instance_id stringlengths 10 57 | file_changes listlengths 1 15 | repo stringlengths 7 53 | base_commit stringlengths 40 40 | problem_statement stringlengths 11 52.5k | patch stringlengths 251 7.06M |
|---|---|---|---|---|---|
ReactiveX__RxPY-537 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rx/__init__.py:hot"
],
"edited_modules": [
"rx/__init__.py:hot"
]
},
"file": "rx/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modul... | ReactiveX/RxPY | f2642a87e6b4d5b3dc9a482323716cf15a6ef570 | zip operator should complete if a single upstream source completes
The following observable `y` ...
``` python
import rx
from rx import operators as rxop
y = rx.range(2).pipe(
rxop.zip(rx.defer(lambda _: y)),
rxop.merge(rx.just(0)),
rxop.share(),
)
y.subscribe(print, on_completed=lambda: prin... | diff --git a/rx/__init__.py b/rx/__init__.py
index b995f2b2..ce18e050 100644
--- a/rx/__init__.py
+++ b/rx/__init__.py
@@ -6,7 +6,6 @@ from typing import Iterable, Callable, Any, Optional, Union, Mapping
from .core import Observable, pipe, typing
from .internal.utils import alias
-
# Please make sure the version h... |
ReactiveX__RxPY-567 | [
{
"changes": {
"added_entities": [
"rx/scheduler/eventloop/asynciothreadsafescheduler.py:AsyncIOThreadSafeScheduler._on_self_loop_or_not_running"
],
"added_modules": null,
"edited_entities": [
"rx/scheduler/eventloop/asynciothreadsafescheduler.py:AsyncIOThreadSafeSchedule... | ReactiveX/RxPY | 1bd44fe68183dcaad1c2a243c2fc4a255e986fbd | Deadlock in AsyncIOThreadSafeScheduler
Fallowing code produces deadlock:
```python
import rx
import rx.operators as ops
from rx.subject.subject import Subject
from rx.scheduler.eventloop import AsyncIOThreadSafeScheduler
import asyncio
import logging
def print_threads_traces(_):
import traceback
p... | diff --git a/rx/scheduler/eventloop/asynciothreadsafescheduler.py b/rx/scheduler/eventloop/asynciothreadsafescheduler.py
index 52f6e30d..79880d41 100644
--- a/rx/scheduler/eventloop/asynciothreadsafescheduler.py
+++ b/rx/scheduler/eventloop/asynciothreadsafescheduler.py
@@ -50,6 +50,10 @@ class AsyncIOThreadSafeSchedul... |
RedHatInsights__insights-core-4219 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"insights/combiners/lspci.py:LsPci.__init__"
],
"edited_modules": [
"insights/combiners/lspci.py:LsPci"
]
},
"file": "insights/combiners/lspci.py"
}
] | RedHatInsights/insights-core | fc8b6397611e78363f264892ac2ed7eb01c7e6be | Lspci combiner missing data
There is a problem in the Lspci combiner that causes it to not include data from `lspci -k`. The following data when parsed will not include all of the `lspci -k` results:
The `lspci -k` data:
```
pcilib: Error reading /sys/bus/pci/devices/0000:00:0c.0/label: Operation not permitted
... | diff --git a/insights/combiners/lspci.py b/insights/combiners/lspci.py
index 42d28acc..6dc9bb33 100644
--- a/insights/combiners/lspci.py
+++ b/insights/combiners/lspci.py
@@ -122,8 +122,8 @@ class LsPci(list):
if lspci_vmmkn:
for dev in lspci_vmmkn:
# use the local copy to prevent... |
RedHatQE__wait_for-19 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"wait_for/__init__.py:wait_for"
],
"edited_modules": [
"wait_for/__init__.py:wait_for"
]
},
"file": "wait_for/__init__.py"
}
] | RedHatQE/wait_for | e027318cd4202c5288246e12e591a86e3296115f | TODO: Convert logging to use standard string formats (%) | diff --git a/wait_for/__init__.py b/wait_for/__init__.py
index d8d2430..2ad0cd7 100644
--- a/wait_for/__init__.py
+++ b/wait_for/__init__.py
@@ -172,24 +172,26 @@ def wait_for(func, func_args=[], func_kwargs={}, logger=None, **kwargs):
tries = 0
out = None
if not very_quiet:
- logger.debug("Starte... |
Refty__mongo-thingy-40 | [
{
"changes": {
"added_entities": [
"mongo_thingy/cursor.py:Cursor.delete",
"mongo_thingy/cursor.py:AsyncCursor.delete"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mongo_thingy/cursor.py:Cursor",
"mongo_thingy/cursor.py:Asy... | Refty/mongo-thingy | 23231d9c34d9425e02b97de78787f466538d42c9 | Implement Cursor.delete()
So that we can remove a bunch of documents that exist from a cursor.
This is useful when we want to reuse a cursor rather than writing a new `remove` query.
For example:
```python
class Foo(Thingy):
def get_bars(self):
return Bar.find({"foo_id": self.id})
def del... | diff --git a/mongo_thingy/cursor.py b/mongo_thingy/cursor.py
index 9539b7f..9636fa9 100644
--- a/mongo_thingy/cursor.py
+++ b/mongo_thingy/cursor.py
@@ -94,6 +94,10 @@ class Cursor(BaseCursor):
document = self.delegate.__getitem__(index)
return self.bind(document)
+ def delete(self):
+ ids... |
RemDelaporteMathurin__FESTIM-555 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"festim/exports/txt_export.py:TXTExport.__init__",
"festim/exports/txt_export.py:TXTExport.is_it_time_to_export",
"festim/exports/txt_export.py:TXTExport.when_is_next_time",
"fest... | RemDelaporteMathurin/FESTIM | 53308f59851b79ba8404d06982cfbe911f5f8d5d | TXT exports don't work in steady state
Related to #509
Users should be able to export the txt fields in 1D for a steady state simulation
| diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index 1bfdf5a0..52a69995 100644
--- a/festim/exports/txt_export.py
+++ b/festim/exports/txt_export.py
@@ -13,19 +13,25 @@ class TXTExport(festim.Export):
Args:
field (str): the exported field ("solute", "1", "retention",
... |
RemDelaporteMathurin__FESTIM-567 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"festim/exports/derived_quantities/derived_quantities.py:DerivedQuantities.is_export"
],
"edited_modules": [
"festim/exports/derived_quantities/derived_quantities.py:DerivedQuantities... | RemDelaporteMathurin/FESTIM | 6716ec58753e16c7f8b10610ea1a4d51788cc6ba | [BUG] DerivedQuantities not exported at final timestep
**Describe the bug**
Derived quantities are not exported at final timestep
**To Reproduce**
Run this with latest FESTIM version:
```python
import numpy as np
import festim as F
my_model = F.Simulation()
my_model.mesh = F.MeshFromVertices(np.linspa... | diff --git a/festim/exports/derived_quantities/derived_quantities.py b/festim/exports/derived_quantities/derived_quantities.py
index 7b67d606..a7798c6e 100644
--- a/festim/exports/derived_quantities/derived_quantities.py
+++ b/festim/exports/derived_quantities/derived_quantities.py
@@ -123,7 +123,7 @@ class DerivedQuan... |
RemDelaporteMathurin__h-transport-materials-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/property.py:ArrheniusProperty.data_T",
"h_transport_materials/property.py:ArrheniusProperty.data_y",
"h_transport_materials/property.py:ArrheniusProperty.fit"
... | RemDelaporteMathurin/h-transport-materials | b4870b7fc221e6912dcfcb4a0019858628ea2479 | Pint for temperature range and data_T data_y | diff --git a/h_transport_materials/property.py b/h_transport_materials/property.py
index d33a6f3..0f16ab4 100644
--- a/h_transport_materials/property.py
+++ b/h_transport_materials/property.py
@@ -236,6 +236,11 @@ class ArrheniusProperty(Property):
if value is None:
self._data_T = value
... |
RemDelaporteMathurin__h-transport-materials-118 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/plotting.py:plot"
],
"edited_modules": [
"h_transport_materials/plotting.py:plot"
]
},
"file": "h_transport_materials/plotting.py"
},
{
"c... | RemDelaporteMathurin/h-transport-materials | 387c90817433e6f4fa5829f3bba0efa5b59f3169 | .value() method should work with units
Users should be able to do:
```python
import h_transport_materials as htm
ureg = htm.ureg
T = ureg.Quantity(900, ureg.K)
D = htm.Diffusivity(1 * ureg.m**2 * ureg.s**-1, 0.1 * ureg.eV)
value = D.value(T)
value.to(ureg.mm**2 * ureg.s**-1)
```
- .value() should... | diff --git a/h_transport_materials/plotting.py b/h_transport_materials/plotting.py
index 3c904ac..35cb638 100644
--- a/h_transport_materials/plotting.py
+++ b/h_transport_materials/plotting.py
@@ -1,7 +1,8 @@
import matplotlib.pyplot as plt
import numpy as np
from numpy.typing import ArrayLike
-from h_transport_mate... |
RemDelaporteMathurin__h-transport-materials-121 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/properties_group.py:PropertiesGroup.filter"
],
"edited_modules": [
"h_transport_materials/properties_group.py:PropertiesGroup"
]
},
"file": "h_tra... | RemDelaporteMathurin/h-transport-materials | fdb8f77447762bb38161f86352c0e7d0684ba803 | Users should be told when filtered group is None | diff --git a/h_transport_materials/properties_group.py b/h_transport_materials/properties_group.py
index 2de20fb..9ecec3d 100644
--- a/h_transport_materials/properties_group.py
+++ b/h_transport_materials/properties_group.py
@@ -2,6 +2,7 @@ import numpy as np
import json
from pybtex.database import BibliographyData
... |
RemDelaporteMathurin__h-transport-materials-169 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/properties_group.py:PropertiesGroup.mean"
],
"edited_modules": [
"h_transport_materials/properties_group.py:PropertiesGroup"
]
},
"file": "h_trans... | RemDelaporteMathurin/h-transport-materials | 1ccf5a11ffbb6a013c50540c1b20cde2ee5302e5 | PropertiesGroup.mean should have units
```python
import h_transport_materials as htm
print(htm.diffusivities.mean().units)
```
Prints
```
dimensionless
``` | diff --git a/h_transport_materials/properties_group.py b/h_transport_materials/properties_group.py
index ccc4b5f..1099a1b 100644
--- a/h_transport_materials/properties_group.py
+++ b/h_transport_materials/properties_group.py
@@ -92,9 +92,15 @@ class PropertiesGroup(list):
default_range (tuple, optional): t... |
RemDelaporteMathurin__h-transport-materials-190 | [
{
"changes": {
"added_entities": [
"h_transport_materials/material.py:Material.__hash__",
"h_transport_materials/material.py:PureMetal.__hash__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"h_transport_materials/material.py:Materia... | RemDelaporteMathurin/h-transport-materials | aaaac2b47fbc86ac80fd5fc969618404cd8fb24a | PropertiesGroup plot add a colour_by argument
Users should be able to colour by properties (default), materials, isotopes, authors with a `colour_by` argument.
Additionally, say users pass a colour_by argument, they should be able to pass a `colours` dict.
