Hello!!
I want to upgrade from v9 to v10 using the documentation. But in the Re-index data section, the commands are not known by the system even so i am in “my-site” directory.
can anybody help ?
Thanks in advance
Hello,
do you have the latest version of invenio-cli?
$ pip show invenio-cli
Name: invenio-cli
Version: 1.0.14
I have the version 1.0.4
You will need to upgrade, see the step Upgrade your invenio-cli, the first step in the upgrade guide.
I did that, but i still have the version 1.0.4
I am not sure what is the command that you have used, I suggest the following:
$ pip uninstall -y invenio-cli
$ pip install invenio-cli
thanks, it’s working.
I got an error when i run pipenv run invenio alembic upgrade
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/bin/invenio", line 8, in <module>
sys.exit(cli())
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask/cli.py", line 357, in decorator
return __ctx.invoke(f, *args, **kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask_alembic/cli/click.py", line 91, in upgrade
base.upgrade(target)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask_alembic/cli/base.py", line 85, in upgrade
get_alembic().upgrade(target)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask_alembic/extension.py", line 327, in upgrade
self.run_migrations(do_upgrade)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask_alembic/extension.py", line 236, in run_migrations
env.run_migrations(**kwargs)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/alembic/runtime/environment.py", line 865, in run_migrations
self.get_context().run_migrations(**kw)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/alembic/runtime/migration.py", line 611, in run_migrations
for step in self._migrations_fn(heads, self):
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/flask_alembic/extension.py", line 325, in do_upgrade
return self.script_directory._upgrade_revs(target, revision)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/alembic/script/base.py", line 439, in _upgrade_revs
return [
File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
self.gen.throw(type, value, traceback)
File "/home/openmrs/.local/share/virtualenvs/invenio-YWY9aZyz/lib/python3.8/site-packages/alembic/script/base.py", line 267, in _catch_revision_errors
raise util.CommandError(err.args[0]) from err
alembic.util.exc.CommandError: Requested revision 41157f1933d6 overlaps with other requested revisions eb9743315a9d
Hello!
Did you try to restore the database at some point?
Can you provide us with the current migrations installed in your system? We can have a look and take it from there. To do so, run the following commands:
List current heads:
invenio alembic heads
then access the database and list all the alembic versions:
psql -U <name_of_your_instance>
<instance_name>=# SELECT * FROM alembic_version;
lastly, paste both results here.
Thank you! 
invenio alembic heads
dbdbc1b19cf2 -> 35c1075e6360 (default) (effective head), Force naming convention.
2da9a03b0833 (2e97565eba72, 862037093962) -> 1ba76da94103 (default, invenio_records_files) (head), Create records files tables.
676dd587542d -> e1146238edd3 (invenio_vocabularies) (head), Create awards table.
862037093962 -> 07fb52561c5c (invenio_records) (head), Alter column from json to jsonb.
bff1f190b9bd (62efc52773d4) -> aaa265b0afa6 (default, invenio_oauthclient) (head), Move UserIdentity to accounts.
dbe499bfda43 -> 04480be1593e (invenio_access) (head), Add ActionSystemRoles.
5b478fe7ef7f -> a3f5a8635cbb (invenio_communities) (head), Remove version table.
12a88921ada2 -> 4e57407b8e4a (default, invenio_oauth2server) (head), Add on delete cascade.
8ae99b034410 -> a29271fd78f8 (invenio_files_rest) (head), Create files object partial unique index.
e655021de0de -> 5d25c1981985 (invenio_oaiserver) (head), Add system_created field.
5cd30a3503c9 -> a14fa442680f (invenio_requests) (effective head), Create tables.
8ed1a438601c, 88d1463de5c0 (de9c14cbb0b2, a14fa442680f) -> 9e0ac518b9df (invenio_rdm_records) (head) (mergepoint), Create records/communities M2M table.
88d1463de5c0 -> a3957490361d (invenio_rdm_records) (head), Remove PIDRelations tables.
62efc52773d4 -> eb9743315a9d (invenio_accounts) (effective head), Add user profile and preferences as JSON fields to the User table.
f615cee99600 -> 999c62899c20 (invenio_pidstore) (head), Create pidstore tables.
c25ef2c50ffa (eb9743315a9d) -> 41157f1933d6 (invenio_userprofiles) (head), Remove table.
and
SELECT * FROM alembic_version
version_num
--------------
1ba76da94103
9e0ac518b9df
a3957490361d
4e57407b8e4a
a29271fd78f8
e655021de0de
04480be1593e
999c62899c20
07fb52561c5c
a3f5a8635cbb
aaa265b0afa6
eb9743315a9d
41157f1933d6
e1146238edd3
I fear your database migrations are currently in an inconsistent state. I have run the migration from a fresh instance and I got the following versions in the database:
1ba76da94103
9e0ac518b9df
a3957490361d
4e57407b8e4a
a29271fd78f8
04480be1593e
999c62899c20
07fb52561c5c
a3f5a8635cbb
aaa265b0afa6
41157f1933d6
e1146238edd3
5d25c1981985
As you can see, I do not have the following migrations:
e655021de0de
eb9743315a9d
And you do not have the following:
5d25c1981985
EDIT: it seems that the migration e655021de0de did not upgrade to 5d25c1981985. They are from invenio-oaiserver (see code) Thus, the difference.
Did you try to restore the database to an older version at some point? If so, it might have caused the issue.
Is your data safe to be wiped? If so, you can simply wipe it and run an upgrade again. To do so:
invenio db drop
invenio alembic upgrade
If the data is not meant to be wiped (e.g. production data), please let me know and we can try to fix the migrations using alembic solely.
It is a development environment. I followed your instructions and everything is fine now. Thanks you
1 Like