bob.db.base issueshttps://gitlab.idiap.ch/bob/bob.db.base/-/issues2017-09-30T18:11:14Zhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/3Database upload breaks if the file already exists at destination2017-09-30T18:11:14ZAndré AnjosDatabase upload breaks if the file already exists at destination*Created by: pkorshunov*
if the file for database 'dbname' already exists at /idiap/group/torch5spro/databases/latest, the command:
bob_dbmanage.py dbname upload
will break with an error 'Operation not permitted'. Once the database fi...*Created by: pkorshunov*
if the file for database 'dbname' already exists at /idiap/group/torch5spro/databases/latest, the command:
bob_dbmanage.py dbname upload
will break with an error 'Operation not permitted'. Once the database file is manually deleted from the destination, the command 'bob_dbmanage.py dbname upload' will work correctly.Manuel Günthersiebenkopf@googlemail.comManuel Günthersiebenkopf@googlemail.comhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/5No test for bob.db.base2017-09-30T18:11:14ZAndré AnjosNo test for bob.db.base*Created by: teodorseglitis*
There is no test for bob.db.base*Created by: teodorseglitis*
There is no test for bob.db.basehttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/6Test server momentarily set to http://beatubulatest.lab.idiap.ch2017-09-30T18:11:14ZAndré AnjosTest server momentarily set to http://beatubulatest.lab.idiap.chDue to problems in the Idiap main server:
https://secure.idiap.ch/bugzilla5/show_bug.cgi?id=12681
For coping with this problem, I have re-implemented the test to allow for an external environment variable to be honoured: `DOCSERVER...Due to problems in the Idiap main server:
https://secure.idiap.ch/bugzilla5/show_bug.cgi?id=12681
For coping with this problem, I have re-implemented the test to allow for an external environment variable to be honoured: `DOCSERVER`.
If it exists, it overrides the current internal setting to use https://www.idiap.ch. We need to remove once that bug is permanently solved.Refactoring 2016 and gitlab migration milestoneTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/7Keyword argument client_id for bob.db.base.File2017-09-30T18:11:14ZTiago de Freitas PereiraKeyword argument client_id for bob.db.base.FileHey,
Just a quick question?
Why the keyword parameter `client_id` was removed from `bob.db.base.File`?
Was because of generality?
We had this argument in `bob.db.verification.utils`
Thanks
Hey,
Just a quick question?
Why the keyword parameter `client_id` was removed from `bob.db.base.File`?
Was because of generality?
We had this argument in `bob.db.verification.utils`
Thanks
https://gitlab.idiap.ch/bob/bob.db.base/-/issues/8Please fix the documentation of `Database.uniquify`2017-09-30T18:11:14ZAndré AnjosPlease fix the documentation of `Database.uniquify`It is generating errors such as this through all DB packages:
```text
/local/gitlab-runner/builds/6b02994f/0/bob/bob.db.utfvp/env/lib/python2.7/site-packages/bob/db/utfvp/__init__.py:docstring of bob.db.utfvp.Database.uniquify:4: ERR...It is generating errors such as this through all DB packages:
```text
/local/gitlab-runner/builds/6b02994f/0/bob/bob.db.utfvp/env/lib/python2.7/site-packages/bob/db/utfvp/__init__.py:docstring of bob.db.utfvp.Database.uniquify:4: ERROR: Unexpected indentation.
```Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/9autosummary is messing up with some namespaces2017-09-30T18:11:14ZAmir MOHAMMADIautosummary is messing up with some namespacesAs a consequence @tiago.pereira is ignoring this in all bob.db packages. Example: https://gitlab.idiap.ch/bob/bob.db.lfw/commit/3d206615699614e07165a74d7a19537468a71b93#8df8c367fbb5bd07a2dd35089ba84b609894aa5e_0_1As a consequence @tiago.pereira is ignoring this in all bob.db packages. Example: https://gitlab.idiap.ch/bob/bob.db.lfw/commit/3d206615699614e07165a74d7a19537468a71b93#8df8c367fbb5bd07a2dd35089ba84b609894aa5e_0_1Refactoring 2016 and gitlab migration milestonehttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/10Missing documentation parts (annotations, objects)2017-09-30T18:11:14ZAndré AnjosMissing documentation parts (annotations, objects)After the migration from `bob.db.verification.utils` of some classes, we still miss the documentation bits.