For example:
```python
import h_transport_materials a... | diff --git a/docs/user/plotting.rst b/docs/user/plotting.rst
index c94eb73..dbc4fa6 100644
--- a/docs/user/plotting.rst
+++ b/docs/user/plotting.rst
@@ -171,6 +171,24 @@ Calculate the mean value and plot it too:
plt.yscale("log")
plt.show()
+The properties can be coloured according to different attributes lik... |
RemDelaporteMathurin__h-transport-materials-224 | [
{
"changes": {
"added_entities": [
"h_transport_materials/property.py:ArrheniusProperty.__mul__",
"h_transport_materials/property.py:ArrheniusProperty.__rmul__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"h_transport_materials/pro... | RemDelaporteMathurin/h-transport-materials | 487452db12b4d4efc02cdac4a50799f1ef7e25d2 | Operations between ArrheniusProperty objects
Users should be able to multiply, divide ArrheniusProperty objects
```python
diff = Diffusivity(...)
solubility = Solubility(...)
permeability = diff * solubility
``` | diff --git a/h_transport_materials/property.py b/h_transport_materials/property.py
index aac6200..566854d 100644
--- a/h_transport_materials/property.py
+++ b/h_transport_materials/property.py
@@ -205,6 +205,43 @@ class ArrheniusProperty(Property):
"""
return val
+ def __mul__(self, other):
+ ... |
RemDelaporteMathurin__h-transport-materials-249 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/properties_group.py:PropertiesGroup.mean"
],
"edited_modules": [
"h_transport_materials/properties_group.py:PropertiesGroup"
]
},
"file": "h_trans... | RemDelaporteMathurin/h-transport-materials | bfc9ed605514d9fce7b1faae4744553c9ab5fb6c | Inf pre-exponential factor on mean permeabilities
On HTM 0.13.1:
```python
import h_transport_materials as htm
perm = htm.permeabilities.filter(material="steel").mean()
print(perm)
```
```
C:\Users\remidm\AppData\Roaming\Python\Python311\site-packages\numpy\core\_methods.py:53: RuntimeWarning: overflow... | diff --git a/h_transport_materials/properties_group.py b/h_transport_materials/properties_group.py
index 60ba476..590fe85 100644
--- a/h_transport_materials/properties_group.py
+++ b/h_transport_materials/properties_group.py
@@ -94,7 +94,11 @@ class PropertiesGroup(list):
# geometric mean of pre-exponential ... |
RemDelaporteMathurin__h-transport-materials-36 | [
{
"changes": {
"added_entities": [
"h_transport_materials/property.py:ArrheniusProperty.range"
],
"added_modules": null,
"edited_entities": [
"h_transport_materials/property.py:ArrheniusProperty.fit"
],
"edited_modules": [
"h_transport_materials/proper... | RemDelaporteMathurin/h-transport-materials | 9434449539499a14ea2bf0b2c00f2a5080a1c7f7 | Temperature range should be determined by data_T | diff --git a/h_transport_materials/property.py b/h_transport_materials/property.py
index 8174d74..4cc3aee 100644
--- a/h_transport_materials/property.py
+++ b/h_transport_materials/property.py
@@ -67,6 +67,16 @@ class ArrheniusProperty(Property):
self.data_y = data_y
super().__init__(**kwargs)
+ ... |
RemDelaporteMathurin__h-transport-materials-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"h_transport_materials/plotting.py:plot"
],
"edited_modules": [
"h_transport_materials/plotting.py:plot"
]
},
"file": "h_transport_materials/plotting.py"
}
] | RemDelaporteMathurin/h-transport-materials | fb641e58eb9c7561940435f7a292bfb3874b99e0 | plot method for PropertiesGRoup | diff --git a/README.md b/README.md
index 3642452..b1f442d 100644
--- a/README.md
+++ b/README.md
@@ -26,8 +26,7 @@ import matplotlib.pyplot as plt
# filter only tungsten and H
diffusivities = htm.diffusivities.filter(material="tungsten").filter(isotope="h")
-for D in diffusivities:
- htm.plotting.plot(D)
+htm.pl... |
RemDelaporteMathurin__h-transport-materials-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "h_transport_materials/materials/vanadium_alloy.py"
},
{
"changes": {
"added_entities": [
"h_transport_materials/properties_group.py:Prop... | RemDelaporteMathurin/h-transport-materials | 7b5c809e34ccd0672db03640b56395dbc65988c6 | Export to JSON
I guess this could be a method of PropertiesGroup | diff --git a/h_transport_materials/materials/vanadium_alloy.py b/h_transport_materials/materials/vanadium_alloy.py
index 3448398..0c6a282 100644
--- a/h_transport_materials/materials/vanadium_alloy.py
+++ b/h_transport_materials/materials/vanadium_alloy.py
@@ -13,7 +13,7 @@ hashizume_diffusivity = Diffusivity(
klepi... |
RenaudLN__dash-pydantic-form-20 | [
{
"changes": {
"added_entities": [
"dash_pydantic_form/fields/base_fields.py:CheckboxField.get_value"
],
"added_modules": null,
"edited_entities": [
"dash_pydantic_form/fields/base_fields.py:BaseField.model_post_init"
],
"edited_modules": [
"dash_pydan... | RenaudLN/dash-pydantic-form | b8d23a6c13641d8fa93ec26ba5ffc499ddd65a40 | Nested Model in Union gives AttributeError: model_fields
Apologies if this is the wrong way to communicate but I am trying get an example working that matches the pydantic models I am trying to render in a dash app.
I have taken the example in your Discriminate Unions doc section and extended it by creating an Offi... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4922739..36c44e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
+## [... |
ReproNim__neurodocker-623 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neurodocker/cli/generate.py:_get_params_for_registered_templates",
"neurodocker/cli/generate.py:_base_generate"
],
"edited_modules": [
"neurodocker/cli/generate.py:_get_param... | ReproNim/neurodocker | a1719727d53aa4f23eeb4f89dde72001acb37bbf | no longer produces `/neurodocker/startup.sh` in docker recipes, in effect ignores neurodocker/templates/_header.yaml?
Discovered while working on
- https://github.com/PeerHerholz/BIDSonym/pull/81
although there is [neurodocker/templates/_header.yaml](https://github.com/ReproNim/neurodocker/blob/77cb740e0b524f8cdb8... | diff --git a/neurodocker/cli/generate.py b/neurodocker/cli/generate.py
index 2626792..d670d31 100644
--- a/neurodocker/cli/generate.py
+++ b/neurodocker/cli/generate.py
@@ -307,6 +307,8 @@ def _get_params_for_registered_templates() -> list[click.Parameter]:
names_tmpls = list(registered_templates_items())
nam... |
ReproNim__reproman-364 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"reproman/resource/aws_ec2.py:AwsEc2.create",
"reproman/resource/aws_ec2.py:AwsEc2.get_session"
],
"edited_modules": [
"reproman/resource/aws_ec2.py:AwsEc2"
]
},
... | ReproNim/reproman | c549a525a284673953348482daad924b23d49752 | enable paramiko/fabric logging (into our handlers) if our debug level < DEBUG
In the light of #344 it is hard to figure out what is going on in fabric, so we need an easy way to enable its debug output. I guess the easiest is just to direct their logger into our handlers | diff --git a/reproman/resource/aws_ec2.py b/reproman/resource/aws_ec2.py
index 65de005..8eb376e 100644
--- a/reproman/resource/aws_ec2.py
+++ b/reproman/resource/aws_ec2.py
@@ -110,8 +110,15 @@ class AwsEc2(Resource):
def create(self):
"""
Create an EC2 instance.
-
- Returns
+
+ ... |
ReproNim__reproman-370 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"reproman/interface/delete.py:Delete.__call__"
],
"edited_modules": [
"reproman/interface/delete.py:Delete"
]
},
"file": "reproman/interface/delete.py"
},
{
"cha... | ReproNim/reproman | 68c82bea9ca5216d7c5140f4318527e1b56297e7 | Add --force to delete to allow remove resource even when actual instance already gone
ATM attempt to remove a resource which requires also removal of some instance (cloud instance, etc) would fail if that thing is already remove through other means. I think we need `--force` option which proceed removing everything it... | diff --git a/reproman/interface/delete.py b/reproman/interface/delete.py
index 72002be..c11a16f 100644
--- a/reproman/interface/delete.py
+++ b/reproman/interface/delete.py
@@ -11,12 +11,10 @@
__docformat__ = 'restructuredtext'
-import re
-
from .base import Interface
-import reproman.interface.base # Needed for ... |
ReproNim__reproman-436 | [
{
"changes": {
"added_entities": [
"reproman/resource/base.py:classify_keys",
"reproman/resource/base.py:ResourceManager._filter_config"
],
"added_modules": [
"reproman/resource/base.py:classify_keys"
],
"edited_entities": [
"reproman/resource/base.p... | ReproNim/reproman | c291a61ba065ecb5da6b1bab1e6e5ba2447e5fd3 | While instantiating resources from the inventory -- guard against parameters read from the file
Should check which are expected from the attr's, and then if there are some additional spurious ones, should filter them out, issue a warning, and then proceed with instantiation using only the "correct" ones. | diff --git a/reproman/resource/base.py b/reproman/resource/base.py
index 46c9642..74c0524 100644
--- a/reproman/resource/base.py
+++ b/reproman/resource/base.py
@@ -99,6 +99,62 @@ def get_resource_backends(cls):
if "doc" in b.metadata}
+def classify_keys(cls, keys):
+ """Classify `keys` according to... |
ReproNim__reproman-488 | [
{
"changes": {
"added_entities": [
"reproman/resource/docker_container.py:_image_latest_default"
],
"added_modules": [
"reproman/resource/docker_container.py:_image_latest_default"
],
"edited_entities": null,
"edited_modules": [
"reproman/resource/dock... | ReproNim/reproman | a5da59d720baf3048a30000632b78e1eae215f5f | create: Default to :latest tag when pulling Docker image
`reproman create` callers that are familiar with the command-line interface to `docker pull` would reasonably expect that, if they omit a tag, the default `:latest` will be used. Instead we download all tags:
```
$ docker images busybox
REPOSITORY ... | diff --git a/reproman/resource/docker_container.py b/reproman/resource/docker_container.py
index 080d6e6..d9d0b2e 100644
--- a/reproman/resource/docker_container.py
+++ b/reproman/resource/docker_container.py
@@ -30,6 +30,16 @@ import logging
lgr = logging.getLogger('reproman.resource.docker_container')
+def _imag... |
ReproNim__reproman-505 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"reproman/distributions/conda.py:get_miniconda_url",
"reproman/distributions/conda.py:CondaDistribution.install_packages",
"reproman/distributions/conda.py:CondaTracer._init",
"re... | ReproNim/reproman | 8b5ce397d9b85deab93f60a944c2774be7dc87e6 | env -0 not supported on macOS
reproman/resource/session.py uses `env -0` to get the environment, but `-0` is not a supported option to `env` on macOS. | diff --git a/reproman/distributions/conda.py b/reproman/distributions/conda.py
index 4cea4e9..21f1599 100644
--- a/reproman/distributions/conda.py
+++ b/reproman/distributions/conda.py
@@ -85,7 +85,9 @@ def get_miniconda_url(conda_platform, python_version):
raise ValueError("Unsupported platform %s for conda i... |
ReproNim__reproman-508 | [
{
"changes": {
"added_entities": [
"reproman/distributions/conda.py:CondaTracer._is_conda_dist_path"
],
"added_modules": null,
"edited_entities": [
"reproman/distributions/conda.py:get_miniconda_url",
"reproman/distributions/conda.py:CondaDistribution.install_pack... | ReproNim/reproman | 2ffa1759a8ced87169f3422bb2a0b0b9fb8e46b9 | Our tracer is incompatible with latest conda
As described in gh-445:
> [...] our distributions.conda isn't compatible
> with the latest conda in at least two ways. We use an environment
> file that doesn't have an extension that conda now expects. That's an
> easy fix, and there's a patch in gh-443. The bigger i... | diff --git a/reproman/distributions/conda.py b/reproman/distributions/conda.py
index db568e5..4cea4e9 100644
--- a/reproman/distributions/conda.py
+++ b/reproman/distributions/conda.py
@@ -85,9 +85,7 @@ def get_miniconda_url(conda_platform, python_version):
raise ValueError("Unsupported platform %s for conda i... |
ReproNim__reproman-539 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"reproman/support/jobs/orchestrators.py:FetchPlainMixin.fetch"
],
"edited_modules": [
"reproman/support/jobs/orchestrators.py:FetchPlainMixin"
]
},
"file": "reproman/sup... | ReproNim/reproman | 98bcaf28682181ad36f5a7a9f8de9f22ad242300 | plain orchestrator: make sure that it at least fetches logs (stdout/err) even if not --output's were specified? | diff --git a/reproman/support/jobs/orchestrators.py b/reproman/support/jobs/orchestrators.py
index 8191a70..2ec5a8a 100644
--- a/reproman/support/jobs/orchestrators.py
+++ b/reproman/support/jobs/orchestrators.py
@@ -890,19 +890,18 @@ class FetchPlainMixin(object):
# treat it as the file.
... |
ReproNim__reproman-544 | [
{
"changes": {
"added_entities": [
"reproman/resource/session.py:Session.transfer_recursive"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"reproman/resource/session.py:Session"
]
},
"file": "reproman/resource/session.py"
},
... | ReproNim/reproman | b82a412ecccce33c885247dbd9464972b0e87c3f | ENH: recursive `get` for sessions (shell, ssh, etc) should support recursive mode of operation
It is necessary for any place where `get` is supposed to obtain a full hierarchy of directories like e.g. getting outputs of the job back to the local system.
