Merge pull request #43 from CCMS-UCSD/create-or-update-readme

Create a readme from Makefile

Makefile.deploytemplate

@@ -58,3 +58,8 @@ view-dependencies:
 update-dependencies:
 	fab2 -H ${USERNAME}@proteomics2.ucsd.edu --prompt-for-login-password \
 	read-dependencies ${WORKFLOW_INPUT} --rewrite-string yes
+
+#Create README
+deploy-update-readme:
+	fab2 -H ${USERNAME}@proteomics2.ucsd.edu --prompt-for-login-password \
+	release-text ${WORKFLOW_INPUT}

fabfile.py

@@ -12,6 +12,65 @@
 
 workflow_components = ['input.xml', 'binding.xml', 'flow.xml', 'result.xml', 'tool.xml']
 
+@task
+def release_text(c, workflow_name):
+    base_dir = '.'
+    tools = read_all_tools('..')
+    dependencies = output_tool_dependencies(workflow_name, base_dir)
+    makefile = read_makefile(base_dir)
+    readme = 'README.md'
+    previous_readme_lines = []
+    if os.path.isfile(readme):
+        with open(readme) as f:
+            for previous_readme_line in f:
+                previous_readme_lines.append(previous_readme_line)
+                if "CCMS_DEPLOYMENTS_HEADER_BREAK_ELEMENT_CAUTION_ANYTHING_ABOVE_WILL_BE_AUTOGENERATED" in previous_readme_line:
+                    previous_readme_lines = []
+
+    version = makefile["WORKFLOW_VERSION"]
+    name = makefile.get("WORKFLOW_LABEL")
+    if name:
+        name = name[1:-1]
+    else:
+        name = workflow_name
+    description = makefile.get("WORKFLOW_DESCRIPTION")
+
+    update_text = "Last updated: {}.".format(makefile['LAST_UPDATED'])
+
+    dependency_text = []
+    seen = {}
+
+    for (dependency, dependency_version) in dependencies:
+
+        status = "N/V"
+        if dependency not in seen or (dependency in seen and seen[dependency] != dependency_version):
+            if dependency in tools:
+
+                local_version, workflow = tools[dependency]
+
+                if dependency_version == local_version:
+                    status = "({})".format(dependency_version)
+                else:
+                    status = "({}, latest is {})".format(dependency_version, local_version)
+
+                dependency_text.append("* {} {}".format(dependency, status))
+            else:
+                dependency_text.append("* {} (untracked)".format(dependency))
+
+        seen[dependency] = dependency_version
+
+    with open(readme, 'w') as w:
+        w.write('## {}\n\n'.format(name))
+        w.write('#### Version: {}\n\n'.format(version))
+        if description:
+            w.write('#### Description: \n{}\n\n'.format(description[1:-1]))
+        if len(dependency_text) > 0:
+            w.write('#### Dependencies: \n{}\n\n'.format("\n".join(dependency_text)))
+        w.write('_{}_\n\n'.format(update_text))
+        w.write('<data id=CCMS_DEPLOYMENTS_HEADER_BREAK_ELEMENT_CAUTION_ANYTHING_ABOVE_WILL_BE_AUTOGENERATED />\n\n')
+        for previous_readme_line in previous_readme_lines:
+            w.write(previous_readme_line)
+
 @task
 def read_branch(c, workflow_name):
     branch_name = None
@@ -28,8 +87,8 @@ def read_makefile(workflow_name):
     with open(makefile_location) as f:
         for l in f:
             split_line = l.rstrip().split('=')
-            if len(split_line) == 2:
-                params[split_line[0]] = split_line[1]
+            if len(split_line) >= 2:
+                params[split_line[0]] = '='.join(split_line[1:])
     params['LAST_UPDATED'] = time.ctime(os.path.getmtime(makefile_location))
     return params