Assaydev persite (#185)

Author: ErinWeisbart

documentation/DCP-documentation/step_2_submit_jobs.md

@@ -60,7 +60,7 @@ As of Distributed-CellProfiler 2.2.0, `run_batch_general.py` has been reformatte
 ### Required inputs
 
 * `step` is the step that you would like to make jobs for.
-Supported steps are `zproj`, `illum`, `qc`, `qc_persite`, `assaydev`, and`analysis`
+Supported steps are `zproj`, `illum`, `qc`, `qc_persite`, `assaydev`, `assaydev_persite`, and `analysis`
 * `identifier` is the project identifier (e.g. "cpg0000-jump-pilot" or "2024_11_07_Collaborator_Cell_Painting")
 * `batch` is the name of the data batch (e.g. "2020_11_04_CPJUMP1")
 * `platelist` is the list of plates to process.

run_batch_general.py

@@ -26,7 +26,7 @@ def scheduleBatch(self, data):
 
 
 def run_batch_general(
-    step,  # (zproj, illum, qc, qc_persite, assaydev, or analysis)
+    step,  # (zproj, illum, qc, qc_persite, assaydev, assaydev_persite, or analysis)
     identifier="",  # (e.g. cpg0000-jump-pilot)
     batch="",  # (e.g. 2020_11_04_CPJUMP1)
     platelist=[],  # (e.g. ['Plate1','Plate2'])
@@ -427,6 +427,71 @@ def run_batch_general(
 
         print("AssayDev job submitted. Check your queue")
 
+    elif step == "assaydev_persite":
+        assaydevqueue = JobQueue(f"{identifier}_AssayDev")
+        if not outpath:
+            outpath = path_dict[path_style]["assaydevoutpath"]
+        if not usebatch:
+            if not pipeline:
+                pipeline = "assaydev.cppipe"
+            if not csvname:
+                csvname = "load_data_with_illum.csv"
+
+            for plate in platelist:
+                if all(len(ele) == 0 for ele in wells):
+                    for eachrow in rows:
+                        for eachcol in columns:
+                            for site in sites:
+                                templateMessage_ad = {
+                                    "Metadata": f"Metadata_Plate={plate},Metadata_Well={eachrow}{int(eachcol):{well_format}},Metadata_Site={str(site)}",
+                                    "pipeline": posixpath.join(pipelinepath, pipeline),
+                                    "output": outpath,
+                                    "input": inputpath,
+                                    "data_file": posixpath.join(datafilepath, plate, csvname),
+                                }
+                                assaydevqueue.scheduleBatch(templateMessage_ad)
+                else:
+                    for well in wells:
+                        for site in sites:
+                            templateMessage_ad = {
+                                "Metadata": f"Metadata_Plate={plate},Metadata_Well={eachwell},Metadata_Site={str(site)}",
+                                "pipeline": posixpath.join(pipelinepath, pipeline),
+                                "output": outpath,
+                                "input": inputpath,
+                                "data_file": posixpath.join(datafilepath, plate, csvname),
+                            }
+                            assaydevqueue.scheduleBatch(templateMessage_ad)
+        else:
+            if not batchfile:
+                batchfile = "Batch_data_assaydev.h5"
+            for plate in platelist:
+                if all(len(ele) == 0 for ele in wells):
+                    for eachrow in rows:
+                        for eachcol in columns:
+                            for site in sites:
+                                templateMessage_ad = {
+                                    "Metadata": f"Metadata_Plate={plate},Metadata_Well={eachrow}{int(eachcol):{well_format}},Metadata_Site={str(site)}",
+                                    "pipeline": posixpath.join(batchpath, batchfile),
+                                    "output": outpath,
+                                    "input": inputpath,
+                                    "data_file": posixpath.join(batchpath, batchfile),
+                                }
+                                assaydevqueue.scheduleBatch(templateMessage_ad)
+                else:
+                    for eachwell in wells:
+                        for site in sites:
+                            templateMessage_ad = {
+                                "Metadata": f"Metadata_Plate={plate},Metadata_Well={eachwell},Metadata_Site={str(site)}",
+                                "pipeline": posixpath.join(batchpath, batchfile),
+                                "output": outpath,
+                                "input": inputpath,
+                                "data_file": posixpath.join(batchpath, batchfile),
+                            }
+                            assaydevqueue.scheduleBatch(templateMessage_ad)
+
+        print("AssayDev job submitted. Check your queue")
+
+
     elif step == "analysis":
         analysisqueue = JobQueue(f"{identifier}_Analysis")
         if not outputstructure:
@@ -512,7 +577,7 @@ def run_batch_general(
     )
     parser.add_argument(
         "step",
-        help="Step to make jobs for. Supported steps are zproj, illum, qc, qc_persite, assaydev, analysis",
+        help="Step to make jobs for. Supported steps are zproj, illum, qc, qc_persite, assaydev, assaydev_persite, analysis",
     )
     parser.add_argument("identifier", help="Project identifier")
     parser.add_argument("batch", help="Name of batch")