'msgpack<1.1,>=1.0.0'


Suggested change

- 'msgpack<1.1,>=1.0.0'

xmnlab · 2023-08-23T22:14:40Z

    - packaging
    - webencodings
    - 'msgpack<1.1,>=1.0.0'
    - markupsafe==2.0.1


Suggested change

- markupsafe==2.0.1

xmnlab · 2023-08-23T22:14:55Z

-    - 'apache-superset>=1.5.0,<2.0.0'
+    - 'apache-superset>=2.0.0,<3.0.0'
+    # https://github.com/apache/superset/issues/23742
+    - 'sqlparse==0.4.3'


Suggested change

- 'sqlparse==0.4.3'

xmnlab · 2023-08-23T22:15:14Z

+    - 'apache-superset>=2.0.0,<3.0.0'
+    # https://github.com/apache/superset/issues/23742
+    - 'sqlparse==0.4.3'
+    - marshmallow-enum


Suggested change

- marshmallow-enum

xmnlab · 2023-08-23T22:15:35Z

    - webencodings
    - 'msgpack<1.1,>=1.0.0'
    - markupsafe==2.0.1
    - 'six>=1.16'


Suggested change

- 'six>=1.16'

xmnlab · 2023-08-23T22:15:54Z

+    - enum34
    - packaging
    - webencodings
    - 'msgpack<1.1,>=1.0.0'


Suggested change

- 'msgpack<1.1,>=1.0.0'

xmnlab · 2023-08-23T22:16:51Z

  - sqlalchemy
  - jsonschema<5,>=3
-  # dependencies from superset 1.5.*
+  # dependencies from superset 2.*


Suggested change

# dependencies from superset 2.*

# dependencies from superset 2.*

- superset 2.1.0

xmnlab · 2023-08-23T22:17:55Z


 set -ex

-# superset


are you planning to move the core data from sqlite to postgresql?

According to this issue, superset is dropping support for SQLite apache/superset#9748

Got it. Thanks for the explanation

…ibilities

luabida · 2023-08-24T13:01:38Z

ERROR w/ Flask-SQLAlchemy >= 3.0:

Traceback (most recent call last):
  File "/opt/conda/envs/epigraphhub/bin/superset", line 6, in <module>
    from superset.cli.main import superset
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/__init__.py", line 21, in <module>
    from superset.app import create_app
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/app.py", line 23, in <module>
    from superset.initialization import SupersetAppInitializer
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/initialization/__init__.py", line 27, in <module>
    from flask_appbuilder import expose, IndexView
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_appbuilder/__init__.py", line 5, in <module>
    from .api import ModelRestApi  # noqa: F401
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_appbuilder/api/__init__.py", line 23, in <module>
    from flask_appbuilder.models.sqla import Model
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_appbuilder/models/sqla/__init__.py", line 5, in <module>
    from flask_sqlalchemy import (
ImportError: cannot import name '_QueryProperty' from 'flask_sqlalchemy' (/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_sqlalchemy/__init__.py)

ERROR w/ sqlalchemy >= 2.0

Traceback (most recent call last):
  File "/opt/conda/envs/epigraphhub/bin/superset", line 6, in <module>
    from superset.cli.main import superset
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/__init__.py", line 21, in <module>
    from superset.app import create_app
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/app.py", line 23, in <module>
    from superset.initialization import SupersetAppInitializer
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/initialization/__init__.py", line 33, in <module>
    from superset.extensions import (
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/superset/extensions/__init__.py", line 119, in <module>
    db = SQLA()
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_sqlalchemy/__init__.py", line 758, in __init__
    _include_sqlalchemy(self, query_class)
  File "/opt/conda/envs/epigraphhub/lib/python3.9/site-packages/flask_sqlalchemy/__init__.py", line 112, in _include_sqlalchemy
    for key in module.__all__:
AttributeError: module 'sqlalchemy' has no attribute '__all__'

Fixed by pinning deps

xmnlab

LGTM! thanks @luabida

chore(superset): bump superset version to 2.*

7392ad8

luabida commented Aug 23, 2023

View reviewed changes

fix superset docker non-root config

1fef79f

xmnlab reviewed Aug 23, 2023

View reviewed changes

Implement requested changes and fixing sqlalchemy dependency incompat…

f4a521a

…ibilities

luabida added 2 commits August 25, 2023 10:21

Fixing static files

17d4b1d

Including driver path to selenium test

f7b01ef

luabida force-pushed the superset-update branch from 3283d81 to 068758b Compare August 25, 2023 16:38

Add script to download google chrome on ci

f18f4b8

luabida force-pushed the superset-update branch 4 times, most recently from 1bb5d75 to 82034e0 Compare August 25, 2023 19:56

include webdriver on PATH

4b222f1

luabida force-pushed the superset-update branch from 82034e0 to 4b222f1 Compare August 25, 2023 20:19

try to fix chrome webdriver crash on CI

9bcb602

luabida force-pushed the superset-update branch from c68e528 to da1e812 Compare August 25, 2023 21:54

Trying downloading latest webdriver from source

f766981

luabida force-pushed the superset-update branch from da1e812 to f766981 Compare August 25, 2023 22:37

Try pinning selenium package

fb9b959

luabida marked this pull request as ready for review August 28, 2023 12:02

luabida requested a review from xmnlab August 28, 2023 12:21

xmnlab approved these changes Aug 28, 2023

View reviewed changes

xmnlab merged commit 76cd35c into thegraphnetwork:main Aug 28, 2023

	# dependencies from superset 2.*
	# dependencies from superset 2.*
	- superset 2.1.0

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luabida commented Aug 23, 2023

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luabida commented Aug 24, 2023

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luabida commented Aug 23, 2023 •

edited

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