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-rw-r--r--qc_app/entry.py7
-rw-r--r--qc_app/templates/index.html8
-rw-r--r--tests/qc_app/test_entry.py97
-rw-r--r--tests/qc_app/test_parse.py6
-rw-r--r--tests/qc_app/test_progress_indication.py24
-rw-r--r--tests/qc_app/test_results_page.py6
-rw-r--r--tests/qc_app/test_uploads_with_zip_files.py49
7 files changed, 91 insertions, 106 deletions
diff --git a/qc_app/entry.py b/qc_app/entry.py
index d23a45a..f2db878 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -100,7 +100,7 @@ def upload_file():
request_errors = errors(request)
if request_errors:
for error in request_errors:
- flash(error, "alert-error error-expr-data")
+ flash(error, "alert-danger error-expr-data")
return redirect(url_for("entry.upload_file"))
filename = secure_filename(request.files["qc_text_file"].filename)
@@ -113,9 +113,8 @@ def upload_file():
zip_errors = zip_file_errors(filepath, upload_dir)
if zip_errors:
for error in zip_errors:
- flash(error, "alert-error error-expr-data")
- return render_template(
- "index.html", species=with_db_connection(species)), 400
+ flash(error, "alert-danger error-expr-data")
+ return redirect(url_for("entry.upload_file"))
return redirect(url_for("parse.parse",
speciesid=request.form["speciesid"],
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 997c1e5..e23dde1 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -26,7 +26,7 @@
<p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
of the methods below can handle.</p>
- <a href={{url_for("upload.rqtl2.select_species")}}
+ <a href="{{url_for('upload.rqtl2.select_species')}}"
title="Upload a zip bundle of R/qtl2 files">
<button class="btn btn-primary">upload R/qtl2 bundle</button></a>
</div>
@@ -60,9 +60,9 @@
</ol>
</div>
- <a href={{url_for("entry.upload_file")}}
+ <a href="{{url_for('entry.upload_file')}}"
title="Upload your expression data"
- class="btn btn-primary">upload Samples/Cases</a>
+ class="btn btn-primary">upload expression data</a>
</div>
<div class="row">
@@ -75,7 +75,7 @@
<p>This section gives you the opportunity to upload any missing samples</p>
</div>
- <a href={{url_for("samples.select_species")}}
+ <a href="{{url_for('samples.select_species')}}"
title="Upload samples/cases/individuals for your data"
class="btn btn-primary">upload Samples/Cases</a>
</div>
diff --git a/tests/qc_app/test_entry.py b/tests/qc_app/test_entry.py
index bfe56ec..0c614a5 100644
--- a/tests/qc_app/test_entry.py
+++ b/tests/qc_app/test_entry.py
@@ -1,80 +1,43 @@
"""Test the entry module in the web-ui"""
import pytest
-from tests.conftest import uploadable_file_object
+@pytest.mark.parametrize(
+ "dataitem,lower",
+ (
+ # expression data UI elements
+ (b'<h2 class="heading">expression data</h2>', True),
+ (b'<a href="/upload"', False),
+ (b'upload expression data</a>', False),
-def test_basic_elements_present_in_index_page(client):
- """
- GIVEN: A flask application testing client
- WHEN: the index page is requested with the "POST" method and no datat
- THEN: verify that the response contains error notifications
- """
- response = client.get("/")
- assert response.status_code == 200
- ## form present
- assert b'<form action="/"' in response.data
- assert b'method="POST"' in response.data
- assert b'enctype="multipart/form-data"' in response.data
- assert b'</form>' in response.data
- ## filetype elements
- assert b'<input type="radio" name="filetype"' in response.data
- assert b'id="filetype_standard_error"' in response.data
- assert b'id="filetype_average"' in response.data
- ## file upload elements
- assert b'<label for="file_upload"' in response.data
- assert b'select file' in response.data
- assert b'<input type="file" name="qc_text_file"' in response.data
- assert b'id="file_upload"' in response.data
- ## submit button
- assert b'<input type="submit" value="upload file"' in response.data
+ # samples/cases data UI elements
+ (b'<h2 class="heading">samples/cases</h2>', True),
+ (b'<a href="/samples/upload/species"', False),
+ (b'upload samples/cases', True),
-def test_post_notifies_errors_if_no_data_is_provided(client):
