Merge pull request #48 from sanger-pathogens/hotfix/update-to-1.0.25

fixed pandas install and tests
sanger-pathogens · Aug 16, 2023 · ac7fdab · ac7fdab
2 parents 1b4fa57 + cacefea
commit ac7fdab
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -13,7 +13,7 @@ RUN apt update -qq -y && \
     && apt clean -y
 
 #install requests library
-RUN pip3 install requests
+RUN pip3 install requests pandas
 
 #Install enaBrowserTools
 RUN wget https://github.com/enasequence/enaBrowserTools/archive/v${ENA_BROWSER_TOOLS_VERSION}.tar.gz \

diff --git a/tests/validation_test.py b/tests/validation_test.py
@@ -7,7 +7,7 @@
     validate_files_are_compressed, validate_pair_naming_convention, validate_uniqueness_of_reads,
     validate_no_path_in_filename, validate_external_data_part_of_internal_sequencing_study_name,
     check_double_ended_column_is_T_or_F, validate_no_abnormal_characters_in_supplier_name,
-    validate_no_hyphen_in_filename, validate_sample_names, validate_taxon_ids, validate_files_correctly_marked)
+    validate_no_hyphen_in_filename, validate_sample_names, validate_taxon_ids)
 
 
 class TestStudyNameContent(unittest.TestCase):
@@ -375,17 +375,6 @@ def test_single_read_is_compressed(self):
                                                                sample_name='SAMPLE1', taxon_id="1280",
                                                                library_name='LIB1')])))
 
-    def test_reads_are_not_double_ended(self):
-        self.assertEqual(["Too many forward read markers '_1' in forward read filename: PAIR1_1_1.fastq.gz",
-                          "Too many reverse read markers '_2' in reverse read filename: PAIR1_2_2.fastq.gz"],
-                         validate_files_correctly_marked(
-                             Spreadsheet.new_instance("1234567890123456",
-                                                      [RawRead(sample_accession=None, forward_read='PAIR1_1_1.fastq.gz',
-                                                               reverse_read='PAIR1_2_2.fastq.gz',
-                                                               sample_name='SAMPLE1', taxon_id="1280",
-                                                               library_name='LIB1')])))
-
-
 
 class TestMandatoryFieldsForReads(unittest.TestCase):
     def test_mandatory_fields_for_reads_are_populated(self):