@amohammadi, since you did this work, could you please patch-up the docs as well?After the migration from `bob.db.verification.utils` of some classes, we still miss the documentation bits.
@amohammadi, since you did this work, could you please patch-up the docs as well?Refactoring 2016 and gitlab migration milestoneAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/11Upload and download commands should be generic2017-09-30T18:11:14ZAndré AnjosUpload and download commands should be genericAs of today, only databases with SQLite files can have external metadata that is downloaded from the Idiap server and placed inside the package before getting it into PyPI.
This is method is also useful for packages which may include me...As of today, only databases with SQLite files can have external metadata that is downloaded from the Idiap server and placed inside the package before getting it into PyPI.
This is method is also useful for packages which may include metadata that is too big to add into the git repository.
In this context, it would be useful to remove this (strange) restriction from this package and let packages decide what is metadata they want to have outside of their git repos. (Example: bob.db.cohface and bob.db.hci_tagging).André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/12bob_dbmanage raises an exception if called w/o parameters2017-09-30T18:11:14ZAndré Anjosbob_dbmanage raises an exception if called w/o parametersHere is the output:
```sh
$ ./bin/bob_dbmanage.py
Traceback (most recent call last):
File "./bin/bob_dbmanage.py", line 23, in <module>
sys.exit(bob.db.base.script.dbmanage.main())
File "/Users/andre/Projects/bob/bob.db.b...Here is the output:
```sh
$ ./bin/bob_dbmanage.py
Traceback (most recent call last):
File "./bin/bob_dbmanage.py", line 23, in <module>
sys.exit(bob.db.base.script.dbmanage.main())
File "/Users/andre/Projects/bob/bob.db.base/bob/db/base/script/dbmanage.py", line 26, in main
return args.func(args)
AttributeError: 'Namespace' object has no attribute 'func'
```
A help message or short usage message should be output in this case.https://gitlab.idiap.ch/bob/bob.db.base/-/issues/13The Database interface lacks a constructor2017-09-30T18:11:14ZManuel Günthersiebenkopf@googlemail.comThe Database interface lacks a constructorThe current `Database` interface contains a function `original_file_names`, which accesses the `self.original_directory` and `self.original_extension` parameters: https://gitlab.idiap.ch/bob/bob.db.base/blob/master/bob/db/base/database.p...The current `Database` interface contains a function `original_file_names`, which accesses the `self.original_directory` and `self.original_extension` parameters: https://gitlab.idiap.ch/bob/bob.db.base/blob/master/bob/db/base/database.py#L147.
In the old `bob.db.verification.utils.Database`, these parameters were passes in the constructor, but here, there is no way to set these parameters, as the `Database` class does not have a constructor.
In several derived classes (for example, `bob.db.mobio`: https://gitlab.idiap.ch/bob/bob.db.mobio/blob/master/bob/db/mobio/query.py#L40), these parameters are passed in the constructor, but as the base class does not accept them anymore as parameters, they are **not used at all**, see bob/bob.db.mobio#7
I remember that we have discussed this issue during the database refactoring. I don't remember, what was the outcome of this discussion. Shall the low-level databases be able to retrieve the original data, e.g., using the `original_file_names` function (in which case we need to provide `original_directory` and `original_extension` as parameters to the constructor), or shall we remove this function?May 2017 HackathonAlain KOMATYAlain KOMATYhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/14Create a low-level database creation guide2017-09-30T18:11:14ZAmir MOHAMMADICreate a low-level database creation guideWe have a guide here: https://gitlab.idiap.ch/biometric/software/wikis/database_creation_guide but it is outdated and full of grammar and spelling errors.
Also see !16We have a guide here: https://gitlab.idiap.ch/biometric/software/wikis/database_creation_guide but it is outdated and full of grammar and spelling errors.