I will send a follow up initial PR for the plain orchestrator... | diff --git a/reproman/resource/session.py b/reproman/resource/session.py
index 776701c..ba80322 100644
--- a/reproman/resource/session.py
+++ b/reproman/resource/session.py
@@ -508,6 +508,50 @@ class Session(object):
raise NotImplementedError
+ def transfer_recursive(self, src_path, dest_path, isdir_fct... |
ResearchObject__ro-crate-py-102 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/entity.py:Entity.__getitem__"
],
"edited_modules": [
"rocrate/model/entity.py:Entity"
]
},
"file": "rocrate/model/entity.py"
}
] | ResearchObject/ro-crate-py | b8668904f18b6d4060d0b29406e2f04c95b6d2f9 | Entity getitem breaks for null JSON values
Example:
```javascript
{
"@id": "sort-and-change-case.ga",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"programmingLanguage": {
"@id": "#galaxy"
},
"name": null
}... | diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py
index 826b564..77d5671 100644
--- a/rocrate/model/entity.py
+++ b/rocrate/model/entity.py
@@ -75,7 +75,7 @@ class Entity(MutableMapping):
def __getitem__(self, key):
v = self._jsonld[key]
- if isinstance(v, str) or key.startswith("@")... |
ResearchObject__ro-crate-py-109 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/cli.py:write_zip"
],
"edited_modules": [
"rocrate/cli.py:write_zip"
]
},
"file": "rocrate/cli.py"
}
] | ResearchObject/ro-crate-py | 5f8f0e83c10018bdb161c6affc3f63eadc53bb08 | write-zip CLI command reinitializes the crate
The `write-zip` CLI command reinitializes the crate, so any changes like adding a workflow or test suite are lost. | diff --git a/rocrate/cli.py b/rocrate/cli.py
index 250a448..7d8dad7 100644
--- a/rocrate/cli.py
+++ b/rocrate/cli.py
@@ -120,7 +120,7 @@ def definition(state, suite, path, engine, engine_version):
@click.argument('dst', type=click.Path(writable=True))
@click.pass_obj
def write_zip(state, dst):
- crate = ROCrate(s... |
ResearchObject__ro-crate-py-111 | [
{
"changes": {
"added_entities": [
"rocrate/cli.py:add_hash",
"rocrate/cli.py:CSVParamType.convert"
],
"added_modules": [
"rocrate/cli.py:add_hash",
"rocrate/cli.py:CSVParamType"
],
"edited_entities": [
"rocrate/cli.py:init",
"rocrate... | ResearchObject/ro-crate-py | 043f7054c28d96128898435144049d1240ea6ea4 | Exclude option for crate init
It would be nice to support an `exclude` option to avoid considering certain sub-paths when initializing an RO-Crate from a directory tree, i.e., `ROCrate(source, init=True)`. For instance, from the command line, you might want to run:
```
rocrate init --exclude .git
```
| diff --git a/rocrate/cli.py b/rocrate/cli.py
index 7d8dad7..a74ec90 100644
--- a/rocrate/cli.py
+++ b/rocrate/cli.py
@@ -23,6 +23,7 @@ from .rocrate import ROCrate
from .model.computerlanguage import LANG_MAP
from .model.testservice import SERVICE_MAP
from .model.softwareapplication import APP_MAP
+from .utils impor... |
ResearchObject__ro-crate-py-116 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/cli.py:cli",
"rocrate/cli.py:init",
"rocrate/cli.py:add",
"rocrate/cli.py:workflow",
"rocrate/cli.py:suite",
"rocrate/cli.py:instance",
"rocrate/c... | ResearchObject/ro-crate-py | aac1df6f5e5b4400696e485e709fe580d35b4e9e | CLI can generate an error when command help is requested
In a non-ro-crate dir:
```console
$ rocrate add workflow --help
Traceback (most recent call last):
File "/home/simleo/git/ro-crate-py/venv/bin/rocrate", line 11, in <module>
load_entry_point('rocrate==0.5.0', 'console_scripts', 'rocrate')()
File "... | diff --git a/rocrate/cli.py b/rocrate/cli.py
index a74ec90..38a20d0 100644
--- a/rocrate/cli.py
+++ b/rocrate/cli.py
@@ -54,58 +54,57 @@ class CSVParamType(click.ParamType):
CSV = CSVParamType()
+OPTION_CRATE_PATH = click.option('-c', '--crate-dir', type=click.Path(), default=os.getcwd)
@click.group()
-@click... |
ResearchObject__ro-crate-py-119 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/file_or_dir.py:FileOrDir.__init__"
],
"edited_modules": [
"rocrate/model/file_or_dir.py:FileOrDir"
]
},
"file": "rocrate/model/file_or_dir.py"
},
{
... | ResearchObject/ro-crate-py | 695004f18175ca70b439534adece9e2242dca778 | Support for non-slash root data entity
The [1.1 spec](https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#direct-properties-of-the-root-data-entity) states that the root data entity SHOULD be the string `./`, but in principle it could be an arbitrary URI. This in contrast with RO-Crate 1.0, where the root... | diff --git a/rocrate/model/file_or_dir.py b/rocrate/model/file_or_dir.py
index d82c2c1..afe3226 100644
--- a/rocrate/model/file_or_dir.py
+++ b/rocrate/model/file_or_dir.py
@@ -45,5 +45,5 @@ class FileOrDir(DataEntity):
if is_url(str(source)):
identifier = os.path.basename(source) if fetch... |
ResearchObject__ro-crate-py-126 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/rocrate.py:ROCrate.__check_metadata"
],
"edited_modules": [
"rocrate/rocrate.py:ROCrate"
]
},
"file": "rocrate/rocrate.py"
}
] | ResearchObject/ro-crate-py | 9c010654dce2b8cd9ca4e99dd73885439885e4fc | Allow root dataset to have more than one type
Fails if root dataset has an array as a value for @type
eg. @type = ['Dataset', 'RepositoryCollection']
Note: @ptsefton says: Can we always code defensively, please.
https://github.com/ResearchObject/ro-crate-py/blob/9c010654dce2b8cd9ca4e99dd73885439885e4fc/rocr... | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index 8ed15de..c0fa0b8 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -151,8 +151,8 @@ class ROCrate():
root = entities[metadata["about"]["@id"]]
except (KeyError, TypeError):
raise ValueError("metadata descriptor does ... |
ResearchObject__ro-crate-py-136 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/dataset.py:Dataset.write"
],
"edited_modules": [
"rocrate/model/dataset.py:Dataset"
]
},
"file": "rocrate/model/dataset.py"
},
{
"changes": {
... | ResearchObject/ro-crate-py | 7380019e81cf3ab4fcffe9292737fff580674142 | Fix behavior wrt "missing" data entities
After the merge of #75, we allow data entities whose `@id` does not map to an existing file or directory, even if local. While this adds flexibility for use cases like #73, such crates are not supported by other libraries. Specifically, I got reports of crates generated with ro-... | diff --git a/rocrate/model/dataset.py b/rocrate/model/dataset.py
index f883a02..b378ea3 100644
--- a/rocrate/model/dataset.py
+++ b/rocrate/model/dataset.py
@@ -18,6 +18,8 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+import errno
+import os
import shuti... |
ResearchObject__ro-crate-py-149 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "rocrate/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/en... | ResearchObject/ro-crate-py | 1e4687a0fb07a56e426a0cb876300de38e54e09c | Allow to attach partials to a crate?
Hi,
For Autosubmit, since the workflow configuration doesn't contain the information needed for RO-Crate, I [used](https://earth.bsc.es/gitlab/es/autosubmit/-/merge_requests/317) the exact same approach from [COMPSs](https://github.com/bsc-wdc/compss/blob/9e79542eef60afa9e288e724... | diff --git a/CITATION.cff b/CITATION.cff
index b255f9b..6599788 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -16,6 +16,9 @@ authors:
- family-names: Huber
given-names: Sebastiaan
orcid: https://orcid.org/0000-0001-5845-8880
+ - family-names: Kinoshita
+ given-names: Bruno
+ orcid: https://orcid.o... |
ResearchObject__ro-crate-py-152 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "rocrate/model/softwareapplication.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | ResearchObject/ro-crate-py | f5281c1c583b1b66bcd8e05e0953635519ba5b2f | Remove software version defaults
E.g., [`PLANEMO_DEFAULT_VERSION = "0.74"`](https://github.com/ResearchObject/ro-crate-py/blob/81d74b3c40241235229500d30b4747a392c65a0b/rocrate/model/softwareapplication.py#L57). No info is better than arbitrary (thus likely wrong) info. | diff --git a/rocrate/model/softwareapplication.py b/rocrate/model/softwareapplication.py
index c7bc8a5..29d8b2b 100644
--- a/rocrate/model/softwareapplication.py
+++ b/rocrate/model/softwareapplication.py
@@ -54,7 +54,6 @@ class SoftwareApplication(ContextEntity, CreativeWork):
PLANEMO_ID = "https://w3id.org/ro/te... |
ResearchObject__ro-crate-py-161 | [
{
"changes": {
"added_entities": [
"rocrate/rocrate.py:ROCrate.__add_parts"
],
"added_modules": null,
"edited_entities": [
"rocrate/rocrate.py:ROCrate.__read_data_entities"
],
"edited_modules": [
"rocrate/rocrate.py:ROCrate"
]
},
"file": ... | ResearchObject/ro-crate-py | dc3f75b0d0390dedbf9a830b6325b76dba468f1f | Support indirect data entity linking from root
Currently we detect data entities only if they are *directly* linked to from the root data entity:
```json
{
"@id": "./",
"@type": "Dataset",
"hasPart": [
{"@id": "spam"},
{"@id": "spam/foo.txt"}
]
},
{
"@id": "spam",
"... | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index d6b12a6..57bcd39 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -147,10 +147,16 @@ class ROCrate():
preview_entity = entities.pop(Preview.BASENAME, None)
if preview_entity and not gen_preview:
self.add(Preview(self, s... |
ResearchObject__ro-crate-py-162 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/metadata.py:Metadata.__init__",
"rocrate/model/metadata.py:Metadata.generate"
],
"edited_modules": [
"rocrate/model/metadata.py:Metadata"
]
},
"fi... | ResearchObject/ro-crate-py | 1e75c3fe87b084f2f91231b775c601cb81e0246e | Add method to include additional contexts at the top level
Right now, it is possible to add additional terms from other contexts to the top level contexts through the attached `Metadata` instance, using the `extra_terms` dictionary:
```python
a_crate = ROCrate(gen_preview=False)
a_crate.metadata.extra_terms.update... | diff --git a/rocrate/model/metadata.py b/rocrate/model/metadata.py
index f4ddb50..49f4aa8 100644
--- a/rocrate/model/metadata.py
+++ b/rocrate/model/metadata.py
@@ -47,6 +47,7 @@ class Metadata(File):
properties=properties
)
# https://www.researchobject.org/ro-crate/1.1/appendix/jsonld.ht... |
ResearchObject__ro-crate-py-163 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/rocrate.py:ROCrate.__read_data_entities",
"rocrate/rocrate.py:ROCrate.__add_parts"
],
"edited_modules": [
"rocrate/rocrate.py:ROCrate"
]
},
"file": "roc... | ResearchObject/ro-crate-py | b3e24baaff92636dc58d910f6f1103d4f86a4c31 | hasPart property on root dataset is assumed to be an array
Loading this dataset causes an error as the hasPart value is not an array but the code assumes it will be :
```json
{
"@id": "./",
"@type": "Dataset",
"hasPart": {"@id": "spam/foo.txt"}
},
{
"@id": "spam/foo.txt",
"@type": "File... | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index 57bcd39..5d5a98d 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -142,7 +142,7 @@ class ROCrate():
root_entity = entities.pop(root_id)
assert root_id == root_entity.pop('@id')
- parts = root_entity.pop('hasPart', [])
+ ... |
ResearchObject__ro-crate-py-166 | [
{
"changes": {
"added_entities": [
"rocrate/rocrate.py:ROCrate.default_entities",
"rocrate/rocrate.py:ROCrate.data_entities",
"rocrate/rocrate.py:ROCrate.contextual_entities"
],
"added_modules": null,
"edited_entities": [
"rocrate/rocrate.py:ROCrate.__init... | ResearchObject/ro-crate-py | 0d3c63946d2a0ab5aeaa5f3bc228db76455c80f8 | Raise an error, warning, or ignore duplicate ID's?
