Resolve "Documentation In-Depth"

Closes #28 (closed)

chipathlon/generators/align_generator.py

@@ -2,26 +2,26 @@ from module_generator import ModuleGenerator
 from chipathlon.result import Result
 
 class AlignGenerator(ModuleGenerator):
+    """
+    :param dax: The workflow graph object
+    :type dax: Peagasus.DAX3.ADAG
+    :param master_jobs: The dictionary mapping job name -> pegasus job object.
+    :type master_jobs: dict
+    :param master_files: The dictionary mapping file name -> pegasus file object.
+    :type master_files: dict
+    :param mdb: A MongoDB database class for fetching sample meta data.
+    :type mdb: :py:class:`~chipathlon.db.MongoDB`
+    :param workflow_module: The actual module being used.
+    :type workflow_module: :py:class:`~chipathlon.workflow_module.WorkflowModule`
+    :param workflow_jobs: Dictionary mapping workflow_job name -> workflow_job instance
+    :type workflow_jobs: dict
+    :param base_path: Base location of the workflow, used to save metadata files.
+    :type base_path: str
+    :param debug: If true, prints out params for each job & module.
+    :type debug: bool
+    """
 
     def __init__(self, dax, master_jobs, master_files, mdb, workflow_module, workflow_jobs, base_path, debug=False):
-        """
-        :param dax: The workflow graph object
-        :type dax: Peagasus.DAX3.ADAG
-        :param master_jobs: The dictionary mapping job name -> pegasus job object.
-        :type master_jobs: dict
-        :param master_files: The dictionary mapping file name -> pegasus file object.
-        :type master_files: dict
-        :param mdb: A MongoDB database class for fetching sample meta data.
-        :type mdb: :py:class:chipathlon.db.MongoDB
-        :param workflow_module: The actual module being used.
-        :type workflow_module: chipathlon.workflow_module.WorkflowModule
-        :param workflow_jobs: Dictionary mapping workflow_job name -> workflow_job instance
-        :type workflow_jobs: dict
-        :param base_path: Base location of the workflow, used to save metadata files.
-        :type base_path: str
-        :param debug: If true, prints out params for each job & module.
-        :type debug: bool
-        """
         super(AlignGenerator, self).__init__(dax, master_jobs, master_files, mdb, workflow_module, workflow_jobs, base_path, debug)
         self.generate_calls = {
             "bwa": {
@@ -40,7 +40,7 @@ class AlignGenerator(ModuleGenerator):
     def _bwa_init(self, run):
         """
         :param run: The run to load genome files for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
 
         Loads required genome files for bwa in to the dictionary structure
         expected by the actual workflow module.  Specifically, this maps:
@@ -60,7 +60,7 @@ class AlignGenerator(ModuleGenerator):
     def _bowtie2_init(self, run):
         """
         :param run: The run to load genome files for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
 
         Loads required genome files for bowtie2 in to the dictionary structure
         expected by the actual workflow module.  Specifically, this maps:
@@ -82,9 +82,9 @@ class AlignGenerator(ModuleGenerator):
     def _bwa_single(self, run, result):
         """
         :param run: The run to generate jobs for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The result to generate jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
 
         Creates inputs, additional_inputs, and outputs for bwa alignment
         jobs with single end reads.  Only the first file in prev_results will
@@ -99,9 +99,9 @@ class AlignGenerator(ModuleGenerator):
     def _bwa_paired(self, run, result):
         """
         :param run: The run to generate jobs for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The result to generate jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
 
         Creates inputs, additional_inputs, and outputs for bwa alignment
         jobs with paired end reads.
@@ -116,9 +116,9 @@ class AlignGenerator(ModuleGenerator):
     def _bowtie2_single(self, run, result):
         """
         :param run: The run to generate jobs for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The result to generate jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
 
         Creates inputs, additional_inputs, and outputs for bowtie2 alignment
         jobs with single end reads.  Only the first file in prev_results will
@@ -134,9 +134,9 @@ class AlignGenerator(ModuleGenerator):
     def _bowtie2_paired(self, run, result):
         """
         :param run: The run to generate jobs for
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The result to generate jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
 
         Creates inputs, additional_inputs, and outputs for bowtie2 alignment
         jobs with paired end reads.
@@ -178,7 +178,7 @@ class AlignGenerator(ModuleGenerator):
     def create_final_results(self, run):
         """
         :param run: The target run to generate jobs for.
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         """
         control_samples = run.get_samples("control")
         signal_samples = run.get_samples("signal")
@@ -214,9 +214,9 @@ class AlignGenerator(ModuleGenerator):
     def find_prev_results(self, run, result):
         """
         :param run: The target run to generate jobs for.
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The target result to create jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
         """
         download_samples = run.get_results("download", "encode.fastq.gz")
         prev_results = []
@@ -231,9 +231,9 @@ class AlignGenerator(ModuleGenerator):
     def parse_result(self, run, result):
         """
         :param run: The target run to generate jobs for.
-        :type run: :py:class:chipathlon.run.Run
+        :type run: :py:class:`~chipathlon.run.Run`
         :param result: The target result to create jobs for.
-        :type result: :py:class:chipathlon.result.Result
+        :type result: :py:class:`~chipathlon.result.Result`
         """
         prev_results = self.get_prev_results(run, result)
         markers, inputs, additional_inputs = self.generate_calls[run.genome.tool][len(prev_results)](run, result)