Also see !16May 2017 HackathonAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/15Circular dependency on bob.db.atnt2017-09-30T18:11:14ZAmir MOHAMMADICircular dependency on bob.db.atntNightlies are failing because of this: https://gitlab.idiap.ch/bob/bob.nightlies/builds/60096
@andre.anjos please take care of this as soon as possible since we want the python 3.6 wheels.Nightlies are failing because of this: https://gitlab.idiap.ch/bob/bob.nightlies/builds/60096
@andre.anjos please take care of this as soon as possible since we want the python 3.6 wheels.May 2017 HackathonAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/16It seems latest changes to bob.db.base breaks bob.pad.base (at least)2017-09-30T18:11:14ZPavel KORSHUNOVIt seems latest changes to bob.db.base breaks bob.pad.base (at least)See build here:https://gitlab.idiap.ch/bob/bob.pad.base/builds/61260
It is possible that bob.bio.base would be broken too
```
ERROR: test01_database (bob.pad.base.test.test_databases.DummyDatabaseSqlTest)
------------------------...See build here:https://gitlab.idiap.ch/bob/bob.pad.base/builds/61260
It is possible that bob.bio.base would be broken too
```
ERROR: test01_database (bob.pad.base.test.test_databases.DummyDatabaseSqlTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/gitlab-runner/builds/0d638152/0/bob/bob.pad.base/build-prefix/lib/python2.7/site-packages/bob/pad/base/test/test_databases.py", line 48, in test01_database
assert db.original_file_name(file) == "original/directory/test/path.orig"
File "/home/gitlab-runner/builds/0d638152/0/bob/bob.pad.base/build-prefix/lib/python2.7/site-packages/bob/db/base/database.py", line 230, in original_file_name
"The original_directory and/or the original_extension were not specified in the constructor.")
ValueError: The original_directory and/or the original_extension were not specified in the constructor.
```May 2017 HackathonAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/18if (Stable releases dbs <> master branches dbs): raise nightlies exception2018-06-07T07:02:43ZTiago de Freitas Pereiraif (Stable releases dbs <> master branches dbs): raise nightlies exceptionI think some of you noticed that already; I'm just writing that to keep it registered (honestly, I don't know if we need that level control).
Currently, the place where the sqlite files are stored are the same no matter we are in a rele...I think some of you noticed that already; I'm just writing that to keep it registered (honestly, I don't know if we need that level control).
Currently, the place where the sqlite files are stored are the same no matter we are in a release or in the master branch.
The effect of that is, when we are updating something related with protocols in the master branch, our nightlies (that tests the released packages) fails (https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/87786).
What should be the best course of action?
1 - Release a new version of the db package as soon as we have a protocol update?
2 - Create different directories for the **stable** and **development** (and we control this via `bob_db_manage`?
One thing that I don't understand (that may solve the issue).
Why the `db.sql3` is not part of the wheels?? This would solve this issue.https://gitlab.idiap.ch/bob/bob.db.base/-/issues/19bob.db.base depends on bob.io.image without declaring that in the requirement...2017-10-18T16:36:36ZManuel Günthersiebenkopf@googlemail.combob.db.base depends on bob.io.image without declaring that in the requirements.txtWhen creating a database from scratch using `bob_db_manage.py`, I have the problem that `bob.io.image` is required, but it is not declared in the `requirements.txt`.
The reason is as follows:
1. While test cases are usually not part of ...When creating a database from scratch using `bob_db_manage.py`, I have the problem that `bob.io.image` is required, but it is not declared in the `requirements.txt`.
The reason is as follows:
1. While test cases are usually not part of the package, `setup.py` https://gitlab.idiap.ch/bob/bob.db.base/blob/15998f2dab6de6da677125c3eb19c42d61172c52/setup.py#L38 links the test database.
2. While `bob_db_manage.py` parses all databases, it tries to `import` the test database.
3. The test database requires `bob.io.image` to be present: https://gitlab.idiap.ch/bob/bob.db.base/blob/15998f2dab6de6da677125c3eb19c42d61172c52/bob/db/base/tests/sample/models.py#L14
* [ ] Quick fix: move the `import bob.io.image` into the function, where it is actually required.