Hi, I just noticed I had a duplicate ID in my crate, is that valid for RO-Crate?
I thought about checking something like `if File(data).id in crate.data_entities`, but I think what identifies uniquely data in the crate are `ID` + JSON-LD data. As I have the date tha... | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index 5d5a98d..d3041a1 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -75,9 +75,6 @@ class ROCrate():
def __init__(self, source=None, gen_preview=False, init=False, exclude=None):
self.exclude = exclude
self.__entity_map = {}
- ... |
ResearchObject__ro-crate-py-168 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/utils.py:is_url"
],
"edited_modules": [
"rocrate/utils.py:is_url"
]
},
"file": "rocrate/utils.py"
}
] | ResearchObject/ro-crate-py | 91376829c2fcf1ecc2376255c1faa055e5f769fe | BUG: If Root Data Entity has an arcp:// ID the arcp:// part gets stripped off it
Here's some code to reproduce the error:
```python
from rocrate.rocrate import ROCrate
import json
import os
test_crate = {
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"@vocab": "http://schema.org/"
... | diff --git a/rocrate/utils.py b/rocrate/utils.py
index 18aa6f2..434fb41 100644
--- a/rocrate/utils.py
+++ b/rocrate/utils.py
@@ -33,7 +33,7 @@ def is_url(string):
parts = urlsplit(string)
if os.name == "nt" and len(parts.scheme) == 1:
return False
- return all((parts.scheme, parts.path))
+ retu... |
ResearchObject__ro-crate-py-169 | [
{
"changes": {
"added_entities": [
"rocrate/model/entity.py:Entity.id"
],
"added_modules": null,
"edited_entities": [
"rocrate/model/entity.py:Entity.__init__"
],
"edited_modules": [
"rocrate/model/entity.py:Entity"
]
},
"file": "rocrate/... | ResearchObject/ro-crate-py | fd5b75e2212698766f8ee10f4f448ed07dd99a47 | Entity id should not be modifiable
It's used to index the entity in the crate's `__entity_map`, so changing it leads to inconsistencies:
```pycon
>>> from rocrate.rocrate import ROCrate
>>> crate = ROCrate()
>>> d = crate.add_dataset("FOO")
>>> crate._ROCrate__entity_map
{..., 'arcp://uuid,2f145cc1-20be-4cd7-ac... | diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py
index 41bf09b..fa26218 100644
--- a/rocrate/model/entity.py
+++ b/rocrate/model/entity.py
@@ -30,9 +30,9 @@ class Entity(MutableMapping):
def __init__(self, crate, identifier=None, properties=None):
self.crate = crate
if identifier:
-... |
ResearchObject__ro-crate-py-170 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/file.py:File.write"
],
"edited_modules": [
"rocrate/model/file.py:File"
]
},
"file": "rocrate/model/file.py"
}
] | ResearchObject/ro-crate-py | 7364e13bf2546f3728e68d6a8c88a6fc66039e58 | Add contentUrl property to files when it's known
E.g., when a remote file is added with `fetch_remote=True`. See https://github.com/ResearchObject/ro-crate/pull/189#issuecomment-1227697348. | diff --git a/rocrate/model/file.py b/rocrate/model/file.py
index 9251aeb..a5d1c43 100644
--- a/rocrate/model/file.py
+++ b/rocrate/model/file.py
@@ -59,6 +59,7 @@ class File(FileOrDir):
if self.fetch_remote:
out_file_path.parent.mkdir(parents=True, exist_ok=True)
... |
ResearchObject__ro-crate-py-171 | [
{
"changes": {
"added_entities": [
"rocrate/cli.py:file",
"rocrate/cli.py:dataset"
],
"added_modules": [
"rocrate/cli.py:file",
"rocrate/cli.py:dataset"
],
"edited_entities": null,
"edited_modules": null
},
"file": "rocrate/cli.py"
}
... | ResearchObject/ro-crate-py | 42aeed481d1c14dab3eaef00c90db7a9a30caf9e | CLI subcommands to add files and directories
Add subcommands to allow this:
```bash
mkdir crate
cd crate
rocrate init # generates minimal metadata file and nothing else
cp /some/other/path/file1 .
cp -rf /some/path/dir1 .
rocrate add file file1
rocrate add dataset dir1
```
| diff --git a/rocrate/cli.py b/rocrate/cli.py
index 9e63e54..8ff4e88 100644
--- a/rocrate/cli.py
+++ b/rocrate/cli.py
@@ -69,6 +69,36 @@ def add():
pass
+@add.command()
+@click.argument('path', type=click.Path(exists=True, dir_okay=False))
+@OPTION_CRATE_PATH
+def file(crate_dir, path):
+ crate = ROCrate(cra... |
ResearchObject__ro-crate-py-172 | [
{
"changes": {
"added_entities": [
"rocrate/cli.py:KeyValueParamType.convert"
],
"added_modules": [
"rocrate/cli.py:KeyValueParamType"
],
"edited_entities": [
"rocrate/cli.py:file",
"rocrate/cli.py:dataset",
"rocrate/cli.py:workflow",
... | ResearchObject/ro-crate-py | 2ea7fae01bca70c5601bcd860582824fb640d4ac | CLI: add a way to set properties
E.g., with a repeatable arg:
```
rocrate add workflow foo.cwl -P name=Foo -P description='Lorem Ipsum'
``` | diff --git a/README.md b/README.md
index dbbe578..76aa7e2 100644
--- a/README.md
+++ b/README.md
@@ -310,7 +310,7 @@ The command acts on the current directory, unless the `-c` option is specified.
### Adding items to the crate
-The `rocrate add` command allows to add workflows and other entity types (currently [te... |
ResearchObject__ro-crate-py-183 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/metadata.py:read_metadata"
],
"edited_modules": [
"rocrate/metadata.py:read_metadata"
]
},
"file": "rocrate/metadata.py"
},
{
"changes": {
"added_... | ResearchObject/ro-crate-py | a551acb4d4084c59e32e2fd79bd82686e6b3aaa2 | FEATURE: Load a crate from a (json) Object
Unless I misunderstand this library can only read crates from disk. It would be very useful to be able to instantiate the library with an object (that would serialise in JSON to an RO-Crate Metadata Document). Eg if I have fetched RO-Crate metadata from an API. | diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 936525e..2069e54 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -19,7 +19,7 @@ jobs:
strategy:
matrix:
os: ['ubuntu-latest', 'macos-latest', 'windows-lates... |
ResearchObject__ro-crate-py-191 | [
{
"changes": {
"added_entities": [
"rocrate/rocrate.py:ROCrate.add_action"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"rocrate/rocrate.py:ROCrate"
]
},
"file": "rocrate/rocrate.py"
}
] | ResearchObject/ro-crate-py | d31f2027b16fb535275c8c8f6c353f58cde64cef | Add function to add a CreateAction to the crate
e.g. `add_action()` which takes the inputs, outputs, instrument, etc as arguments and builds a CreateAction entity.
CreateAction entities are fiddly to create, but essential for WRROC - so many workflow managers need to create them and have written the code themselves ... | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index 5597d54..63f2eb3 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -556,6 +556,22 @@ class ROCrate():
self.metadata.extra_terms.update(TESTING_EXTRA_TERMS)
return definition
+ def add_action(self, instrument, identifier=None, ob... |
ResearchObject__ro-crate-py-192 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/entity.py:Entity.__init__"
],
"edited_modules": [
"rocrate/model/entity.py:Entity"
]
},
"file": "rocrate/model/entity.py"
}
] | ResearchObject/ro-crate-py | d31f2027b16fb535275c8c8f6c353f58cde64cef | Allow entities to be passed in as `properties` values when initialising an entity
Example demonstrating the issue:
```python
from rocrate.model import ContextEntity, Person
from rocrate.rocrate import ROCrate
crate = ROCrate()
alice = crate.add(
Person(
crate,
"https://orcid.org/0000-000... | diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py
index c18096e..22e69a5 100644
--- a/rocrate/model/entity.py
+++ b/rocrate/model/entity.py
@@ -34,12 +34,13 @@ class Entity(MutableMapping):
self.__id = self.format_id(identifier)
else:
self.__id = f"#{uuid.uuid4()}"
+ ... |
ResearchObject__ro-crate-py-193 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/entity.py:Entity.__setitem__"
],
"edited_modules": [
"rocrate/model/entity.py:Entity"
]
},
"file": "rocrate/model/entity.py"
}
] | ResearchObject/ro-crate-py | 1419ddc3b6a95a24577ac5a5ee3635204021608b | Setting/Accessing nested properties on entities without @id
RO-Crates aim to write the metadata file as flattend and compacted JSON-LD. I have noticed some inconsistencies with enforcing this behavior in this library.
Currently, it is possible to write nested properties to an entity, even if this property is a dict... | diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py
index 22e69a5..fc23ead 100644
--- a/rocrate/model/entity.py
+++ b/rocrate/model/entity.py
@@ -102,6 +102,9 @@ class Entity(MutableMapping):
if key.startswith("@"):
raise KeyError(f"cannot set '{key}'")
values = value if isinst... |
ResearchObject__ro-crate-py-217 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/dataset.py:Dataset._copy_folder",
"rocrate/model/dataset.py:Dataset._stream_folder_from_path"
],
"edited_modules": [
"rocrate/model/dataset.py:Dataset"
]
... | ResearchObject/ro-crate-py | d1ee55ac3c0b9b0c569043b087adbebeca8d3eb1 | Support percent-encoding of data entity paths
In [Describing entities in JSON-LD](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#describing-entities-in-json-ld) the spec says:
> Care must be taken to express any relative paths using `/` separator and escape special characters like spa... | diff --git a/README.md b/README.md
index 3800030..87feb62 100644
--- a/README.md
+++ b/README.md
@@ -166,6 +166,22 @@ for n in "Mickey_Mouse", "Scrooge_McDuck":
donald.append_to("follows", p)
```
+#### Handling of special characters
+
+Since RO-Crate entity identifiers are URIs (relative or absolute), special c... |
ResearchObject__ro-crate-py-37 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "rocrate/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/da... | ResearchObject/ro-crate-py | 4ab8975b9478b7ba2f13fb0d13bd1b3b5287ac54 | Ensure Entity.properties yields ready-to-write JSON
This line in the root dataset code auto-converts `datePublished` into a Python datetime object:
https://github.com/ResearchObject/ro-crate-py/blob/4ab8975b9478b7ba2f13fb0d13bd1b3b5287ac54/rocrate/model/root_dataset.py#L28
Things are fine when writing an RO-Crate, ... | diff --git a/requirements.txt b/requirements.txt
index 4eca3b0..869d0d0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,3 +7,4 @@ urllib3==1.25.6
arcp==0.2.1
galaxy2cwl
jinja2
+python-dateutil
diff --git a/rocrate/_version.py b/rocrate/_version.py
index 3d718ba..b5fdc75 100644
--- a/rocrate/_version.py
++... |
ResearchObject__ro-crate-py-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/dataset.py:Dataset.write_zip"
],
"edited_modules": [
"rocrate/model/dataset.py:Dataset"
]
},
"file": "rocrate/model/dataset.py"
},
{
"changes": {
... | ResearchObject/ro-crate-py | 21736196aece64f9dc43aa39e456acb889d83fcc | Track files/dirs not listed in the metadata file
From the spec:
> Payload files may appear directly in the RO-Crate Root alongside the RO-Crate Metadata File, and/or appear in sub-directories of the RO-Crate Root. Each file and directory MAY be represented as Data Entities in the RO-Crate Metadata File.
