Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

changeset 2:bd56ac4cca16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 704e7cba33e85648198babefb4d82df66c6709f8
author pimarin
date Fri, 17 Feb 2023 08:04:44 +0000
parents 9ef108e34063
children 5ffc68b4ec04
files data_manager/plasmidfinder_fetch_database.py data_manager/plasmidfinder_fetch_database.xml test-data/plasmidfinder.loc.test test-data/plasmidfinder_test_data_manager_2.1.json test-data/plasmidfinder_test_data_manager_latest.json
diffstat 5 files changed, 9 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/plasmidfinder_fetch_database.py	Wed Feb 15 10:35:15 2023 +0000
+++ b/data_manager/plasmidfinder_fetch_database.py	Fri Feb 17 08:04:44 2023 +0000
@@ -55,7 +55,7 @@
         data_info = dict(value=plasmidfinder_value,
                          name=plasmidfinder_name,
                          date=self._plasmidfinder_date_version,
-                         path=self._db_name)
+                         path="plasmidfinder_database")
         self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]
         return self.plasmidfinder_table_list
 
--- a/data_manager/plasmidfinder_fetch_database.xml	Wed Feb 15 10:35:15 2023 +0000
+++ b/data_manager/plasmidfinder_fetch_database.xml	Fri Feb 17 08:04:44 2023 +0000
@@ -26,7 +26,7 @@
             <param name="database_select" value="latest"/>
             <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
                 <assert_contents>
-                    <has_text_matching expression='\{"data_tables":\ \{\"plasmidfinder_database\"\:\ \[\{\"date\"\:\ \"\d\d\d\d\w\d\d\w\d\d\", \"name\"\: \"\w\w\w\w\w\w\w\w\w\w\w\w\d\d\d\d-\d\d-\d\d\",\ \"path\"\:\ \"plasmidfinder-db\",\ \"value\"\:\ \"plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d\"' />
+                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;:\ \[\{&quot;date&quot;:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;:\ &quot;c18e08c17a59_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;:\ &quot;plasmidfinder_c18e08c17a59_2023-02-15&quot;\}\]\}\}"/>
                 </assert_contents>
             </output>
         </test>
@@ -35,7 +35,7 @@
             <param name="database_select" value="2.1"/>
             <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
                 <assert_contents>
-                    <has_text_matching expression='"data_tables": \{"plasmidfinder_database": \[\{"date": "\d\d\d\\d-\d\d-\d\d", "name": "2\.1_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d"' />
+                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;:\ \[\{&quot;date&quot;:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;:\ &quot;2.1_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;:\ &quot;plasmidfinder_1307168b1ce7_2023-02-15&quot;\}\]\}\}"/>
                 </assert_contents>
             </output>
         </test>
--- a/test-data/plasmidfinder.loc.test	Wed Feb 15 10:35:15 2023 +0000
+++ b/test-data/plasmidfinder.loc.test	Fri Feb 17 08:04:44 2023 +0000
@@ -1,12 +1,4 @@
-plasmidfinder_9002e7282dd0_2022-12-20	9002e7282dd0_2022-12-20	2022-12-20	plasmidfinder-db
-plasmidfinder_1307168b1ce7_2022-12-20	2.1_2022-12-20	2022-12-20	plasmidfinder-db
-plasmidfinder_c18e08c17a59_2023-02-14	c18e08c17a59_2023-02-14	2023-02-14	/tmp/tmpuox8103m/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14
-plasmidfinder_1307168b1ce7_2023-02-14	2.1_2023-02-14	2023-02-14	/tmp/tmpuox8103m/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14
-plasmidfinder_c18e08c17a59_2023-02-14	c18e08c17a59_2023-02-14	2023-02-14	/tmp/tmpn3vh0q7x/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14
-plasmidfinder_1307168b1ce7_2023-02-14	2.1_2023-02-14	2023-02-14	/tmp/tmpn3vh0q7x/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14
-plasmidfinder_c18e08c17a59_2023-02-14	c18e08c17a59_2023-02-14	2023-02-14	/tmp/tmp2rmtj19j/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14
-plasmidfinder_1307168b1ce7_2023-02-14	2.1_2023-02-14	2023-02-14	/tmp/tmp2rmtj19j/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14
-plasmidfinder_c18e08c17a59_2023-02-14	c18e08c17a59_2023-02-14	2023-02-14	/tmp/tmp1py50qws/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14
-plasmidfinder_1307168b1ce7_2023-02-14	2.1_2023-02-14	2023-02-14	/tmp/tmp1py50qws/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14
-plasmidfinder_c18e08c17a59_2023-02-14	c18e08c17a59_2023-02-14	2023-02-14	/tmp/tmpyavtigve/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-14
-plasmidfinder_1307168b1ce7_2023-02-14	2.1_2023-02-14	2023-02-14	/tmp/tmpyavtigve/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-14
+plasmidfinder_c18e08c17a59_2023-02-15	c18e08c17a59_2023-02-15	2023-02-15	plasmidfinder_database
+plasmidfinder_1307168b1ce7_2023-02-15	2.1_2023-02-15	2023-02-15	plasmidfinder_database
+plasmidfinder_c18e08c17a59_2023-02-15	c18e08c17a59_2023-02-15	2023-02-15	/tmp/tmp19jlq5v4/galaxy-dev/tool-data/plasmidfinder-db/c18e08c17a59_2023-02-15
+plasmidfinder_1307168b1ce7_2023-02-15	2.1_2023-02-15	2023-02-15	/tmp/tmp19jlq5v4/galaxy-dev/tool-data/plasmidfinder-db/2.1_2023-02-15
--- a/test-data/plasmidfinder_test_data_manager_2.1.json	Wed Feb 15 10:35:15 2023 +0000
+++ b/test-data/plasmidfinder_test_data_manager_2.1.json	Fri Feb 17 08:04:44 2023 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"plasmidfinder_database": [{"date": "2023-01-27", "name": "2.1_2023-01-27", "path": "plasmidfinder-db", "value": "plasmidfinder_1307168b1ce7_2023-01-27"}]}}
\ No newline at end of file
+{"data_tables": {"plasmidfinder_database": [{"date": "2023-02-15", "name": "2.1_2023-02-15", "path": "plasmidfinder_database", "value": "plasmidfinder_1307168b1ce7_2023-02-15"}]}}
\ No newline at end of file
--- a/test-data/plasmidfinder_test_data_manager_latest.json	Wed Feb 15 10:35:15 2023 +0000
+++ b/test-data/plasmidfinder_test_data_manager_latest.json	Fri Feb 17 08:04:44 2023 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"plasmidfinder_database": [{"date": "2022-12-19", "name": "9002e7282dd0_2022-12-19", "path": "plasmidfinder-db", "value": "plasmidfinder_9002e7282dd0_2022-12-19"}]}}
\ No newline at end of file
+{"data_tables": {"plasmidfinder_database": [{"date": "2023-02-15", "name": "c18e08c17a59_2023-02-15", "path": "plasmidfinder_database", "value": "plasmidfinder_c18e08c17a59_2023-02-15"}]}}
\ No newline at end of file