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Merge pull request #14906 from jmchilton/reset_metadata_testing

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Fix resetting metadata on many repositories at once via the shed API
This commit is contained in:
John Chilton
2023-05-18 09:55:07 -04:00
committed by GitHub
parent 0e576afdba 83c85d79da
commit fef73a4f2e
12 changed files with 720 additions and 12 deletions
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lib/tool_shed/test/base/populators.py
+61 -1
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@@ -1,3 +1,6 @@
import tarfile
from pathlib import Path
from tempfile import NamedTemporaryFile
from typing import (
List,
Optional,
@@ -7,6 +10,7 @@ from typing import (
import requests
from galaxy.util.resources import (
files,
resource_path,
Traversable,
)
@@ -43,6 +47,28 @@ DEFAULT_PREFIX = "repofortest"
COLUMN_MAKER_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar")
COLUMN_MAKER_1_1_1_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar")
DEFAULT_COMMIT_MESSAGE = "a test commit message"
TEST_DATA_REPO_FILES = files("tool_shed.test.test_data")
def repo_files(test_data_path: str) -> List[Path]:
repos = TEST_DATA_REPO_FILES.joinpath(f"repos/{test_data_path}")
paths = sorted(Path(str(x)) for x in repos.iterdir())
return paths
def repo_tars(test_data_path: str) -> List[Path]:
tar_paths = []
for path in repo_files(test_data_path):
if path.is_dir():
prefix = f"shedtest_{test_data_path}_{path.name}_"
tf = NamedTemporaryFile(delete=False, prefix=prefix)
with tarfile.open(tf.name, "w:gz") as tar:
tar.add(str(path.absolute()), arcname=test_data_path or path.name)
tar_path = tf.name
else:
tar_path = str(path)
tar_paths.append(Path(tar_path))
return tar_paths
class ToolShedPopulator:
@@ -55,6 +81,23 @@ class ToolShedPopulator:
self._admin_api_interactor = admin_api_interactor
self._api_interactor = api_interactor
def setup_test_data_repo(self, test_data_path: str) -> Repository:
prefix = test_data_path.replace("_", "")
category_id = self.new_category(prefix=prefix).id
repository = self.new_repository(category_id, prefix=prefix)
repository_id = repository.id
assert repository_id
for index, repo_tar in enumerate(repo_tars(test_data_path)):
commit_message = f"Updating {test_data_path} with index {index} with tar {repo_tar}"
response = self.upload_revision(
repository_id,
repo_tar,
commit_message=commit_message,
)
assert response.is_ok
return repository
def setup_column_maker_repo(self, prefix=DEFAULT_PREFIX) -> Repository:
category_id = self.new_category(prefix=prefix).id
repository = self.new_repository(category_id, prefix=prefix)
@@ -110,7 +153,19 @@ class ToolShedPopulator:
self, repository: HasRepositoryId, path: Traversable, commit_message: str = DEFAULT_COMMIT_MESSAGE
):
response = self.upload_revision_raw(repository, path, commit_message)
api_asserts.assert_status_code_is_ok(response)
if response.status_code != 200:
response_json = None
err_msg = None
try:
response_json = response.json()
except Exception:
pass
if response_json and "err_msg" in response_json:
err_msg = response_json["err_msg"]
if err_msg and "No changes" in err_msg:
assert_msg = f"Updating repository [{repository}] with path [{path}] and commit_message {commit_message} failed to update repository contents, no changes found. Response: [{response_json}]"
raise AssertionError(assert_msg)
api_asserts.assert_status_code_is_ok(response)
return RepositoryUpdate(__root__=response.json())
def new_repository(self, category_id, prefix=DEFAULT_PREFIX) -> Repository:
@@ -169,6 +224,11 @@ class ToolShedPopulator:
api_asserts.assert_status_code_is_ok(revisions_response)
return OrderedInstallableRevisions(__root__=revisions_response.json())
def assert_has_n_installable_revisions(self, repository: Repository, n: int):
revisions = self.get_ordered_installable_revisions(repository.owner, repository.name)
actual_n = len(revisions.__root__)
assert actual_n == n, f"Expected {n} repository revisions, found {actual_n} for {repository}"
def get_repository_for(self, owner: str, name: str, deleted: str = "false") -> Optional[Repository]:
request = RepositoryIndexRequest(
owner=owner,
lib/tool_shed/test/functional/test_shed_repositories.py
+55
View File
@@ -1,5 +1,11 @@
import os
import tempfile
from galaxy.tool_util.parser import get_tool_source
from galaxy.util.compression_utils import CompressedFile
from galaxy.util.resources import resource_path
from galaxy_test.base import api_asserts
from tool_shed.test.base.populators import repo_tars
from ..base.api import ShedApiTestCase
COLUMN_MAKER_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar")
@@ -101,3 +107,52 @@ class TestShedRepositoriesApi(ShedApiTestCase):
first_hit = results.hits[0]
assert first_hit.repository.name == repository.name
assert first_hit.repository.times_downloaded == 0
def test_repo_tars(self):
for index, repo_path in enumerate(repo_tars("column_maker")):
path = CompressedFile(repo_path).extract(tempfile.mkdtemp())
tool_xml_path = os.path.join(path, "column_maker.xml")
tool_source = get_tool_source(config_file=tool_xml_path)
tool_version = tool_source.parse_version()
if index == 0:
assert tool_version == "1.1.0"
elif index == 1:
assert tool_version == "1.2.0"
elif index == 2:
assert tool_version == "1.3.0"
else:
raise AssertionError("Wrong number of repo tars returned...")
def test_reset_on_simple_repository(self):
populator = self.populator
repository = populator.setup_test_data_repo("column_maker")
populator.assert_has_n_installable_revisions(repository, 3)
response = self.api_interactor.post(
"repositories/reset_metadata_on_repository", data={"repository_id": repository.id}
)
api_asserts.assert_status_code_is_ok(response)
populator.assert_has_n_installable_revisions(repository, 3)
def test_reset_with_uninstallable_revisions(self):
populator = self.populator
# setup a repository with 4 revisions but only 3 installable ones due to no version change in a tool
repository = populator.setup_test_data_repo("column_maker_with_download_gaps")
populator.assert_has_n_installable_revisions(repository, 3)
response = self.api_interactor.post(
"repositories/reset_metadata_on_repository", data={"repository_id": repository.id}
)
api_asserts.assert_status_code_is_ok(response)
populator.assert_has_n_installable_revisions(repository, 3)
def test_reset_all(self):
populator = self.populator
repository = populator.setup_test_data_repo("column_maker_with_download_gaps")
populator.assert_has_n_installable_revisions(repository, 3)
# reseting one at a time or resetting everything via the web controllers works...
# reseting all at once via the API does not work - it breaks the repository
response = self.api_interactor.post(
"repositories/reset_metadata_on_repositories",
data={"payload": "can not be empty because bug in controller"},
)
api_asserts.assert_status_code_is_ok(response)
populator.assert_has_n_installable_revisions(repository, 3)
lib/tool_shed/test/test_data/__init__.py
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lib/tool_shed/test/test_data/repos/column_maker/1/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.1.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker/2/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.2.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="50" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker/3/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.3.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="50" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker_with_download_gaps/1/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.1.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="40" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker_with_download_gaps/2/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.2.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="50" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker_with_download_gaps/3/column_maker.xml
+85
View File
@@ -0,0 +1,85 @@
<tool id="Add_a_column1" name="Compute" version="1.2.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="50" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
Modified help text.