> It is i... | diff --git a/rocrate/model/dataset.py b/rocrate/model/dataset.py
index 4a47c41..2944dff 100644
--- a/rocrate/model/dataset.py
+++ b/rocrate/model/dataset.py
@@ -79,4 +79,5 @@ class Dataset(DataEntity):
# iterate over the entries
for file_src, rel_path in self.directory_entries():
dest_pat... |
ResearchObject__ro-crate-py-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/rocrate.py:ROCrate.write_zip"
],
"edited_modules": [
"rocrate/rocrate.py:ROCrate"
]
},
"file": "rocrate/rocrate.py"
}
] | ResearchObject/ro-crate-py | 41f7646303bb27a148d5f964f24cd70a1db6fbc2 | write_zip should not include the new archive in itself
If one calls `write_zip` with an output path that is within the RO-crate directory, the new zip file ends up inside itself. As `write_zip` walks the directory tree it'll find the partially written zip file and copy it into the archive. | diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py
index 5c3969d..a968f10 100644
--- a/rocrate/rocrate.py
+++ b/rocrate/rocrate.py
@@ -510,6 +510,8 @@ class ROCrate():
root = Path(root)
for name in files:
source = root / name
+ if source.samefi... |
ResearchObject__ro-crate-py-75 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/cli.py:cli",
"rocrate/cli.py:init",
"rocrate/cli.py:add",
"rocrate/cli.py:workflow",
"rocrate/cli.py:suite",
"rocrate/cli.py:instance",
"rocrate/c... | ResearchObject/ro-crate-py | 44e730c9bee4ffd312e8f81772deee47a509ba0a | Bug? Fails to load a crate file without its data entities (directories)
I think this is a bug.
On loading a directory with ONLY the sample file from here: https://raw.githubusercontent.com/ResearchObject/example-ro-sample-image-crate/main/sample-crate/ro-crate-metadata.jsonld
```
from rocrate.rocrate import ROC... | diff --git a/rocrate/cli.py b/rocrate/cli.py
index 7512383..0f02132 100644
--- a/rocrate/cli.py
+++ b/rocrate/cli.py
@@ -39,25 +39,23 @@ class State:
@click.pass_context
def cli(ctx, crate_dir):
ctx.obj = state = State()
- state.crate_dir = crate_dir
+ state.crate_dir = os.getcwd() if not crate_dir else os... |
ResearchObject__ro-crate-py-76 | [
{
"changes": {
"added_entities": [
"rocrate/model/data_entity.py:DataEntity.write",
"rocrate/model/data_entity.py:DataEntity.write_zip"
],
"added_modules": null,
"edited_entities": [
"rocrate/model/data_entity.py:DataEntity.__init__"
],
"edited_modules... | ResearchObject/ro-crate-py | 7421fadf3836bb275a770999450059ef0219867e | Bug: Won't load a crate with hasPart reference to a RepositoryCollection.
Loading the below test data gives an error:
```
File "/Users/pt/working/ro-crate-py/test.py", line 3, in <module>
crate = ROCrate("haspart")
File "/Users/pt/rocrate/lib/python3.9/site-packages/rocrate/rocrate.py", line 92, in __init_... | diff --git a/rocrate/model/data_entity.py b/rocrate/model/data_entity.py
index d04d364..e9acbe5 100644
--- a/rocrate/model/data_entity.py
+++ b/rocrate/model/data_entity.py
@@ -24,13 +24,14 @@ from .entity import Entity
class DataEntity(Entity):
- def __init__(self, crate, identifier, properties=None):
- ... |
ResearchObject__ro-crate-py-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/dataset.py:Dataset.write"
],
"edited_modules": [
"rocrate/model/dataset.py:Dataset"
]
},
"file": "rocrate/model/dataset.py"
}
] | ResearchObject/ro-crate-py | e48fa3482cd519082f5a9edc1b54808b5926be63 | Adding a directory to a new crate gives an error when trying to write the crate: AttributeError: 'str' object has no attribute 'exists'
Adding a directory to a new crate gives an error when trying to write the crate: `AttributeError: 'str' object has no attribute 'exists'`
See the below example:
```python
import... | diff --git a/rocrate/model/dataset.py b/rocrate/model/dataset.py
index 15489b5..4746e9a 100644
--- a/rocrate/model/dataset.py
+++ b/rocrate/model/dataset.py
@@ -48,7 +48,7 @@ class Dataset(FileOrDir):
self.__get_parts(out_path)
else:
out_path.mkdir(parents=True, exist_ok=True)
- ... |
ResearchObject__ro-crate-py-95 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rocrate/model/preview.py:Preview.__init__"
],
"edited_modules": [
"rocrate/model/preview.py:Preview"
]
},
"file": "rocrate/model/preview.py"
},
{
"changes": {
... | ResearchObject/ro-crate-py | 7a5d25f3f4f8f4ca68f42cc582cf61378589bbe2 | Duplicate preview entry in output crate
```python
import shutil
from rocrate.rocrate import ROCrate
shutil.rmtree("/tmp/out_crate", ignore_errors=True)
crate = ROCrate("test/test-data/read_crate")
crate.write("/tmp/out_crate")
```
The output crate has:
```javascript
{
"@id": "ro-crat... | diff --git a/rocrate/model/preview.py b/rocrate/model/preview.py
index 553eacc..03013b9 100644
--- a/rocrate/model/preview.py
+++ b/rocrate/model/preview.py
@@ -32,8 +32,8 @@ class Preview(File):
"""
BASENAME = "ro-crate-preview.html"
- def __init__(self, crate, source=None):
- super().__init__(cr... |
ResearchObject__runcrate-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/runcrate/convert.py:ProvCrateBuilder.add_action_params",
"src/runcrate/convert.py:ProvCrateBuilder.convert_param",
"src/runcrate/convert.py:ProvCrateBuilder._map_input_data",
... | ResearchObject/runcrate | c27ed1181e0781a22481f1efd7a79879cb33505c | CWLProv conversion: include creation datetime, size, checksum, format
See https://github.com/RenskeW/runcrate-analysis/issues/2
Mappings:
* creation datetime: [dateCreated](https://schema.org/dateCreated) (there's a `prov:time` field in `wasGeneratedBy` entries)
* size: [contentSize](https://schema.org/contentSi... | diff --git a/src/runcrate/convert.py b/src/runcrate/convert.py
index 0d76432..ff48935 100644
--- a/src/runcrate/convert.py
+++ b/src/runcrate/convert.py
@@ -566,6 +566,8 @@ class ProvCrateBuilder:
))
if len(action_p["exampleOfWork"]) == 1:
action_p["exampleOfWork"] = action_p[... |
ReviewNB__treon-25 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"treon/treon.py:get_notebooks_to_test"
],
"edited_modules": [
"treon/treon.py:get_notebooks_to_test"
]
},
"file": "treon/treon.py"
}
] | ReviewNB/treon | c90f964ae714cb7ac78aede2f86753e3d21104ec | Allow multiple PATHs to be provided
According to `treon --help`, treon is meant to be invoked as
```
treon [PATH] [--threads=<number>] [-v] [--exclude=<string>]...
```
However, it is currently not possible to pass multiple PATHs, unlike many command-line tools (e.g., `cat`). If multiple PATHs are provided, the... | diff --git a/treon/treon.py b/treon/treon.py
index 60c75f0..f34f9fe 100644
--- a/treon/treon.py
+++ b/treon/treon.py
@@ -2,7 +2,7 @@
"""
Usage:
treon
- treon [PATH] [--threads=<number>] [-v] [--exclude=<string>]...
+ treon [PATH]... [--threads=<number>] [-v] [--exclude=<string>]...
Arguments:
PATH ... |
RhodiumGroup__rhg_compute_tools-38 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rhg_compute_tools/gcs.py:_get_path_types",
"rhg_compute_tools/gcs.py:cp_gcs",
"rhg_compute_tools/gcs.py:sync_gcs"
],
"edited_modules": [
"rhg_compute_tools/gcs.py:_ge... | RhodiumGroup/rhg_compute_tools | b7c9a7b87804449627ac10f7028e4e458ca5db05 | KubeCluster.adapt() does not work
we get rapid increases and decreases of the number of workers. Also, this doesn't play nice with multiple threads | diff --git a/requirements.txt b/requirements.txt
index 6603199..d19ea9f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
-matplotlib==3.0.3
google-cloud-storage==1.16.1
dask-kubernetes==0.8.0
+matplotlib==3.0.3
+numpy>=1.14
diff --git a/rhg_compute_tools/gcs.py b/rhg_compute_tools/gcs.py
index 1a4... |
RhodiumGroup__rhg_compute_tools-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rhg_compute_tools/cli.py:repdirstruc"
],
"edited_modules": [
"rhg_compute_tools/cli.py:repdirstruc"
]
},
"file": "rhg_compute_tools/cli.py"
},
{
"changes": {
... | RhodiumGroup/rhg_compute_tools | 3a937a614adf9645db1b2603ff1b386c41a708fe | replicate_directory_structure_on_gcs: Add options for authenticating using `gcloud init`
If you set up a session and cache credentials using the gcloud or gsutil tools, we should be able to pull from these by simply creating a client | diff --git a/HISTORY.rst b/HISTORY.rst
index 053b986..dd1fc91 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -8,7 +8,7 @@ v0.2.0
------
* Add CLI tools (:issue:`37`). See ``rctools gcs repdirstruc --help`` to start
-* Add new function ``rhg_compute_tools.gcs.replicate_directory_structure_on_gcs`` to copy directory t... |
RightBrain-Networks__auto-semver-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"semver/__init__.py:SemVer.get_branches",
"semver/__init__.py:SemVer.version_repo",
"semver/__init__.py:main"
],
"edited_modules": [
"semver/__init__.py:SemVer",
... | RightBrain-Networks/auto-semver | eaebfcc3297fd1adb355069691cbf5e95eb31731 | Semver fails with double quotes in a commit
**Version of Auto-Semver:**
0.6.2
**Environment:**
docker
**Issue description:**
Having a double quote anywhere in the commit message will cause versioning to fail. For example:
this will work:
```
[klucas@klucas-wks ui-build-config] (master)$ git log -1... | diff --git a/Jenkinsfile b/Jenkinsfile
index cbbd435..10aee15 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -1,4 +1,4 @@
-library('pipeline-library')
+library('pipeline-library@bugfix/durable-task-workaround')
pipeline {
options { timestamps() }
@@ -18,7 +18,7 @@ pipeline {
stage('Self Version') {
ste... |
RobinL__fuzzymatcher-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fuzzymatcher/data_getter_sqlite.py:DataGetter._tokens_to_matches"
],
"edited_modules": [
"fuzzymatcher/data_getter_sqlite.py:DataGetter"
]
},
"file": "fuzzymatcher/data... | RobinL/fuzzymatcher | 5f0b19d50d5dcbcd930f9634d2bf429007b5efcc | OperationalError: malformed MATCH expression
Using `fuzzy_left_join`, I came across the above error while matching addresses.