+ # R/qtl2 data UI elements
+ (b'<h2 class="heading">r/qtl2 bundles</h2>', True),
+ (b'<a href="/upload/rqtl2/select-species"', False),
+ (b'upload r/qtl2 bundle', True)
+ ))
+def test_landing_page_has_sections(client, dataitem, lower):
"""
GIVEN: A flask application testing client
- WHEN: the index page is requested with the "POST" method and with no
- data provided
- THEN: ensure the system responds woit the appropriate error messages
+ WHEN: the index page is requested
+ THEN: ensure the page has the expected UI elements
"""
- response = client.post("/", data={})
- assert response.status_code == 400
- assert b'Invalid file type provided.' in response.data
- assert b'No file was uploaded.' in response.data
+ resp = client.get("/")
+ assert resp.status_code == 200
+ assert dataitem in (resp.data.lower() if lower else resp.data)
-def test_post_with_correct_data(client):
- """
- GIVEN: A flask application testing client
- WHEN: the index page is requested with the "POST" method and with the
- appropriate data provided
- THEN: ensure the system redirects to the parse endpoint with the filename
- and filetype
- """
- response = client.post(
- "/", data={
- "speciesid": 1,
- "filetype": "average",
- "qc_text_file": uploadable_file_object("no_data_errors.tsv")
- })
-
- assert response.status_code == 302
- assert b'Redirecting...' in response.data
- assert (
- b'/parse/parse?speciesid=1&amp;filename=no_data_errors.tsv&amp;filetype=average'
- in response.data)
-@pytest.mark.parametrize(
- "request_data,error_message",
- (({"filetype": "invalid_choice",
- "qc_text_file": uploadable_file_object("no_data_errors.tsv")},
- b'Invalid file type provided.'),
- ({"filetype": "average"}, b'No file was uploaded.'),
- ({"filetype": "standard-error"}, b'No file was uploaded.')))
-def test_post_with_missing_or_invalid_data(client, request_data,error_message):
+def test_landing_page_fails_with_post(client):
"""
GIVEN: A flask application testing client
- WHEN: the index page is requested with the "POST" method and with data
- either being missing or invalid
- THEN: ensure that the system responds with the appropriate error message
+ WHEN: the index page is requested with the "POST" method
+ THEN: ensure the system fails
"""
- response = client.post("/", data=request_data)
- assert response.status_code == 400
- assert error_message in response.data
+ resp = client.post("/")
+ assert resp.status_code == 405
+ assert (
+ b'<h1>405: The method is not allowed for the requested URL.</h1>'
+ in resp.data)
diff --git a/tests/qc_app/test_parse.py b/tests/qc_app/test_parse.py
index 187af76..3915a4d 100644
--- a/tests/qc_app/test_parse.py
+++ b/tests/qc_app/test_parse.py
@@ -30,7 +30,7 @@ def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments]
filename = "no_data_errors.tsv"
filetype = "average"
client.post(
- "/", data={
+ "/upload", data={
"speciesid": speciesid,
"filetype": filetype,
"qc_text_file": uploadable_file_object(filename)})
@@ -81,7 +81,7 @@ def test_parse_with_non_uploaded_file(client, filename, uri, error_msgs):
## Conditionally upload files
if filename and filename != "non_existent.file":
client.post(
- "/", data={
+ "/upload", data={
"filetype": "average",
"qc_text_file": uploadable_file_object(filename)})
# Trigger
@@ -89,7 +89,7 @@ def test_parse_with_non_uploaded_file(client, filename, uri, error_msgs):
## Check that there was exactly one redirect
assert len(resp.history) == 1 and resp.history[0].status_code == 302
## Check that redirect is to home page and is successful
- assert resp.request.path == "/"
+ assert resp.request.path == "/upload"
assert resp.status_code == 200
## Check that error(s) are displayed
for error_msg in error_msgs:
diff --git a/tests/qc_app/test_progress_indication.py b/tests/qc_app/test_progress_indication.py
index 8eba970..14a1050 100644
--- a/tests/qc_app/test_progress_indication.py
+++ b/tests/qc_app/test_progress_indication.py
@@ -15,7 +15,7 @@ def test_with_non_existing_job(client, redis_conn_with_fresh_job): # pylint: dis
assert (
b"No job, with the id '<em>non-existent-job-id</em>' was found!"
