test: add org param tests

Log.out

@@ -0,0 +1,39 @@
+STAR version=2.7.10b
+STAR compilation time,server,dir=2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
+STAR git: On branch master ; commit c6f8efc2c7043ef83bf8b0d9bed36bbb6b9b1133 ; diff files: CHANGES.md 
+##### Command Line:
+STAR --runMode genomeGenerate --genomeSAindexNbases 5 --genomeChrBinNbits 18 --runThreadN 1 --genomeDir /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index --genomeFastaFiles /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/invalid
+##### Initial USER parameters from Command Line:
+###### All USER parameters from Command Line:
+runMode                       genomeGenerate        ~RE-DEFINED
+genomeSAindexNbases           5     ~RE-DEFINED
+genomeChrBinNbits             18     ~RE-DEFINED
+runThreadN                    1     ~RE-DEFINED
+genomeDir                     /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index     ~RE-DEFINED
+genomeFastaFiles              /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/invalid        ~RE-DEFINED
+##### Finished reading parameters from all sources
+
+##### Final user re-defined parameters-----------------:
+runMode                           genomeGenerate   
+runThreadN                        1
+genomeDir                         /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index
+genomeFastaFiles                  /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/invalid   
+genomeSAindexNbases               5
+genomeChrBinNbits                 18
+
+-------------------------------
+##### Final effective command line:
+STAR   --runMode genomeGenerate      --runThreadN 1   --genomeDir /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index   --genomeFastaFiles /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/invalid      --genomeSAindexNbases 5   --genomeChrBinNbits 18
+----------------------------------------
+
+Number of fastq files for each mate = 1
+ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:  3000 0.99 10
+Finished loading and checking parameters
+--genomeDir directory exists and will be overwritten: /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index/
+!!!!! WARNING: Could not move Log.out file from ./Log.out into /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/index/Log.out. Will keep ./Log.out
+
+Oct 31 16:40:53 ... starting to generate Genome files
+
+EXITING because of INPUT ERROR: could not open genomeFastaFile: /scratch/pytest-of-balajt0000/pytest-29/test_create_star_index_star_pr0/invalid
+
+Oct 31 16:40:53 ...... FATAL ERROR, exiting

tests/test_get_library_source.py

@@ -264,6 +264,52 @@ def test_evaluate_min_freq_ratio(self, tmpdir):
             file_2=Source()
         )
 
+    def test_evaluate_org_id_not_none(self):
+        """Test when self.org_id is not None."""
+        CONFIG.args.org_id = 7227  # An example taxon ID
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        test_instance = GetLibSource(config=CONFIG)
+        result = test_instance.evaluate()
+
+        assert result.file_1.taxon_id == 7227
+        assert result.file_1.short_name == "dmelanogaster"
+
+    def test_evaluate_org_id_none_with_path_2(self, tmpdir, monkeypatch):
+        """Test when self.org_id is None and self.paths[1] is not None."""
+        CONFIG.args.org_id = None
+        CONFIG.args.path_1_processed = FILE_MATE_1
+        CONFIG.args.path_2_processed = FILE_MATE_2
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        CONFIG.args.tmp_dir = tmpdir
+        CONFIG.args.out_dir = tmpdir
+        test_instance = GetLibSource(config=CONFIG)
+
+        # Mock the get_source method to return a specific result
+        monkeypatch.setattr(
+            'htsinfer.get_library_source.GetLibSource.get_source',
+            lambda *args, **kwargs: SOURCE_HUMAN,
+        )
+
+        result = test_instance.evaluate()
+
+        assert result.file_2.taxon_id == SOURCE_HUMAN.taxon_id
+        assert result.file_2.short_name == SOURCE_HUMAN.short_name
+
+    def test_evaluate_org_id_not_none_with_path_2(self, tmpdir):
+        """Test when self.org_id is not None and self.paths[1] is not None."""
+        CONFIG.args.org_id = 7227
+        CONFIG.args.path_1_processed = FILE_MATE_1
+        CONFIG.args.path_2_processed = FILE_MATE_2
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        CONFIG.args.tmp_dir = tmpdir
+        CONFIG.args.out_dir = tmpdir
+        test_instance = GetLibSource(config=CONFIG)
+
+        result = test_instance.evaluate()
+
+        assert result.file_2.taxon_id == 7227
+        assert result.file_2.short_name == "dmelanogaster"
+
     def test_create_kallisto_index_problem(self, tmpdir):
         """Pass invalid file as transcripts.fasta file
         to simulate KallistoProblem."""
@@ -276,3 +322,36 @@ def test_create_kallisto_index_problem(self, tmpdir):
         test_instance = GetLibSource(config=CONFIG)
         with pytest.raises(KallistoProblem):
             test_instance.create_kallisto_index()
+
+    def test_get_organism_name_found(self):
+        """Test the function when the taxon_id
+        is found in the organism dictionary."""
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        test_instance = GetLibSource(config=CONFIG)
+        taxon_id = 7227
+        result = test_instance.get_organism_name(
+            taxon_id, CONFIG.args.t_file_processed
+        )
+        assert result == "dmelanogaster"
+
+    def test_get_organism_name_not_found(self):
+        """Test the function when the taxon_id
+        is not found in the organism dictionary."""
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        test_instance = GetLibSource(config=CONFIG)
+        taxon_id = 12345  # A tax ID that doesn't exist in transcripts
+        result = test_instance.get_organism_name(
+            taxon_id, CONFIG.args.t_file_processed
+        )
+        assert result is None
+
+    def test_get_organism_name_file_problem(self):
+        """Test the function when there's a
+        file problem while processing the FASTA file."""
+        CONFIG.args.t_file_processed = FILE_DUMMY
+        test_instance = GetLibSource(config=CONFIG)
+        taxon_id = 7227
+        with pytest.raises(FileProblem):
+            test_instance.get_organism_name(
+                taxon_id, CONFIG.args.t_file_processed
+            )