It seems to relate to the following string: `'16 Orchard Court, Near Stepaside Park, Stepaside, Dublin, ireland'`
(note: I swapped out the street name for another for privacy reasons, but ... | diff --git a/fuzzymatcher/data_getter_sqlite.py b/fuzzymatcher/data_getter_sqlite.py
index c54eec8..e97808e 100644
--- a/fuzzymatcher/data_getter_sqlite.py
+++ b/fuzzymatcher/data_getter_sqlite.py
@@ -177,10 +177,21 @@ class DataGetter:
"""
# This fails if the special tokens 'and' or 'or' are in... |
RockefellerArchiveCenter__DACSspace-39 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dacsspace/reporter.py:CSVReporter.__init__",
"dacsspace/reporter.py:CSVReporter.write_report"
],
"edited_modules": [
"dacsspace/reporter.py:CSVReporter"
]
},
"f... | RockefellerArchiveCenter/DACSspace | c6a6042607540fd0522a9b0e1aaf2b43fe389e6d | Create reporting class
As part of #21, create a class which handles reporting logic. Currently this is written to a CSV but we could also print it to stdout, or possibly other formats. | diff --git a/dacsspace/reporter.py b/dacsspace/reporter.py
index 731b7a8..514a247 100644
--- a/dacsspace/reporter.py
+++ b/dacsspace/reporter.py
@@ -1,10 +1,13 @@
+import csv
+
class CSVReporter:
"""Creates CSV reports."""
- def __init__(self):
- # TODO: set filepath for CSV
- pass
+ def _... |
RockefellerArchiveCenter__DACSspace-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dacsspace/dacsspace.py:DACSspace.run"
],
"edited_modules": [
"dacsspace/dacsspace.py:DACSspace"
]
},
"file": "dacsspace/dacsspace.py"
},
{
"changes": {
"a... | RockefellerArchiveCenter/DACSspace | 35d9e7686b660844a831391c4ac3d2fd3ce0be86 | Allow users to specify a schema to validate against
**Is your feature request related to a problem? Please describe.**
DACSspace will ship with a schema for single-level minimum requirement and (maybe) a custom RAC schema. Users may also want to supply their own schema to validate against.
**Describe the solution y... | diff --git a/dacsspace/dacsspace.py b/dacsspace/dacsspace.py
index fcecea7..b953a5b 100644
--- a/dacsspace/dacsspace.py
+++ b/dacsspace/dacsspace.py
@@ -6,9 +6,10 @@ from .validator import Validator
class DACSspace:
"""Base DACSspace class. Fetches data from AS, validates and reports results."""
- def run(se... |
RockefellerArchiveCenter__DACSspace-52 | [
{
"changes": {
"added_entities": [
"dacsspace/dacsspace.py:DACSspace.__init__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"dacsspace/dacsspace.py:DACSspace"
]
},
"file": "dacsspace/dacsspace.py"
}
] | RockefellerArchiveCenter/DACSspace | 1fc1a52c2404e97be7ff26fc38660f5ffcb806e2 | Address filename conventions/extension
@daremiyo discovered that troublesome filenames (filenames with spaces and no extensions provided) will pass tests. We might want to consider building out a solution to this:
- Enhance the TestReporter class to include testing for specific filenames/characters/extensions
- Hav... | diff --git a/dacsspace/dacsspace.py b/dacsspace/dacsspace.py
index b953a5b..35118e7 100644
--- a/dacsspace/dacsspace.py
+++ b/dacsspace/dacsspace.py
@@ -1,3 +1,5 @@
+import re
+
from .client import ArchivesSpaceClient
from .reporter import CSVReporter
from .validator import Validator
@@ -6,6 +8,14 @@ from .validator... |
RockefellerArchiveCenter__DACSspace-61 | [
{
"changes": {
"added_entities": [
"dacsspace.py:main"
],
"added_modules": [
"dacsspace.py:main"
],
"edited_entities": null,
"edited_modules": null
},
"file": "dacsspace.py"
},
{
"changes": {
"added_entities": null,
"added_modules":... | RockefellerArchiveCenter/DACSspace | 85311540f820991e820e1b1af631bb9fdba17276 | Allow package to be run from the command line
**Is your feature request related to a problem? Please describe.**
DACSspace is primarily designed to be run from the command line. We should make sure this is actually possible!
**Describe the solution you'd like**
DACSspace should support something like the following... | diff --git a/.gitignore b/.gitignore
index 3890670..630d230 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,6 @@ log.txt
*__pycache__
.coverage
.tox
+build
+*.egg-info
+.pytest_cache
diff --git a/dacsspace.py b/dacsspace/command_line.py
similarity index 64%
rename from dacsspace.py
rename to dacsspace/command_li... |
RockefellerArchiveCenter__DACSspace-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dacsspace/client.py:ArchivesSpaceClient.__init__"
],
"edited_modules": [
"dacsspace/client.py:ArchivesSpaceClient"
]
},
"file": "dacsspace/client.py"
},
{
"chan... | RockefellerArchiveCenter/DACSspace | 7741871f59be04cb57a89673e78681ec41992f8f | Rethink handling of AS configs
**Is your feature request related to a problem? Please describe.**
The current implementation of this library asks for a config file with ArchivesSpace credentials. This works with a standalone script, but not with an installable package.
**Describe the solution you'd like**
Rethink ... | diff --git a/.gitignore b/.gitignore
index 630d230..34a30bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,4 @@
-local_settings.cfg
+as_config.cfg
log.txt
*.csv
*__pycache__
diff --git a/README.md b/README.md
index 35f3965..3649ae3 100644
--- a/README.md
+++ b/README.md
@@ -24,29 +24,23 @@ Download and install ... |
RockefellerArchiveCenter__DACSspace-70 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dacsspace/reporter.py:CSVReporter.write_report"
],
"edited_modules": [
"dacsspace/reporter.py:CSVReporter"
]
},
"file": "dacsspace/reporter.py"
},
{
"changes": ... | RockefellerArchiveCenter/DACSspace | 7741871f59be04cb57a89673e78681ec41992f8f | Add the number of errors per resource to the csv
When a resource has many missing fields, it would be useful to know how many required fields are missing.
To do this, we should add the number of validation errors to a column in the .csv
- Add the number of validation errors, as an integer, to the dictionary that... | diff --git a/dacsspace/reporter.py b/dacsspace/reporter.py
index 67bec10..6d79184 100644
--- a/dacsspace/reporter.py
+++ b/dacsspace/reporter.py
@@ -23,6 +23,7 @@ class CSVReporter:
fieldnames = [
"uri",
"valid",
+ "error_count",
"explanatio... |
RockefellerArchiveCenter__DACSspace-81 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dacsspace/command_line.py:main"
],
"edited_modules": [
"dacsspace/command_line.py:main"
]
},
"file": "dacsspace/command_line.py"
},
{
"changes": {
"added_... | RockefellerArchiveCenter/DACSspace | 5edc66932c21b5d718e0ffa90d7347e11de04784 | TypeError when running dacsspace
**Describe the bug**
When running dacsspace I get this error:
`TypeError: _StoreAction.__init__() got an unexpected keyword argument 'typ'`
**To Reproduce**
Steps to reproduce the behavior:
1. `dacsspace test.csv`
4. See error `TypeError: _StoreAction.__init__() got an unexpecte... | diff --git a/dacsspace/command_line.py b/dacsspace/command_line.py
index d96267a..78bf994 100644
--- a/dacsspace/command_line.py
+++ b/dacsspace/command_line.py
@@ -14,7 +14,7 @@ def main():
parser.add_argument(
'--as_config',
help='Filepath for ArchivesSpace configuration file',
- typ=str... |
RockefellerArchiveCenter__rac_aspace-85 | [
{
"changes": {
"added_entities": [
"rac_aspace/serializers.py:BaseSerializer.write_data",
"rac_aspace/serializers.py:BaseSerializer.read_data"
],
"added_modules": [
"rac_aspace/serializers.py:BaseSerializer",
"rac_aspace/serializers.py:CSVSerializer",
"r... | RockefellerArchiveCenter/rac_aspace | 7d8c39cf471c548476e14d5c8bf14e36347f9d73 | Add function to open data files and return an iterable
**Is your feature request related to a problem? Please describe.**
To address #30 @daremiyo and I think it would be good to have a function that can turn a file into something that a script can use natively.
**Describe the solution you'd like**
Create a function t... | diff --git a/rac_aspace/serializers.py b/rac_aspace/serializers.py
index 9c327c4..534804f 100644
--- a/rac_aspace/serializers.py
+++ b/rac_aspace/serializers.py
@@ -1,7 +1,7 @@
import csv
-class Serializer:
+class BaseSerializer:
def __init__(self, filename, filemode="w"):
"""Sets initial attribute... |
Roguelazer__muttdown-14 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"muttdown/config.py:Config.merge_config",
"muttdown/config.py:Config.smtp_password"
],
"edited_modules": [
"muttdown/config.py:Config"
]
},
"file": "muttdown/con... | Roguelazer/muttdown | 61809de9a445bda848d4933822070e0dd705c192 | Error when trying to run gpg command as smtp_password_command
Hello, I've just switched machines and have been setting things up as I usually have them. I seem to be having an issue with the `smtp_password_command` parameter. My yaml file looks like this:
```yaml
smtp_host: smtp.gmail.com
smtp_port: 465
smtp_ssl:... | diff --git a/muttdown/config.py b/muttdown/config.py
index 236d16f..a09e9c7 100644
--- a/muttdown/config.py
+++ b/muttdown/config.py
@@ -80,6 +80,7 @@ class Config(object):
if self._config['smtp_password'] and self._config['smtp_password_command']:
raise ConfigError('Cannot set smtp_password *and*... |
Roguelazer__muttdown-21 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"muttdown/main.py:convert_tree"
],
"edited_modules": [
"muttdown/main.py:convert_tree"
]
},
"file": "muttdown/main.py"
}
] | Roguelazer/muttdown | a8d8b954fa0dcc51a215df36041c2d330d7f1c19 | Most header information seems to be going missing somewhere
Hello, I don't send a huge amount of email from Mutt so I'm not sure how long this has been going on, but I've recently realised that when I send emails, almost all the header information appears to get discarded. At the receiving end I can't see the "Subject"... | diff --git a/muttdown/main.py b/muttdown/main.py
index d9c551f..0816c28 100644
--- a/muttdown/main.py
+++ b/muttdown/main.py
@@ -59,7 +59,7 @@ def _move_headers(source, dest):
del source[k]
-def convert_tree(message, config, indent=0):
+def convert_tree(message, config, indent=0, wrap_alternative=True)... |
SALib__SALib-457 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/Problem/multi_output.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"e... | SALib/SALib | 4012c1313ee360d0cc3be0fba084f4f86048e2ea | Add parallel analysis
Users are currently expected to apply the desired analysis method to every column in the result array.
```python
# example taken from readme
sobol_indices = [sobol.analyze(problem, Y) for Y in y.T]
```
The hybrid OO/functional approach introduced in v1.4 handles this [automatically](https... | diff --git a/examples/Problem/multi_output.py b/examples/Problem/multi_output.py
index a308bff..717aec0 100644
--- a/examples/Problem/multi_output.py
+++ b/examples/Problem/multi_output.py
@@ -18,7 +18,7 @@ sp = ProblemSpec({
'outputs': ['max_P', 'Utility', 'Inertia', 'Reliability']
})
-(sp.sample_saltelli(1000... |
SALib__SALib-484 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/SALib/util/problem.py:ProblemSpec.__init__",
"src/SALib/util/problem.py:ProblemSpec.analyze"
],
"edited_modules": [
"src/SALib/util/problem.py:ProblemSpec"
]
},... | SALib/SALib | b20ee38be0756eebc4e3947a669c48a04307c25d | MorrisAnalyzer fails for single group
I am using v 1.4.5 of the SALib and I'm getting the following error when analyzing one single variable:
```
File "C:\...\SALib\sample\morris\morris.py", line 113, in sample
sample_morris = _sample_morris(problem, N, num_levels)
File "C:\...\SALib\sample\morris\morris.py... | diff --git a/src/SALib/util/problem.py b/src/SALib/util/problem.py
index 896e37f..f49a154 100644
--- a/src/SALib/util/problem.py
+++ b/src/SALib/util/problem.py
@@ -38,6 +38,8 @@ class ProblemSpec(dict):
self._analysis = None
self['num_vars'] = len(self['names'])
+ if 'groups' not in self:
+ ... |
SALib__SALib-628 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/SALib/analyze/delta.py:calc_delta",
"src/SALib/analyze/delta.py:sobol_first"
],
"edited_modules": [
"src/SALib/analyze/delta.py:calc_delta",
"src/SALib/analyze/de... | SALib/SALib | da19e0901f9355de02f9691b394154354fbe4792 | Migrate to numpy>=2.0.0
Numpy 2.0.0 was released at June 16. It seems that SALib is incompatible with the new numpy now.