in resp.data)
- assert b'<meta http-equiv="refresh" content="5;url=/">' in resp.data
+ assert b'<meta http-equiv="refresh" content="5;url=/upload">' in resp.data
def test_with_unstarted_job(client, job_id, redis_conn_with_fresh_job): # pylint: disable=[unused-argument]
"""
@@ -29,9 +29,9 @@ def test_with_unstarted_job(client, job_id, redis_conn_with_fresh_job): # pylint
resp = client.get(f"/parse/status/{job_id}")
assert b'<meta http-equiv="refresh" content="5">' in resp.data
assert (
- b'<progress id="job_' +
- (f'{job_id}').encode("utf8") +
- b'" value="0.0">0.0</progress>') in resp.data
+ b'<progress id="job_' + (f'{job_id}').encode("utf8") + b'"') in resp.data
+ assert b'value="0.0"' in resp.data
+ assert b'0.0</progress>' in resp.data
def test_with_in_progress_no_error_job(
client, job_id, redis_conn_with_in_progress_job_no_errors): # pylint: disable=[unused-argument]
@@ -48,9 +48,9 @@ def test_with_in_progress_no_error_job(
resp = client.get(f"/parse/status/{job_id}")
assert b'<meta http-equiv="refresh" content="5">' in resp.data
assert (
- b'<progress id="job_' +
- (f'{job_id}').encode("utf8") +
- b'" value="0.32242342">32.242342</progress>') in resp.data
+ b'<progress id="job_' + (f'{job_id}').encode("utf8") + b'"') in resp.data
+ assert b'value="0.32242342"' in resp.data
+ assert b'32.242342</progress>' in resp.data
assert (
b'<span >No errors found so far</span>'
in resp.data)
@@ -72,13 +72,13 @@ def test_with_in_progress_job_with_errors(
resp = client.get(f"/parse/status/{job_id}")
assert b'<meta http-equiv="refresh" content="5">' in resp.data
assert (
- b'<progress id="job_' +
- (f'{job_id}').encode("utf8") +
- b'" value="0.4534245">45.34245</progress>') in resp.data
+ b'<progress id="job_' + (f'{job_id}').encode("utf8") + b'"') in resp.data
+ assert b'value="0.4534245"' in resp.data
+ assert b'45.34245</progress>' in resp.data
assert (
- b'<p class="alert-error">We have found the following errors so far</p>'
+ b'<p class="alert-danger">We have found the following errors so far</p>'
in resp.data)
- assert b'table class="reports-table">' in resp.data
+ assert b'table class="table reports-table">' in resp.data
assert b'Duplicate Header' in resp.data
assert b'Invalid Value' in resp.data
diff --git a/tests/qc_app/test_results_page.py b/tests/qc_app/test_results_page.py
index 57f1531..bb596d7 100644
--- a/tests/qc_app/test_results_page.py
+++ b/tests/qc_app/test_results_page.py
@@ -56,12 +56,12 @@ def test_results_with_completed_job_some_errors(
1. the system redirects to the results page
2. the results page displays the errors found
"""
- resp = client.get(f"/parse/status/{job_id}", follow_redirects=True)
+ resp = client.get(f"/parse/status/{job_id}", follow_redirects=True);import sys;print(resp.data, file=sys.stderr)
assert len(resp.history) == 1
assert (
- b'<p class="alert-error">We found the following errors</p>'
+ b'<p class="alert-danger">We found the following errors</p>'
in resp.data)
- assert b'<table class="reports-table">' in resp.data
+ assert b'<table class="table reports-table">' in resp.data
