fixed broken link

src/software/automation_pipeline_developer.md

@@ -7,7 +7,7 @@ lang: en-US
 
 The Ephys/Imaging Automation Pipeline in BRAINCoGS main goals are:
 
-+ Automate spike sorting and imaging segmentation for all recordings 
++ Automate spike sorting and imaging segmentation for all recordings
 + Centralize/Standardize paths for Recording Data Storage
 + Unify & Register Ephys/Imaging Processing
 + Store processed data in BRAINCoGS Database (DJ)
@@ -16,7 +16,7 @@ To accomplish this we developed three tools:
 
 + Ephys/Imaging Automation GUI (<a href="https://github.com/BrainCOGS/RecordingProcessJobGUI">RecordingProcessJobGUI</a>)
 + Recording Workflow management (<a href="https://github.com/BrainCOGS/U19-pipeline_python/tree/master/u19_pipeline/automatic_job">Automatic_job directory in U19-pipeline_python </a>)
-+ Collab reposiotries to handle Ephys/Imaging Processing (<a href="https://github.com/BrainCOGS/BrainCogsEphysSorters">BrainCogsEphysSorters </a> and <a href="https://github.com/BrainCOGS/BrainCogsImagingSegmentation">BrainCogsImagingSegmentation </a>) 
++ Collab reposiotries to handle Ephys/Imaging Processing (<a href="https://github.com/BrainCOGS/BrainCogsEphysSorters">BrainCogsEphysSorters </a> and <a href="https://github.com/BrainCOGS/BrainCogsImagingSegmentation">BrainCogsImagingSegmentation </a>)
 
 
  ## Ephys/Imaging Automation GUI
@@ -33,24 +33,24 @@ Workflow management is composed mainly by two classes that handles recordings an
  + Ephys recordings are composed by one or many independent probe electrophysiology recordings. Each probe recording correspond to a job in the workflow management
  + Calcium imaging recordings are composed by one or many independent field of views image stacks. Each field of view image stack correspond to a job in the workflow management.
 
-The class that manages workflow at the recording level is (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>)
+The class that manages workflow at the recording level is (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>)
 
  <figure>
 <img src='./assets/images/automation_pipeline_developer/workflow_manager_recordings.png'>
 <center><figcaption>Workflow manager diagam at the recording level</figcaption></center>
  </figure>
 
-### Main functions and variables in recording workflow manager 
+### Main functions and variables in recording workflow manager
 
 + **recording_status_dict** in (<a href="https://https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/params_config.py">Params Config file</a>): This dictionary defines status definitions and corresponding functions to execute.
 + **pipeline_handler_main** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main function in recording workflow
 1. Executes corresponding functions based in status.
 2. Executed every 30 minutes to check for new recordings to be handled.
 3. Send notifications for processed and failed functions.
 +  **exception_handler** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Python decorator for error handling.
-+  **modality_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main ingestion function from recording to recording_process tables. There are subcalls depending on modality of recording (ephys or imaging). 
++  **modality_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main ingestion function from recording to recording_process tables. There are subcalls depending on modality of recording (ephys or imaging).
 
-#### Imaging preingestion main steps: 
+#### Imaging preingestion main steps:
 
 +  **imaging_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Ingestion to recording_process table for an imaging recording. Get all FOVs (TIFF stacks) for the recording and assign a new job for each one with corresponding parameters fetched from selection done in automation GUI.
 **AcquiredTiff populate function** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/imaging_pipeline.py">Imaging pipeline</a>): Auxiliar script to call **populate_Imaging_AcquiredTiff** script in MATLAB.
@@ -66,7 +66,7 @@ The class that manages workflow at the recording level is (<a href="https://gith
 <center><figcaption>ERD for imaging pipeline at the recording level</figcaption></center>
  </figure>
 
-#### Ephys preingestion main steps: 
+#### Ephys preingestion main steps:
 
  +  **electrophysiology_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Ingestion to recording_process table for an ephys recording. Get all probes for the recording and assign a new job for each one with corresponding parameters fetched from selection done in automation GUI.
  1. Ingest **ephys_pipeline.EphysPipelineSession** table
@@ -81,7 +81,7 @@ The class that manages workflow at the recording level is (<a href="https://gith
 <center><figcaption>ERD for ephys pipeline at the recording level</figcaption></center>
  </figure>
 
- ### Main functions and variables in recording_process workflow manager 
+ ### Main functions and variables in recording_process workflow manager
 
  + **recording_process_status_dict** in (<a href="https://https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/params_config.py">Params Config file</a>): This dictionary defines status definitions and corresponding functions to execute.
 + **pipeline_handler_main** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording__process_handler.py">RecProcessHandler</a>): Main function in recording process workflow
@@ -110,4 +110,4 @@ The class that manages workflow at the recording level is (<a href="https://gith
 
 #### Set up instructions for BrainCogsEphysSorters in cluster system
 
-1. 
+1.