E.g., the quick start example, if run this after `pip install SALib --force-reinstall`
```python
from SALib.sample import saltelli
from SALib.analyze import sobol
from SALib.test_functions imp... | diff --git a/src/SALib/analyze/delta.py b/src/SALib/analyze/delta.py
index f80cad7..783b603 100644
--- a/src/SALib/analyze/delta.py
+++ b/src/SALib/analyze/delta.py
@@ -137,13 +137,13 @@ def calc_delta(Y, Ygrid, X, m):
# if not np.all(np.equal(Y_ix, Y_ix[0])):
Y_ix = Y[ix]
- if Y_ix.ptp() != ... |
SALib__SALib-636 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/SALib/analyze/pawn.py:analyze"
],
"edited_modules": [
"src/SALib/analyze/pawn.py:analyze"
]
},
"file": "src/SALib/analyze/pawn.py"
}
] | SALib/SALib | 6fb0a9c144692be5993e50dc99575eab44c192be | PAWN analysis not working when problem uses groups attribute
If I have a problem that was set using groups, sampling (using `sobol_sample`, for example) and analyze with PAWN:
```python
from SALib.util import read_param_file
from SALib import ProblemSpec
from SALib.test_functions import Ishigami
param_file = "... | diff --git a/src/SALib/analyze/pawn.py b/src/SALib/analyze/pawn.py
index 3ad4e45..729c584 100644
--- a/src/SALib/analyze/pawn.py
+++ b/src/SALib/analyze/pawn.py
@@ -149,8 +149,9 @@ def analyze(
# Take the mean of effects from parameters that are grouped together
unique_grps = np.array(unique_grps)
+... |
SAP__cf-python-logging-support-14 | [
{
"changes": {
"added_entities": [
"sap/cf_logging/formatters/json_formatter.py:_default_serializer"
],
"added_modules": [
"sap/cf_logging/formatters/json_formatter.py:_default_serializer"
],
"edited_entities": [
"sap/cf_logging/formatters/json_formatter.py:... | SAP/cf-python-logging-support | 396ba738098024745205cbff22b2646a5337d1d1 | Problem with object logging
Hello,
we run into trouble using this package in combination with the pika package (http://pika.readthedocs.io/en/0.10.0/). After initialization of the logger using cf_logging.init() the pika packages produces exceptions while trying to perform the following log operation:
LOGGER.info... | diff --git a/.gitignore b/.gitignore
index e6ff992..4a314cd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ __pycache__/
# Distribution / packaging
.Python
+.env
env/
env3/
venv/
@@ -25,6 +26,7 @@ lib/
dist/
lib64/
parts/
+.pytest_cache/
sdist/
var/
*.egg-info/
diff --git a/sap/cf_logging/format... |
SAP__cloud-pysec-73 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "sap/xssec/constants.py"
}
] | SAP/cloud-pysec | de3cff1b5dd6930091bde36c7a691634a037cb52 | Timeout during IAS API requests
While creating a security context for IAS, the API requests made to IAS times out. The current timeout is 2s.
Endpoints that currently timeout-
1. `/.well-known/openid-configuration`
2. `verification_key_url`
This happens mostly in AP regions where IAS broker and main tenant are in dif... | diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9983d27..120dab6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,7 +10,7 @@ on:
jobs:
build:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
strategy:
matrix:
diff --git a/CHANGELOG.md b... |
SAP__data-attribute-recommendation-python-sdk-108 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sap/aibus/dar/client/dar_session.py:DARSession.__init__"
],
"edited_modules": [
"sap/aibus/dar/client/dar_session.py:DARSession"
]
},
"file": "sap/aibus/dar/client/dar_... | SAP/data-attribute-recommendation-python-sdk | 70a9af6f275d0bc5ad6f1c541fe5b1126e7b2aa9 | Allow http://localhost for local testing; skip HTTPSRequired exception | diff --git a/.flake8 b/.flake8
index 53496e9..307dd28 100644
--- a/.flake8
+++ b/.flake8
@@ -3,4 +3,5 @@
max-line-length = 88
# E203 clashes with black, see https://github.com/PyCQA/pycodestyle/pull/914
# W503 is already deprecated: https://www.flake8rules.com/rules/W503.html
-ignore = E203, W503
+# B011: pytest use... |
SAP__data-attribute-recommendation-python-sdk-67 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sap/aibus/dar/client/inference_client.py:InferenceClient.do_bulk_inference"
],
"edited_modules": [
"sap/aibus/dar/client/inference_client.py:InferenceClient"
]
},
"file... | SAP/data-attribute-recommendation-python-sdk | a6f0b6f95755e0ce934879a46275b438c9a9e4e0 | InferenceClient: document retry parameter | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4859204..a64742c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versi... |
SAP__data-attribute-recommendation-python-sdk-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sap/aibus/dar/client/data_manager_client.py:DataManagerClient.wait_for_dataset_validation"
],
"edited_modules": [
"sap/aibus/dar/client/data_manager_client.py:DataManagerClient"
... | SAP/data-attribute-recommendation-python-sdk | efa9a5a9ff52575d641f8c5290ecde5133870cd6 | Expose validationMessage in DatasetValidationFailed
Having an error message as follows is not good enough:
```
sap.aibus.dar.client.exceptions.DatasetValidationFailed: Validation for Dataset '0992af67-bf6e-4b8c-b45c-76078e1e6eff' failed with status: 'INVALID_DATA'
```
We should additionally show the validationM... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23cdc12..4859204 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,7 +20,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed
* Log message missing model deployment ID [#59]
+* Expose a Dataset's `validationMessage` in `Data... |
SAP__python-pyodata-149 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyodata/v2/model.py:EdmDateTimeTypTraits.from_json"
],
"edited_modules": [
"pyodata/v2/model.py:EdmDateTimeTypTraits"
]
},
"file": "pyodata/v2/model.py"
}
] | SAP/python-pyodata | 9a3694d553c64e781923e11f6fbc28af67b01bc3 | Date out of range error
According to #80 we facing the same error. We're just consumer using the api to receive data for our DWH. Currently one of our job fails because of this error.
Is it possible to implement a fix for this problem on pyodata side?
Json:
```
{
"d": {
"results": {
"... | diff --git a/pyodata/v2/model.py b/pyodata/v2/model.py
index 5412ca9..67cc1ad 100644
--- a/pyodata/v2/model.py
+++ b/pyodata/v2/model.py
@@ -21,6 +21,8 @@ from lxml import etree
from pyodata.exceptions import PyODataException, PyODataModelError, PyODataParserError
LOGGER_NAME = 'pyodata.model'
+FIX_SCREWED_UP_MINIM... |
SAP__python-pyodata-232 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyodata/v2/model.py:EdmDateTimeOffsetTypTraits.from_json"
],
"edited_modules": [
"pyodata/v2/model.py:EdmDateTimeOffsetTypTraits"
]
},
"file": "pyodata/v2/model.py"
}... | SAP/python-pyodata | 5d1490871f4b824a82dd6eaa148444a99ea4f47d | Malformed value for primitive Edm.DateTimeOffset type
We are using pyodata v1.7.1 the whole time and I'm tried to update to the latest v1.10.0 version. But now I get this error when querying data from the odata service:
```
Traceback (most recent call last):
File "/workspace/tmp/venv/odatavenv/lib/python3.10/sit... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0f876b9..7175a5d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
## [Unreleased]
+- model: fix edge case for Edm.DateTimeOffset.from_json() without offset - Petr Hanak
+
## [1.10.0]
... |
SAP__python-pyodata-259 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyodata/v2/service.py:EntityProxy.__init__"
],
"edited_modules": [
"pyodata/v2/service.py:EntityProxy"
]
},
"file": "pyodata/v2/service.py"
}
] | SAP/python-pyodata | ea558f504532e378e182952db5e78aead3d23a6e | Expanded properties don't have their own results wrapper in V2 like this library expects
In OData V2 JSON, expanded properties are simple arrays of the contained entities.
See https://www.odata.org/documentation/odata-version-2-0/json-format/
Section 9, 9. Inline Representation of Associated Entries
However, py... | diff --git a/pyodata/v2/service.py b/pyodata/v2/service.py
index 0da3463..e84d2f7 100644
--- a/pyodata/v2/service.py
+++ b/pyodata/v2/service.py
@@ -873,10 +873,12 @@ class EntityProxy:
# if there are no entities available, received data consists of
# metadata propertie... |
SAP__python-pyodata-264 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyodata/v2/service.py:EntityProxy.__init__"
],
"edited_modules": [
"pyodata/v2/service.py:EntityProxy"
]
},
"file": "pyodata/v2/service.py"
}
] | SAP/python-pyodata | 0d5c9dabfc7e5b99837eaf7fdccc592bc344d623 | AttributeError in PyOData v1.11.0 When Executing CustomerCollection Query
After updating to PyOData version 1.11.0, I encountered a significant issue with a previously functional query. The purpose of the query is to retrieve a list of customers using the CustomerCollection.get_entities() method, with additional parame... | diff --git a/pyodata/v2/service.py b/pyodata/v2/service.py
index e84d2f7..0ed7741 100644
--- a/pyodata/v2/service.py
+++ b/pyodata/v2/service.py
@@ -876,7 +876,7 @@ class EntityProxy:
# available entities are serialized in results array
for entity in proprties[p... |
SCons__scons-4532 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"SCons/Errors.py:convert_to_BuildError"
],
"edited_modules": [
"SCons/Errors.py:convert_to_BuildError"
]
},
"file": "SCons/Errors.py"
}
] | SCons/scons | 37c74732fefe7a9efd6cee5d86b422f712787eb6 | SCons may convert another exception to BuildError incorrectly
An internal SCons routine, `SCons.Errors.convert_to_BuildError`, attempts to synthesize a `BuildError` exception from whatever exception may have been raised when the Taskmaster executes an action. This can go wrong in certain circumstances. The docstring ... | diff --git a/CHANGES.txt b/CHANGES.txt
index 8815a2061..0a36b9405 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -63,6 +63,9 @@ RELEASE VERSION/DATE TO BE FILLED IN LATER
old Python 2-only code block in a test.
