From edccba84838d43fa694e8cd7623ac633ff8d7e54 Mon Sep 17 00:00:00 2001
From: Nicholas Bokulich <nbokulich@gmail.com>
Date: Thu, 16 Jul 2020 13:39:36 -0700
Subject: [PATCH] MAINT: port Bowtie2Index to q2-types (#16)

---
 ci/recipe/meta.yaml       |  2 ++
 q2_shogun/__init__.py     |  4 ----
 q2_shogun/_formats.py     | 45 ---------------------------------------
 q2_shogun/_shogun.py      |  2 +-
 q2_shogun/_types.py       | 14 ------------
 q2_shogun/plugin_setup.py |  8 +------
 6 files changed, 4 insertions(+), 71 deletions(-)
 delete mode 100644 q2_shogun/_formats.py
 delete mode 100644 q2_shogun/_types.py

diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
index bc8e15d..3da8502 100644
--- a/ci/recipe/meta.yaml
+++ b/ci/recipe/meta.yaml
@@ -19,6 +19,8 @@ requirements:
 
   run:
     - python {{ python }}
+    - qiime2 {{ release }}.*
+    - q2-types {{ release }}.*
     - SHOGUN
     - bowtie2
     - cytoolz
diff --git a/q2_shogun/__init__.py b/q2_shogun/__init__.py
index 14e1301..a16ad2d 100644
--- a/q2_shogun/__init__.py
+++ b/q2_shogun/__init__.py
@@ -7,11 +7,7 @@
 # ----------------------------------------------------------------------------
 
 from ._version import get_versions
-from ._formats import (Bowtie2IndexFileFormat, Bowtie2IndexDirFmt)
-from ._types import Bowtie2Index
 
 
 __version__ = get_versions()['version']
 del get_versions
-
-__all__ = ['Bowtie2IndexFileFormat', 'Bowtie2IndexDirFmt', 'Bowtie2Index']
diff --git a/q2_shogun/_formats.py b/q2_shogun/_formats.py
deleted file mode 100644
index 1cac54a..0000000
--- a/q2_shogun/_formats.py
+++ /dev/null
@@ -1,45 +0,0 @@
-# ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import itertools
-
-from qiime2.plugin import model
-
-
-class Bowtie2IndexFileFormat(model.BinaryFileFormat):
-    def _validate_(self, level):
-        # It's not clear if there is any way to tell if a Bowtie2 index is
-        # correct or not.
-        # bowtie2 does have an inspect method — this inspects at the dir level
-        # not on the file level.
-        # may also want to validate that all files have the same basename
-        pass
-
-
-class Bowtie2IndexDirFmt(model.DirectoryFormat):
-    idx1 = model.File(r'.+(?<!\.rev)\.1\.bt2l?', format=Bowtie2IndexFileFormat)
-    idx2 = model.File(r'.+(?<!\.rev)\.2\.bt2l?', format=Bowtie2IndexFileFormat)
-    ref3 = model.File(r'.+\.3\.bt2l?', format=Bowtie2IndexFileFormat)
-    ref4 = model.File(r'.+\.4\.bt2l?', format=Bowtie2IndexFileFormat)
-    rev1 = model.File(r'.+\.rev\.1\.bt2l?', format=Bowtie2IndexFileFormat)
-    rev2 = model.File(r'.+\.rev\.2\.bt2l?', format=Bowtie2IndexFileFormat)
-
-    def get_basename(self):
-        paths = [str(x.relative_to(self.path)) for x in self.path.iterdir()]
-        prefix = _get_prefix(paths)
-        return prefix[:-1]  # trim trailing '.'
-
-
-# SO: https://stackoverflow.com/a/6718380/579416
-def _get_prefix(strings):
-    def all_same(x):
-        return all(x[0] == y for y in x)
-
-    char_tuples = zip(*strings)
-    prefix_tuples = itertools.takewhile(all_same, char_tuples)
-    return ''.join(x[0] for x in prefix_tuples)
diff --git a/q2_shogun/_shogun.py b/q2_shogun/_shogun.py
index 7c0d166..49aeab4 100644
--- a/q2_shogun/_shogun.py
+++ b/q2_shogun/_shogun.py
@@ -17,7 +17,7 @@
 from qiime2.util import duplicate
 from q2_types.feature_data import DNAFASTAFormat
 
-from q2_shogun._formats import Bowtie2IndexDirFmt
+from q2_types.bowtie2 import Bowtie2IndexDirFmt
 
 
 def _run_command(cmd, verbose=True):
diff --git a/q2_shogun/_types.py b/q2_shogun/_types.py
deleted file mode 100644
index c26b673..0000000
--- a/q2_shogun/_types.py
+++ /dev/null
@@ -1,14 +0,0 @@
-# ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-from qiime2.plugin import SemanticType
-
-# Technically there is a bit more to this, for instance the ref sequences may
-# or may not be present in an index, or may be the only thing in an index,
-# but let's not worry about that just yet.
-Bowtie2Index = SemanticType('Bowtie2Index')
diff --git a/q2_shogun/plugin_setup.py b/q2_shogun/plugin_setup.py
index 8075304..9414ea7 100644
--- a/q2_shogun/plugin_setup.py
+++ b/q2_shogun/plugin_setup.py
@@ -10,9 +10,8 @@
 
 from q2_types.feature_data import FeatureData, Sequence, Taxonomy
 from q2_types.feature_table import FeatureTable, Frequency
+from q2_types.bowtie2 import Bowtie2Index
 
-from ._formats import Bowtie2IndexDirFmt
-from ._types import Bowtie2Index
 from ._shogun import minipipe, nobunaga
 import q2_shogun
 
@@ -30,11 +29,6 @@
     citations=[citations['Hillmann320986']]
 )
 
-plugin.register_views(Bowtie2IndexDirFmt,
-                      citations=[citations['langmead2012fast']])
-plugin.register_semantic_types(Bowtie2Index)
-plugin.register_semantic_type_to_format(Bowtie2Index, Bowtie2IndexDirFmt)
-
 plugin.methods.register_function(
     function=nobunaga,
     inputs={'query': FeatureData[Sequence],