assert b'Duplicate Header' in resp.data
assert b'<td>Heading &#39;DupHead&#39; is repeated</td>' in resp.data
assert b'Invalid Value' in resp.data
diff --git a/tests/qc_app/test_uploads_with_zip_files.py b/tests/qc_app/test_uploads_with_zip_files.py
index fb101ad..1506cfa 100644
--- a/tests/qc_app/test_uploads_with_zip_files.py
+++ b/tests/qc_app/test_uploads_with_zip_files.py
@@ -8,10 +8,17 @@ def test_upload_zipfile_with_zero_files(client):
THEN: Ensure that the system responds with the appropriate error message and
status code
"""
- resp = client.post("/", data={
- "filetype": "average",
- "qc_text_file": uploadable_file_object("empty.zip")})
- assert resp.status_code == 400
+ resp = client.post("/upload",
+ data={
+ "filetype": "average",
+ "qc_text_file": uploadable_file_object("empty.zip")},
+ follow_redirects=True)
+ assert len(resp.history) == 1
+ redirect = resp.history[0]
+ assert redirect.status_code == 302
+ assert redirect.location == "/upload"
+
+ assert resp.status_code == 200
assert (b"Expected exactly one (1) member file within the uploaded zip "
b"file. Got 0 member files.") in resp.data
@@ -22,10 +29,18 @@ def test_upload_zipfile_with_multiple_files(client):
THEN: Ensure that the system responds with the appropriate error message and
status code
"""
- resp = client.post("/", data={
- "filetype": "average",
- "qc_text_file": uploadable_file_object("multiple_files.zip")})
- assert resp.status_code == 400
+ resp = client.post(
+ "/upload",
+ data={
+ "filetype": "average",
+ "qc_text_file": uploadable_file_object("multiple_files.zip")},
+ follow_redirects=True)
+ assert len(resp.history) == 1
+ redirect = resp.history[0]
+ assert redirect.status_code == 302
+ assert redirect.location == "/upload"
+
+ assert resp.status_code == 200
assert (b"Expected exactly one (1) member file within the uploaded zip "
b"file. Got 3 member files.") in resp.data
@@ -35,7 +50,7 @@ def test_upload_zipfile_with_one_tsv_file(client):
WHEN: A zip file with exactly one valid TSV file is uploaded
THEN: Ensure that the system redirects to the correct next URL
"""
- resp = client.post("/", data={
+ resp = client.post("/upload", data={
"speciesid": 1,
"filetype": "average",
"qc_text_file": uploadable_file_object("average.tsv.zip")})
@@ -53,9 +68,17 @@ def test_upload_zipfile_with_one_non_tsv_file(client):
THEN: Ensure that the system responds with the appropriate error message and
status code
"""
- resp = client.post("/", data={
- "filetype": "average",
- "qc_text_file": uploadable_file_object("non_tsv.zip")})
- assert resp.status_code == 400
+ resp = client.post(
+ "/upload",
+ data={
+ "filetype": "average",
+ "qc_text_file": uploadable_file_object("non_tsv.zip")},
+ follow_redirects=True)
+ assert len(resp.history) == 1
+ redirect = resp.history[0]
+ assert redirect.status_code == 302
+ assert redirect.location == "/upload"
+
+ assert resp.status_code == 200
assert (b"Expected the member text file in the uploaded zip file to "
b"be a tab-separated file.") in resp.data
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 03:47:15 +0000