- scons-time tests now supply a "filter" argument to tarfile.extract
to quiet a warning wh... |
SDXorg__pysd-390 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pysd/cli/parser.py:split_subview_sep",
"pysd/cli/parser.py:split_vars"
],
"edited_modules": [
"pysd/cli/parser.py:split_subview_sep",
"pysd/cli/parser.py:split_vars"
... | SDXorg/pysd | f3f3c56cd5851ef161e6bae299592b7571014df3 | Issues with subview-sep
When translating a model with views, subviews and subsubviews (hence two separators required) with split-views=True, and you get the order of the separators wrong in the CLI (i.e. ".,-" when it should be "-,."), the separation of views gets messed up. We could try to improve this, possibly by id... | diff --git a/docs/command_line_usage.rst b/docs/command_line_usage.rst
index b959ee8..ee1afbe 100644
--- a/docs/command_line_usage.rst
+++ b/docs/command_line_usage.rst
@@ -58,7 +58,15 @@ In order to split the Vensim model views in different files, as explained in :do
.. code-block:: text
- python -m pysd --spl... |
SDXorg__pysd-430 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pysd/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pysd/builders/pytho... | SDXorg/pysd | 3b98bb903eafd81816434143837d5df2ec55cb78 | Warning for user when non-constant functions are modified by 'params'
Say the user wants to set the initial conditions for the simulation, but they accidentally use the 'params' keyword. This will overwrite the stock calling functions with the values they meant to use as initial conditions, and they will get very unusu... | diff --git a/docs/advanced_usage.rst b/docs/advanced_usage.rst
index 0c8f775..c583b19 100644
--- a/docs/advanced_usage.rst
+++ b/docs/advanced_usage.rst
@@ -145,6 +145,8 @@ A submodel of a translated model can be run as a standalone model. This can be d
.. automethod:: pysd.py_backend.model.Model.select_submodel
:... |
SMART-Lab__smartlearner-35 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"smartlearner/batch_scheduler.py:MiniBatchScheduler.__init__"
],
"edited_modules": [
"smartlearner/batch_scheduler.py:MiniBatchScheduler"
]
},
"file": "smartlearner/batc... | SMART-Lab/smartlearner | b0877d3b961deceb273139f064985e39239351a7 | Move tests at the root of the library.
That way test won't appear in the autocomplete of your preferred python IDE. | diff --git a/smartlearner/batch_scheduler.py b/smartlearner/batch_scheduler.py
index 664cfb5..99f33ec 100644
--- a/smartlearner/batch_scheduler.py
+++ b/smartlearner/batch_scheduler.py
@@ -26,6 +26,11 @@ class MiniBatchScheduler(BatchScheduler):
self.batch_size = batch_size
self.shared_batch_count = t... |
SNEWS2__snewpy-198 | [
{
"changes": {
"added_entities": [
"python/snewpy/neutrino.py:MassHierarchy.derive_from_dm2",
"python/snewpy/neutrino.py:MixingParameters3Flavor.__iter__",
"python/snewpy/neutrino.py:MixingParameters3Flavor.__getitem__",
"python/snewpy/neutrino.py:MixingParameters3Flavor.__... | SNEWS2/snewpy | e8f1677290e908d620deebb356267d9c51ce0831 | `MixingParameters` presets
Currently, the `snewpy.neutrino.MixingParameters` class contains two sets of default oscillation parameters (for NMO and IMO), both from NuFit 5.0 (July 2020). Since then, there’s been a 5.1 update in October 2021 and NuFit 6.0 is likely to come out later this year. We should regularly update... | diff --git a/python/snewpy/neutrino.py b/python/snewpy/neutrino.py
index 63a6a87..20ad140 100644
--- a/python/snewpy/neutrino.py
+++ b/python/snewpy/neutrino.py
@@ -3,14 +3,26 @@
from enum import IntEnum
from astropy import units as u
-
+from dataclasses import dataclass
+from typing import Optional
+import numpy a... |
SNEWS2__snewpy-302 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"python/snewpy/models/ccsn.py:Fornax_2022.__init__"
],
"edited_modules": [
"python/snewpy/models/ccsn.py:Fornax_2022"
]
},
"file": "python/snewpy/models/ccsn.py"
}
] | SNEWS2/snewpy | 9a77fc9f016ceaa82a685fbdba20193c55166f66 | Change Fornax_2022 input parameters
I missed the discussion in #283, and looking at the new model class now. It has two input parameters `progenitor` and `progenitor_mass` which, if provided, should match each other (checked by validator):
https://github.com/SNEWS2/snewpy/blob/7a2176ffa54f95ca987bcf7ae1c16bfd578b6aeb/... | diff --git a/python/snewpy/models/ccsn.py b/python/snewpy/models/ccsn.py
index eb891a2..4b167cb 100644
--- a/python/snewpy/models/ccsn.py
+++ b/python/snewpy/models/ccsn.py
@@ -414,18 +414,19 @@ _fornax_2022_progenitors = [ '9.0', '9.25', '9.5', '9.75', '10
'22.00', '22.30', '... |
SODALITE-EU__iac-blueprint-builder-6 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/blueprint2CSAR.py:to_CSAR",
"src/blueprint2CSAR.py:validate_csar"
],
"edited_modules": [
"src/blueprint2CSAR.py:to_CSAR",
"src/blueprint2CSAR.py:validate_csar"
... | SODALITE-EU/iac-blueprint-builder | 344a294164876727fb9d8d53c4e3304934ff69e5 | Upgrade to cover new KB features and TOSCA upgrade
Has to support:
- TOSCA 1.3 valid creation (constraints, operation defininitions)
- artifact uploads
- Ansible playbook uploads
- optimisation DSL
| diff --git a/src/blueprint2CSAR.py b/src/blueprint2CSAR.py
index a470f37..36f2d68 100644
--- a/src/blueprint2CSAR.py
+++ b/src/blueprint2CSAR.py
@@ -82,7 +82,8 @@ def to_CSAR(blueprint_name: str, blueprint_dir: Path, no_meta: bool = False, ent
yaml_files = glob.glob(str(tmp_blueprint_path) + "/*.yaml") + glo... |
SODALITE-EU__iac-blueprint-builder-7 | [
{
"changes": {
"added_entities": [
"src/iacparser.py:extract_dependency"
],
"added_modules": [
"src/iacparser.py:extract_dependency"
],
"edited_entities": [
"src/iacparser.py:innerdicts",
"src/iacparser.py:parse",
"src/iacparser.py:parse_data... | SODALITE-EU/iac-blueprint-builder | a1de65bbebf6bb37396a33d0408fa040f9b95f6c | Upgrade to cover new KB features and TOSCA upgrade
Has to support:
- TOSCA 1.3 valid creation (constraints, operation defininitions)
- artifact uploads
- Ansible playbook uploads
- optimisation DSL
| diff --git a/Dockerfile b/Dockerfile
index a538008..9149596 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,5 +3,4 @@ ADD . /parser
WORKDIR /parser
RUN pip3 install -r requirements.txt
EXPOSE 80
-CMD python src/main.py
-
+CMD python src/main.py
\ No newline at end of file
diff --git a/src/iacparser.py b/src/iacp... |
Sage-Bionetworks__Genie-380 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie_registry/maf.py:_check_tsa1_tsa2",
"genie_registry/maf.py:_check_allele_col",
"genie_registry/maf.py:maf._validate"
],
"edited_modules": [
"genie_registry/maf.p... | Sage-Bionetworks/Genie | ae02ff83314c6b33de1bd7f39b0213b3c14300b1 | Strip white space from Reference_Allele and TSA2.
Duplicated variants masked due to extra white space in the end | diff --git a/genie_registry/maf.py b/genie_registry/maf.py
index e90e4eb..512c998 100644
--- a/genie_registry/maf.py
+++ b/genie_registry/maf.py
@@ -27,7 +27,7 @@ def _check_tsa1_tsa2(df):
)
if not (tsa1_eq_ref or tsa1_eq_tsa2):
error = (
- "Mutation File: Contains both "
+... |
Sage-Bionetworks__Genie-427 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie_registry/clinical.py:Clinical._validate"
],
"edited_modules": [
"genie_registry/clinical.py:Clinical"
]
},
"file": "genie_registry/clinical.py"
}
] | Sage-Bionetworks/Genie | b18aebbb3d2b3ad43f8981f94a5cb9271911eddb | Validation of clinical files fails with numpy error
I have encountered the following error when performing validation on patient and sample clinical files.
```
docker run -v $(pwd):/data --rm sagebionetworks/genie genie --syn_user ###### --syn_pass ############ validate /data/data_clinical_supp_patient_PROV.txt /da... | diff --git a/genie_registry/clinical.py b/genie_registry/clinical.py
index 5ebd360..90fca60 100644
--- a/genie_registry/clinical.py
+++ b/genie_registry/clinical.py
@@ -898,11 +898,11 @@ class Clinical(FileTypeFormat):
# CHECK: SAMPLE_CLASS is optional attribute
have_column = process_functions.checkCo... |
Sage-Bionetworks__Genie-437 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie/process_functions.py:check_col_and_values"
],
"edited_modules": [
"genie/process_functions.py:check_col_and_values"
]
},
"file": "genie/process_functions.py"
},... | Sage-Bionetworks/Genie | 0485b7e1599c4894714a92d5e12e99cc2b0cd02d | Make validation of SEQ_ASSAY_IDs case-insensitive
The SEQ_ASSAY_IDs in the assay_information.yaml are being compared to the 'Sample Clinical Database' table (syn7517674), which converts the SEQ_ASSAY_IDs to all uppercase. If the SEQ_ASSAY_IDs assay_information.yaml contain lowercase characters, they will be erroneousl... | diff --git a/genie/process_functions.py b/genie/process_functions.py
index ef0b745..3cd5e65 100644
--- a/genie/process_functions.py
+++ b/genie/process_functions.py
@@ -876,18 +876,21 @@ def check_col_and_values(
final.extend(value.split(sep))
check_values = pd.Series(final)
if no... |
Sage-Bionetworks__Genie-438 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie_registry/maf.py:_check_tsa1_tsa2"
],
"edited_modules": [
"genie_registry/maf.py:_check_tsa1_tsa2"
]
},
"file": "genie_registry/maf.py"
}
] | Sage-Bionetworks/Genie | ef4b90520b2b7664e8ab19e001a2cc9c9724437c | Modify error message for maf.py check
for _check_tsa1_tsa2 in maf.py, modify error message.
https://github.com/Sage-Bionetworks/Genie/blob/develop/genie_registry/maf.py#L25
Instead of
> The values in TUMOR_SEQ_ALLELE1 must be the same as all the values in REFERENCE_ALLELE OR TUMOR_SEQ_ALLELE2
maybe
> All... | diff --git a/genie_registry/maf.py b/genie_registry/maf.py
index f4dae91..714233a 100644
--- a/genie_registry/maf.py
+++ b/genie_registry/maf.py
@@ -25,8 +25,8 @@ def _check_tsa1_tsa2(df):
error = (
"maf: Contains both "
"TUMOR_SEQ_ALLELE1 and TUMOR_SEQ_ALLELE2 columns. "
... |
Sage-Bionetworks__Genie-444 | [
{
"changes": {
"added_entities": [
"genie/process_functions.py:validate_genie_identifier"
],
"added_modules": [
"genie/process_functions.py:validate_genie_identifier"
],
"edited_entities": null,
"edited_modules": null
},
"file": "genie/process_function... | Sage-Bionetworks/Genie | 0c14a6055cf5e7872fa7e7b75860cf7b03e8cc39 | Add validation check for SAMPLE_ID
cBioPortal file imports have an undocumented character limit of 50 for SAMPLE_IDs. This caused issues with the 12.2-consortium release with one site's IDs. | diff --git a/genie/process_functions.py b/genie/process_functions.py
index 033e1ec..fed9e3b 100644
--- a/genie/process_functions.py
+++ b/genie/process_functions.py
@@ -174,6 +174,32 @@ def checkColExist(DF, key):
return result
+def validate_genie_identifier(
+ identifiers: pd.Series, center: str, filename:... |
Sage-Bionetworks__Genie-450 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie_registry/clinical.py:_check_int_dead_consistency"
],
"edited_modules": [
"genie_registry/clinical.py:_check_int_dead_consistency"
]
},
"file": "genie_registry/cli... | Sage-Bionetworks/Genie | 044479d77e7a12626cb6dc366edfc181908c62f7 | Modify check for DEAD variable in clinical file
if DEAD is False, then YEAR_DEATH and INT_DOD must be ‘Not Applicable’
https://www.synapse.org/#!Synapse:syn3380222/wiki/412290 | diff --git a/genie_registry/clinical.py b/genie_registry/clinical.py
index 90fca60..7739b2e 100644
--- a/genie_registry/clinical.py
+++ b/genie_registry/clinical.py
@@ -95,10 +95,10 @@ def _check_int_dead_consistency(clinicaldf: DataFrame) -> str:
# Check that all string values are equal each other
is_equal =... |
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