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Fixes and tests for data fetch models.
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@jmchilton
jmchilton committed Sep 13, 2024
1 parent b46bdd4 commit a157d33
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Showing 3 changed files with 202 additions and 1 deletion.
9 changes: 8 additions & 1 deletion lib/galaxy/schema/fetch_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,13 @@ class ExtraFiles(FetchBaseModel):
)


class DatasetHash(Model):
hash_function: Literal["MD5", "SHA-1", "SHA-256", "SHA-512"]
hash_value: str

model_config = ConfigDict(extra="forbid")


class BaseDataElement(FetchBaseModel):
name: Optional[CoercedStringType] = None
dbkey: str = Field("?")
Expand All @@ -115,7 +122,7 @@ class BaseDataElement(FetchBaseModel):
auto_decompress: bool = AutoDecompressField
items_from: Optional[ElementsFromType] = Field(None, alias="elements_from")
collection_type: Optional[str] = None
MD5: Optional[str] = None
hashes: Optional[List[DatasetHash]] = None
description: Optional[str] = None
model_config = ConfigDict(extra="forbid")

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62 changes: 62 additions & 0 deletions lib/galaxy_test/api/test_tools_upload.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import json
import os
import urllib.parse
from base64 import b64encode

import pytest
from tusclient import client
Expand All @@ -25,6 +26,9 @@
)
from ._framework import ApiTestCase

B64_FOR_1_2_3 = b64encode(b"1 2 3").decode("utf-8")
URI_FOR_1_2_3 = f"base64://{B64_FOR_1_2_3}"


class TestToolsUpload(ApiTestCase):
dataset_populator: DatasetPopulator
Expand Down Expand Up @@ -927,6 +931,64 @@ def test_upload_and_validate_valid(self):
terminal_validated_state = self.dataset_populator.validate_dataset_and_wait(history_id, dataset_id)
assert terminal_validated_state == "ok", terminal_validated_state

def test_upload_and_validate_hash_valid(self):
with self.dataset_populator.test_history() as history_id:
destination = {"type": "hdas"}
targets = [
{
"destination": destination,
"items": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [
{"hash_function": "SHA-1", "hash_value": "65e9d53484d28eef5447bc06fe2d754d1090975a"}
],
},
],
}
]
payload = {
"history_id": history_id,
"targets": targets,
"validate_hashes": True,
}
fetch_response = self.dataset_populator.fetch(payload)
self._assert_status_code_is(fetch_response, 200)
outputs = fetch_response.json()["outputs"]
new_dataset = outputs[0]
self.dataset_populator.wait_for_history(history_id, assert_ok=True)

def test_upload_and_validate_hash_invalid(self):
with self.dataset_populator.test_history() as history_id:
destination = {"type": "hdas"}
targets = [
{
"destination": destination,
"items": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [{"hash_function": "SHA-1", "hash_value": "invalidhash"}],
},
],
}
]
payload = {
"history_id": history_id,
"targets": targets,
"validate_hashes": True,
}
fetch_response = self.dataset_populator.fetch(payload, assert_ok=True, wait=False)
self._assert_status_code_is(fetch_response, 200)
outputs = fetch_response.json()["outputs"]
new_dataset = outputs[0]
self.dataset_populator.wait_for_history(history_id, assert_ok=False)
dataset_details = self.dataset_populator.get_history_dataset_details(
history_id, dataset=new_dataset, assert_ok=False
)
assert dataset_details["state"] == "error"

def _velvet_upload(self, history_id, extra_inputs):
payload = self.dataset_populator.upload_payload(
history_id,
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132 changes: 132 additions & 0 deletions test/unit/app/tools/test_data_fetch.py
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Original file line number Diff line number Diff line change
@@ -1,13 +1,17 @@
import json
import os
import tempfile
from base64 import b64encode
from contextlib import contextmanager
from shutil import rmtree
from tempfile import mkdtemp

from galaxy.tools.data_fetch import main
from galaxy.util.unittest_utils import skip_if_github_down

B64_FOR_1_2_3 = b64encode(b"1 2 3").decode("utf-8")
URI_FOR_1_2_3 = f"base64://{B64_FOR_1_2_3}"


def test_simple_path_get():
with _execute_context() as execute_context:
Expand Down Expand Up @@ -55,6 +59,134 @@ def test_simple_uri_get():
assert hda_result["ext"] == "bed"


def test_correct_md5():
with _execute_context() as execute_context:
request = {
"targets": [
{
"destination": {
"type": "hdas",
},
"elements": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [
{
"hash_function": "MD5",
"hash_value": "5ba48b6e5a7c4d4930fda256f411e55b",
}
],
}
],
}
],
"validate_hashes": True,
}
execute_context.execute_request(request)
output = _unnamed_output(execute_context)
hda_result = output["elements"][0]
assert hda_result["state"] == "ok"
assert hda_result["ext"] == "txt"


def test_incorrect_md5():
with _execute_context() as execute_context:
request = {
"targets": [
{
"destination": {
"type": "hdas",
},
"elements": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [
{
"hash_function": "MD5",
"hash_value": "thisisbad",
}
],
}
],
}
],
"validate_hashes": True,
}
execute_context.execute_request(request)
output = _unnamed_output(execute_context)
hda_result = output["elements"][0]
assert (
hda_result["error_message"]
== "Failed to validate upload with [MD5] - expected [thisisbad] got [5ba48b6e5a7c4d4930fda256f411e55b]"
)


def test_correct_sha1():
with _execute_context() as execute_context:
request = {
"targets": [
{
"destination": {
"type": "hdas",
},
"elements": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [
{
"hash_function": "SHA-1",
"hash_value": "65e9d53484d28eef5447bc06fe2d754d1090975a",
}
],
}
],
}
],
"validate_hashes": True,
}
execute_context.execute_request(request)
output = _unnamed_output(execute_context)
hda_result = output["elements"][0]
assert hda_result["state"] == "ok"
assert hda_result["ext"] == "txt"


def test_incorrect_sha1():
with _execute_context() as execute_context:
request = {
"targets": [
{
"destination": {
"type": "hdas",
},
"elements": [
{
"src": "url",
"url": URI_FOR_1_2_3,
"hashes": [
{
"hash_function": "SHA-1",
"hash_value": "thisisbad",
}
],
}
],
}
],
"validate_hashes": True,
}
execute_context.execute_request(request)
output = _unnamed_output(execute_context)
hda_result = output["elements"][0]
assert (
hda_result["error_message"]
== "Failed to validate upload with [SHA-1] - expected [thisisbad] got [65e9d53484d28eef5447bc06fe2d754d1090975a]"
)


@skip_if_github_down
def test_deferred_uri_get():
with _execute_context() as execute_context:
Expand Down

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