Merge in the library list, detail, and results downloading feature from

[htsworkflow.git] / htsworkflow / frontend / samples / results.py

diff --git a/htsworkflow/frontend/samples/results.py b/htsworkflow/frontend/samples/results.py
new file mode 100644 (file)
index 0000000..d7cb77e
--- /dev/null
+++ b/htsworkflow/frontend/samples/results.py
@@ -0,0 +1,134 @@
+from htsworkflow.frontend import settings
+
+import glob
+import os
+import re
+
+s_paren = re.compile("^\w+")
+
+def get_flowcell_result_dict(flowcell_id):
+    """
+    returns a dictionary following the following pattern for
+    a given flowcell_id:
+    
+     
+    d['C1-33']['summary']           # Summary.htm file path
+    d['C1-33']['eland_results'][5]  # C1-33 lane 5 file eland results file path
+    d['C1-33']['run_xml']           # run_*.xml file path
+    d['C1-33']['scores']            # scores.tar.gz file path
+    """
+    flowcell_id = flowcell_id.strip()
+    
+    d = {}
+    
+    ################################
+    # Flowcell Directory
+    fc_dir = glob.glob(os.path.join(settings.RESULT_HOME_DIR, flowcell_id))
+    
+    # Not found
+    if len(fc_dir) == 0:
+        return None
+    
+    # No duplicates!
+    assert len(fc_dir) <= 1
+    
+    # Found fc dir
+    fc_dir = fc_dir[0]
+    
+    ################################
+    # C#-## dirs
+    c_dir_list = glob.glob(os.path.join(fc_dir, 'C*'))
+    
+    # Not found
+    if len(c_dir_list) == 0:
+        return d
+    
+    for c_dir_path in c_dir_list:
+        summary_file = glob.glob(os.path.join(c_dir_path, 'Summary.htm'))
+        pathdir, c_dir = os.path.split(c_dir_path)
+        
+        # Create sub-dictionary
+        d[c_dir] = {}
+        
+        
+        ###############################
+        # Summary.htm file
+        
+        # Not found
+        if len(summary_file) == 0:
+            d[c_dir]['summary'] = None
+            
+        # Found
+        else:
+            # No duplicates!
+            assert len(summary_file) == 1
+            
+            summary_file = summary_file[0]
+            d[c_dir]['summary'] = summary_file
+            
+        ###############################
+        # Result files
+        
+        d[c_dir]['eland_results'] = {}
+        
+        result_filepaths = glob.glob(os.path.join(c_dir_path, 's_*_eland_result.txt*'))
+        
+        for filepath in result_filepaths:
+            
+            junk, result_name = os.path.split(filepath)
+            
+            #lanes 1-8, single digit, therefore s_#; # == index 2
+            lane = int(result_name[2])
+            d[c_dir]['eland_results'][lane] = filepath
+            
+        ###############################
+        # run*.xml file
+        run_xml_filepath = glob.glob(os.path.join(c_dir_path, 'run_*.xml'))
+        
+        if len(run_xml_filepath) == 0:
+            d[c_dir]['run_xml'] = None
+        else:
+            # No duplicates
+            assert len(run_xml_filepath) == 1
+            
+            d[c_dir]['run_xml'] = run_xml_filepath[0]
+            
+        ###############################
+        # scores.tar.gz
+        scores_filepath = glob.glob(os.path.join(c_dir_path, 'scores*'))
+        
+        if len(scores_filepath) == 0:
+            d[c_dir]['scores'] = None
+        else:
+            # No duplicates
+            assert len(scores_filepath) == 1
+            
+            d[c_dir]['scores'] = scores_filepath[0]
+        
+    return d
+
+    
+def cn_mTobp(cn_m):
+    """
+    Converts CN-M (i.e. C1-33, C1-26, C4-28) cycle information into
+    number of base pairs.
+    """
+    pass
+
+
+def parse_flowcell_id(flowcell_id):
+    """
+    Return flowcell id and any status encoded in the id
+  
+    We stored the status information in the flowcell id name.
+    this was dumb, but database schemas are hard to update.
+    """
+    fields = flowcell_id.split()
+    fcid = None
+    status = None
+    if len(fields) > 0:
+        fcid = fields[0]
+    if len(fields) > 1:
+        status = fields[1]
+    return fcid, status
+