adding tgz to artifacts

qiita-spots · Aug 7, 2023 · ce3f1bf · ce3f1bf
1 parent 228f198
commit ce3f1bf
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Showing 2 changed files with 27 additions and 10 deletions.
diff --git a/qp_woltka/tests/test_woltka.py b/qp_woltka/tests/test_woltka.py
@@ -185,7 +185,7 @@ def test_woltka_to_array_rep82(self):
             'wait\n',
             '\n',
             f'cd {out_dir}; tar -cvf alignment.tar *.sam.xz; '
-            'tar zxvf coverages.tgz coverages\n',
+            'tar zxvf coverages.tgz artifact.cov coverages\n',
             'fi\n',
             f'finish_woltka {url} {job_id} {out_dir}\n',
             'date\n']
@@ -314,7 +314,7 @@ def test_woltka_to_array_wol(self):
             'wait\n',
             '\n',
             f'cd {out_dir}; tar -cvf alignment.tar *.sam.xz; '
-            'tar zxvf coverages.tgz coverages\n',
+            'tar zxvf coverages.tgz artifact.cov coverages\n',
             'fi\n',
             f'finish_woltka {url} {job_id} {out_dir}\n',
             'date\n']

diff --git a/qp_woltka/woltka.py b/qp_woltka/woltka.py
@@ -5,9 +5,10 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from os import environ
+from os import environ, mkdir
 from os.path import join, basename, exists, dirname
 from glob import glob
+from shutil import copy2
 
 from qiita_client import ArtifactInfo
 
@@ -141,7 +142,7 @@ def woltka_to_array(files, output, database_bowtie2, prep, url, name):
              "wait",
              '\n'.join(fcmds),
              f'cd {output}; tar -cvf alignment.tar *.sam.xz; '
-             'tar zxvf coverages.tgz coverages\n'
+             'tar zxvf coverages.tgz artifact.cov coverages\n'
              'fi',
              f'finish_woltka {url} {name} {output}\n'
              "date"]  # end time
@@ -248,13 +249,22 @@ def woltka(qclient, job_id, parameters, out_dir):
     """
     db_files = _process_database_files(parameters['Database'])
 
+    def _coverage_copy(dest):
+        fp_coverages = f'{out_dir}/coverages.tgz'
+        mkdir(dest)
+        dest = f'{dest}/coverages.tgz'
+        copy2(fp_coverages, dest)
+
+        return dest
+
     errors = []
     ainfo = []
     fp_biom = f'{out_dir}/free.biom'
     fp_alng = f'{out_dir}/alignment.tar'
     if exists(fp_biom) and exists(fp_alng):
         ainfo = [ArtifactInfo('Alignment Profile', 'BIOM', [
-            (fp_biom, 'biom'), (fp_alng, 'log')])]
+            (fp_biom, 'biom'), (fp_alng, 'log'),
+            (_coverage_copy(f'{out_dir}/alignment/'), 'plan_text')])]
     else:
         ainfo = []
         errors.append('Missing files from the "Alignment Profile"; please '
@@ -263,7 +273,8 @@ def woltka(qclient, job_id, parameters, out_dir):
     fp_biom = f'{out_dir}/none.biom'
     if exists(fp_biom):
         ainfo.append(ArtifactInfo('Per genome Predictions', 'BIOM', [
-            (fp_biom, 'biom')]))
+            (fp_biom, 'biom'),
+            (_coverage_copy(f'{out_dir}/none/'), 'plan_text')]))
     else:
         errors.append('Table none/per-genome was not created, please contact '
                       'qiita.help@gmail.com for more information')
@@ -272,7 +283,8 @@ def woltka(qclient, job_id, parameters, out_dir):
         fp_biom = f'{out_dir}/per-gene.biom'
         if exists(fp_biom):
             ainfo.append(ArtifactInfo('Per gene Predictions', 'BIOM', [
-                (fp_biom, 'biom')]))
+                (fp_biom, 'biom'),
+                (_coverage_copy(f'{out_dir}/per_gene/'), 'plan_text')]))
         else:
             errors.append('Table per-gene was not created, please contact '
                           'qiita.help@gmail.com for more information')
@@ -283,7 +295,8 @@ def woltka(qclient, job_id, parameters, out_dir):
             fp_biom = f'{out_dir}/ko.biom'
             if exists(fp_biom):
                 ainfo.append(ArtifactInfo('KEGG Ontology (KO)', 'BIOM', [
-                    (fp_biom, 'biom')]))
+                    (fp_biom, 'biom'),
+                    (_coverage_copy(f'{out_dir}/ko/'), 'plan_text')]))
             else:
                 errors.append('Table KEGG Ontology was not created, please '
                               'contact qiita.help@gmail.com for more '
@@ -293,7 +306,8 @@ def woltka(qclient, job_id, parameters, out_dir):
             fp_biom = f'{out_dir}/ec.biom'
             if exists(fp_biom):
                 ainfo.append(ArtifactInfo('KEGG Enzyme (EC)', 'BIOM', [
-                    (fp_biom, 'biom')]))
+                    (fp_biom, 'biom'),
+                    (_coverage_copy(f'{out_dir}/ec/'), 'plan_text')]))
             else:
                 errors.append('Table KEGG Enzyme was not created, please '
                               'contact qiita.help@gmail.com for more '
@@ -305,7 +319,10 @@ def woltka(qclient, job_id, parameters, out_dir):
             fp_biom = f'{out_dir}/pathway.biom'
             if exists(fp_biom):
                 ainfo.append(
-                    ArtifactInfo('KEGG Pathway', 'BIOM', [(fp_biom, 'biom')]))
+                    ArtifactInfo('KEGG Pathway', 'BIOM', [
+                        (fp_biom, 'biom'),
+                        (_coverage_copy(f'{out_dir}/pathway/'),
+                         'plan_text')]))
             else:
                 errors.append('Table KEGG Pathway was not created, please '
                               'contact qiita.help@gmail.com for more '