Merge pull request #23 from pepkit/dev

version 0.8.1 bugfix release
pepkit · Apr 2, 2018 · 67e24d1 · 67e24d1
2 parents dbfb0d9 + 13028d0
commit 67e24d1
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Showing 6 changed files with 35 additions and 18 deletions.
diff --git a/.gitignore b/.gitignore
@@ -66,6 +66,7 @@ open_pipelines/
 # pytest-related
 .cache/
 .coverage
+.pytest_cache
 
 # Reserved files for comparison
 *RESERVE*

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Detailed instructions are in the [Read the Docs documentation](http://looper.rea
 
 
 ```
-pip install --user looper
+pip install --user https://github.com/pepkit/looper/zipball/master
 export PATH=$PATH:~/.local/bin
 ```
 

diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -1,12 +1,16 @@
 Changelog
 ******************************
 
-- **v0.8.1** (*2018-02-27*):
+- **v0.8.1** (*2018-04-02*):
 
   - Changed
 
     - Minor documentation and packaging updates for first Pypi release.
 
+    - Fix a bug that incorrectly mapped protocols due to case sensitive issues
+
+    - Fix a bug with ``report_figure`` that made it output pandas code
+
 
 - **v0.8.0** (*2018-01-19*):
 

diff --git a/looper/looper.py b/looper/looper.py
@@ -565,7 +565,7 @@ def __call__(self):
 
         columns = []
         stats = []
-        figs = []
+        figs = _pd.DataFrame()
 
         for sample in self.prj.samples:
             _LOGGER.info(self.counter.show(sample.sample_name, sample.protocol))
@@ -612,14 +612,8 @@ def __call__(self):
 
             t = _pd.read_table(
                 figs_file, header=None, names=['key', 'value', 'pl'])
-
-            t.drop_duplicates(subset=['key', 'pl'], keep='last', inplace=True)
-
-            t.loc[:, 'plkey'] = t['pl'] + ":" + t['key']
-            dupes = t.duplicated(subset=['key'], keep=False)
-            t.loc[dupes, 'key'] = t.loc[dupes, 'plkey']
-
-            figs.append(t)
+            t['sample_name'] = sample.name
+            figs = figs.append(t, ignore_index=True)
 
         # all samples are parsed. Produce file.
 
@@ -646,11 +640,22 @@ def __call__(self):
             root=os.path.join(self.prj.metadata.output_dir, self.prj.name))
 
         figs_html_file = open(figs_html_path, 'w')
-
-        img_code = "<h1>{key}</h1><a href='{path}'><img src='{path}'></a>\n"
-        for fig in figs:
-            figs_html_file.write(img_code.format(
-                key=str(fig['key']), path=fig['value']))
+        html_header = "<html><h1>Summary of sample figures for project {}</h1>\n".format(self.prj.name)
+        figs_html_file.write(html_header)
+        sample_img_header = "<h3>{sample_name}</h3>\n"
+        sample_img_code = "<p><a href='{path}'><img src='{path}'>{key}</a></p>\n"
+
+        figs.drop_duplicates(keep='last', inplace=True)
+        for sample_name in figs['sample_name'].drop_duplicates().sort_values():
+            f = figs[figs['sample_name'] == sample_name]
+            figs_html_file.write(sample_img_header.format(sample_name=sample_name))
+
+            for i, row in f.iterrows():
+                figs_html_file.write(sample_img_code.format(
+                    key=str(row['key']), path=row['value']))
+
+        html_footer = "</html>"
+        figs_html_file.write(html_footer)
 
         figs_html_file.close()
         _LOGGER.info(

diff --git a/looper/pipeline_interface.py b/looper/pipeline_interface.py
@@ -74,7 +74,9 @@ def __init__(self, config):
                 pipe_data["path"] = pipe_path
 
         self.pipe_iface = self.pipe_iface_config["pipelines"]
-        self.protomap = self.pipe_iface_config["protocol_mapping"]
+        self.protomap = {utils.alpha_cased(proto): pipekey
+                         for proto, pipekey in
+                         self.pipe_iface_config["protocol_mapping"].items()}
 
 
     def __getitem__(self, item):

diff --git a/looper/project.py b/looper/project.py
@@ -95,6 +95,8 @@ def build_submission_bundles(self, protocol, priority=True):
             those already mapped and those not yet mapped
         """
 
+        protocol = alpha_cased(protocol)
+
         if not priority:
             raise NotImplementedError(
                 "Currently, only prioritized protocol mapping is supported "
@@ -110,11 +112,12 @@ def build_submission_bundles(self, protocol, priority=True):
                 self.interfaces_by_protocol[protocol]
         except KeyError:
             # Messaging can be done by the caller.
+            _LOGGER.debug("No interface for protocol: %s", protocol)
             return []
 
         job_submission_bundles = []
         pipeline_keys_used = set()
-        _LOGGER.debug("Building pipelines for {} PIs...".
+        _LOGGER.debug("Building pipelines for {} interface(s)...".
                       format(len(pipeline_interfaces)))
 
         bundle_by_strict_pipe_key = {}
@@ -131,6 +134,8 @@ def build_submission_bundles(self, protocol, priority=True):
 
             this_protocol_pipelines = pipe_iface.fetch_pipelines(protocol)
             if not this_protocol_pipelines:
+                _LOGGER.debug("No pipelines; available: {}".format(
+                        ", ".join(pipe_iface.protomap.keys())))
                 continue
 
             # TODO: update once dependency-encoding logic is in place.