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/test/test_data/repos/column_maker_with_download_gaps/4/column_maker.xml
+83
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@@ -0,0 +1,83 @@
<tool id="Add_a_column1" name="Compute" version="1.3.0">
<description>an expression on every row</description>
<command interpreter="python">
column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
</command>
<inputs>
<param name="cond" size="50" type="text" value="c3-c2" label="Add expression"/>
<param format="tabular" name="input" type="data" label="as a new column to" help="Query missing? See TIP below"/>
<param name="round" type="select" label="Round result?">
<option value="no">NO</option>
<option value="yes">YES</option>
</param>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input"/>
</outputs>
<tests>
<test>
<param name="cond" value="c3-c2"/>
<param name="input" value="1.bed"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out1.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="no"/>
<output name="out_file1" file="column_maker_out2.interval"/>
</test>
<test>
<param name="cond" value="c4*1"/>
<param name="input" value="1.interval"/>
<param name="round" value="yes"/>
<output name="out_file1" file="column_maker_out3.interval"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-----
**What it does**
This tool computes an expression for every row of a query and appends the result as a new column (field).
- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
- **c3-c2** will add a length column to the query if **c2** and **c3** are start and end position
-----
**Example**
If this is your input::
chr1 151077881 151077918 2 200 -
chr1 151081985 151082078 3 500 +
computing "c4*c5" will produce::
chr1 151077881 151077918 2 200 - 400.0
chr1 151081985 151082078 3 500 + 1500.0
if, at the same time, "Round result?" is set to **YES** results will look like this::
chr1 151077881 151077918 2 200 - 400
chr1 151081985 151082078 3 500 + 1500
You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
chr1 151077881 151077918 2 200 - True
chr1 151081985 151082078 3 500 + True
or computing "type(c2)==type('') for Input will return::
chr1 151077881 151077918 2 200 - False
chr1 151081985 151082078 3 500 + False
</help>
</tool>
lib/tool_shed/webapp/api/repositories.py
+18 -11
View File
@@ -564,10 +564,17 @@ class RepositoriesController(BaseAPIController):
"""
def handle_repository(trans, rmm, repository, results):
def handle_repository(trans, repository, results):
log.debug(f"Resetting metadata on repository {repository.name}")
try:
rmm.set_repository(repository)
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=self.app,
user=trans.user,
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
repository=repository,
persist=False,
)
rmm.reset_all_metadata_on_repository_in_tool_shed()
rmm_invalid_file_tups = rmm.get_invalid_file_tups()
if rmm_invalid_file_tups:
@@ -587,13 +594,6 @@ class RepositoriesController(BaseAPIController):
results["repository_status"].append(status)
return results
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=self.app,
user=trans.user,
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
persist=False,
)
start_time = strftime("%Y-%m-%d %H:%M:%S")
results = dict(start_time=start_time, repository_status=[], successful_count=0, unsuccessful_count=0)
handled_repository_ids = []
@@ -612,6 +612,13 @@ class RepositoriesController(BaseAPIController):
my_writable = util.asbool(payload.get("my_writable", False))
else:
my_writable = True
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=self.app,
user=trans.user,
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
persist=False,
)
query = rmm.get_query_for_setting_metadata_on_repositories(my_writable=my_writable, order=False)
# First reset metadata on all repositories of type repository_dependency_definition.
for repository in query:
@@ -623,7 +630,7 @@ class RepositoriesController(BaseAPIController):
encoded_ids_to_skip,
)
elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
results = handle_repository(trans, repository, results)
# Now reset metadata on all remaining repositories.
for repository in query:
encoded_id = trans.security.encode_id(repository.id)
@@ -634,7 +641,7 @@ class RepositoriesController(BaseAPIController):
encoded_ids_to_skip,
)
elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
results = handle_repository(trans, rmm, repository, results)
results = handle_repository(trans, repository, results)
stop_time = strftime("%Y-%m-%d %H:%M:%S")
results["stop_time"] = stop_time
return json.dumps(results, sort_keys=True, indent=4)
pyproject.toml
+3
View File
@@ -159,6 +159,9 @@ target-version = "py37"
# E402 module level import not at top of file # TODO, we would like to improve this.
# E501 is line length (delegated to black)
ignore = ["B008", "B9", "E402", "E501"]
exclude = [
"lib/tool_shed/test/test_data/repos"
]
[tool.ruff.isort]
# We are not selecting "I" rules in ruff yet because support for all the isort