* [ ] Real fix (includes the quick fix): add `bob.io.image` to the **test** requirementshttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/21The file-based databases should not have an option of original_extension2021-06-24T12:53:33ZAmir MOHAMMADIThe file-based databases should not have an option of original_extension@andre.anjos raised this issue yesterday. Since the discussions we do offline tend to get lost and ignored, I am opening an issue for it here.@andre.anjos raised this issue yesterday. Since the discussions we do offline tend to get lost and ignored, I am opening an issue for it here.Bob 9.0.0https://gitlab.idiap.ch/bob/bob.db.base/-/issues/22Loading data from databases with minimal parameters provided2021-06-24T12:54:01ZAmir MOHAMMADILoading data from databases with minimal parameters providedAs of now it seems that we do not have a single way to load a sample in our databases.
The old db's load like this:
```python
db = Database(original_directory='/some/path')
sample = db.objects()[0]
data = sample.load(db.original_directo...As of now it seems that we do not have a single way to load a sample in our databases.
The old db's load like this:
```python
db = Database(original_directory='/some/path')
sample = db.objects()[0]
data = sample.load(db.original_directory, db.original_extension)
```
The current guide advices this:
```python
db = Database(original_directory='/some/path')
sample = db.objects()[0]
data = sample.load()
```
but this requires changes in all db interfaces because it suggests that each db sample object will carry a reference to `original_directory`.
I suggest we do like this:
```python
db = Database(original_directory='/some/path')
sample = db.objects()[0]
data = db.load(sample)
```
This is similar in how annotations are returned in high-level interfaces and hides away the fact that the database is a file-based one.
It can be easily implemented for all current databases that we have like this:
```python
class bob.db.base.Database:
def load(self, file):
return file.load(self.original_directory, self.original_extension)
```
What do you think?Bob 9.0.0https://gitlab.idiap.ch/bob/bob.db.base/-/issues/23Add bob.db.nist_sre16 package2018-05-08T12:09:42ZSaeed SARFJOOAdd bob.db.nist_sre16 packagePlease create this package in the bob project and give me the owner permission.Please create this package in the bob project and give me the owner permission.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.db.base/-/issues/24bob_dbmanage.py breaks when one of the dbs are broken2018-06-05T16:33:00ZAmir MOHAMMADIbob_dbmanage.py breaks when one of the dbs are brokenHere is what I faced today:
```
Traceback (most recent call last):
File "bin/bob_dbmanage.py", line 85, in <module>
sys.exit(bob.db.base.script.dbmanage.main())
File "src/bob.db.base/bob/db/base/script/dbmanage.py", line 24, in m...Here is what I faced today:
```
Traceback (most recent call last):
File "bin/bob_dbmanage.py", line 85, in <module>
sys.exit(bob.db.base.script.dbmanage.main())
File "src/bob.db.base/bob/db/base/script/dbmanage.py", line 24, in main
formatter_class=RawDescriptionHelpFormatter)
File "src/bob.db.base/bob/db/base/manage.py", line 185, in create_parser
driver.add_commands(subparsers)
File "src/bob.db.swan/bob/db/swan/driver.py", line 153, in add_commands
from .create import create_subparser
File "src/bob.db.swan/bob/db/swan/create.py", line 8, in <module>
from .common import swan_bio_file_metadata
ImportError: cannot import name 'swan_bio_file_metadata'
```
This kind of errors should be handled.https://gitlab.idiap.ch/bob/bob.db.base/-/issues/26Let's talk about Pandas2021-06-24T12:51:47ZTiago de Freitas PereiraLet's talk about PandasHi guys,
I was discussing with @cverzat about how to create a database package for her problem.
The database that she's working with is basically some excel files containing some information (floats, categories, structured data in gener...Hi guys,
I was discussing with @cverzat about how to create a database package for her problem.
The database that she's working with is basically some excel files containing some information (floats, categories, structured data in general).
Pandas is way easier and more convenient to handle this kind of data than to craft database APIs the way we are used to craft.
I'm wondering if it makes sense create a pandas "backend" in `bob.db.base`.
Would be easier to incorporate this kind of data.
what do you think?
ping @andre.anjos