add tests

galaxyproject · Dec 3, 2024 · dc403a1 · dc403a1
1 parent 61a42bc
commit dc403a1
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Showing 2 changed files with 62 additions and 3 deletions.
diff --git a/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml b/data_managers/data_manager_dada2/data_manager/dada2_fetcher.xml
@@ -91,6 +91,29 @@
         <data name="out_file" format="data_manager_json" />
     </outputs>
     <tests>
+        <test>
+            <param name="db_cond|db_select" value="silva"/>
+            <param name="db_cond|version_select" value="138.2_toGenus"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Silva version 138.2 to Genus (for short read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="db_cond|db_select" value="silva"/>
+            <param name="db_cond|version_select" value="138.2_toSpecies"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Silva version 138.2 to Species (for long read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="db_cond|db_select" value="silva"/>
+            <param name="db_cond|version_select" value="138"/>
+            <output name="out_file" file="silva138_json"/>
+        </test>
         <test>
             <param name="db_cond|db_select" value="silva"/>
             <param name="db_cond|version_select" value="138"/>
@@ -101,14 +124,50 @@
             <param name="db_cond|version_select" value="132"/>
             <output name="out_file" file="silva132_json"/>
         </test>
+        <test>
+            <param name="db_cond|db_select" value="rdp"/>
+            <param name="db_cond|version_select" value="19_toSpecies"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="RDP trainset 19 to Species (for long read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="db_cond|db_select" value="rdp"/>
+            <param name="db_cond|version_select" value="19_toGenus"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="RDP trainset 19 to Genus (for short read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="db_cond|db_select" value="rdp"/>
             <param name="db_cond|version_select" value="16"/>
             <output name="out_file" file="rdp16_json"/>
         </test>
+        <test>
+            <param name="db_cond|db_select" value="greengenes2"/>
+            <param name="db_cond|version_select" value="2024.09_toGenus"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="GreenGenes2 release 2024.09 to Genus (for short read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="db_cond|db_select" value="greengenes2"/>
+            <param name="db_cond|version_select" value="2024.09_toSpecies"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="GreenGenes2 release 2024.09 to Species (for long read 16S)"/>
+                </assert_contents>
+            </output>
+        </test>
         <test>
             <param name="db_cond|db_select" value="greengenes"/>
-            <param name="db_cond|version_select" value="13.84"/>
+            <param name="db_cond|version_select" value=""/>
             <output name="out_file" file="greengenes13.84_json"/>
         </test>
         <test>

diff --git a/data_managers/data_manager_dada2/data_manager/data_manager.py b/data_managers/data_manager_dada2/data_manager/data_manager.py
@@ -43,8 +43,8 @@
     "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1",
     "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
     "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
-    "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip",
-    "unite_8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip",
+    "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip",
+    "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip",
     "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
     "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1",
     "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1",