bugfixes

README.md

@@ -1,6 +1,6 @@
 ## Automatic Processing tool aka Apocalypse (apo)
 
-Apocalypse (apo) is a library that provides the SwissFEL  user platform to effortlessly run (and re run) their scripts on the the SwissFEL infrastructure --  compute cluster "Eris" (login node: sf-eris) with [sf-daq](https://github.com/paulscherrerinstitute/sf_daq_broker) output files.
+Apocalypse (apo) is a library that provides the SwissFEL  user platform to effortlessly run (and re run) their scripts on the SwissFEL infrastructure --  compute cluster "Eris" (login node: sf-eris) with [sf-daq](https://github.com/paulscherrerinstitute/sf_daq_broker) output files.
 
 More information about [Eris](https://hpc-sysadmins.gitpages.psi.ch/swissfel/compute.html)
 
@@ -16,16 +16,21 @@ ssh sf-cn-#
 <pth_script> --input <filename>.h5
 ```
 - `sf-cn-#` -- corresponds to the node allocated for interactive use and displayed after `salloc`
-- `<pth_script>` -- is top level script that should run exactly as stated. That means any additional actions (e.g. setting enviroment, adding pmodules, additional parameter handling) should be included in it. See [examples](https://gitea.psi.ch/woznic_n/dummy_apocalypse/src/branch/main/examples)
+- `<pth_script>` -- is top level script that should run exactly as stated. That means any additional actions (e.g. setting environment, adding pmodules, additional parameter handling) should be included in it. See [examples](https://gitea.psi.ch/woznic_n/dummy_apocalypse/src/branch/main/examples)
 - `<filename>.h5` is the path to file that you would like to process on `/sf/<endstation>/data/<pgroup>/raw/`
 
-Once your tests are succesfull remember to cancel your allocation by:
+Once your tests are successful remember to cancel your allocation by:
 ```bash
 scancel <JID>
 ```
 - `<JID>` is slurm's job ID, displayed when allocating resources, you can also check it by `squeue -u $USER`
 
 #### Setup
+Run apo from Eris:
+```bash
+ssh sf-eris
+```
+
 If you have `/sf/daq/bin` on your path, there is no need to do anything, otherwise:
 ```bash
 export PATH=$PATH:/sf/daq/bin
@@ -92,4 +97,4 @@ buffer - file type correspondence:
 - data3buffer = BSDATA.h5
 - imagebuffer = CAMERAS.h5
 - detector_buffer = JF.h5
-- apocalypse = all files when "re-run"
+- apocalypse = all files when "re-run"

apocalypse/send_done.py

@@ -112,7 +112,9 @@ def setup_msg(args, msg, tstamp):
 
 
 def parse_apo_meta(pth):
-    loader = LOADER.get(pth.suffix, lambda x: x)
+    loader = LOADER.get(pth.suffix, lambda x: {
+        "table": x
+        })
     with open(pth, "r") as f:
         data = f.read()
     try:

apocalypse/wait_for_file.py

@@ -49,8 +49,8 @@ def on_status(chn, _method_frame, header_frame, body, args):
     local_args.header = header
     local_args.request = request
     local_args.correlation_id = header_frame.correlation_id
-    if request.get("metadata", {}).get("general/instrument") == local_args.endstation:
-        print(header)
+    # if request.get("metadata", {}).get("general/instrument") == local_args.endstation:
+        # print(header)
         # print(body)
     if (
         header.get("action") is None or request.get("writer_type") is None

examples/simple1/pixi.toml

@@ -11,4 +11,4 @@ version = "0.1.0"
 python = "==3.12"
 sfdata = "*"
 logzero = "*"
-
+bitshuffle = {version="==0.5.2",build="py312h5fdea32_5"}

examples/simple1/run_simple1.sh

@@ -1,5 +1,5 @@
 #! /bin/bash
 
 SCRIPT_PTH=./examples/simple1/
-
-pixi run --manifest-path ${SCRIPT_PTH}pixi.toml python ${SCRIPT_PTH}simple1.py -f $2
+unset PIXI_IN_SHELL
+pixi run --manifest-path $SCRIPT_PTH python ${SCRIPT_PTH}simple1.py -f $2

examples/simple2/pixi.toml

@@ -12,3 +12,4 @@ python="==3.12"
 sfdata="*"
 numpy="*"
 logzero = "*"
+bitshuffle = {version="==0.5.2",build="py312h5fdea32_5"}

examples/simple2/run_simple2.sh

@@ -1,4 +1,5 @@
 #! /bin/bash
 
-SCRIPT_PTH=./examples/
-pixi run --manifest-path ${SCRIPT_PTH}pixi.toml python ${SCRIPT_PTH}simple2.py -f $2 -b bg.CAMERAS.h5
+SCRIPT_PTH=./examples/simple2/
+unset PIXI_IN_SHELL
+pixi run --manifest-path ${SCRIPT_PTH} python ${SCRIPT_PTH}simple2.py -f $2 -b bg.CAMERAS.h5

tests/apo/test_send_msg.py

@@ -268,7 +268,9 @@ def test_send_msg_body_req_succ_double_meta(mock_apo_input):
         }, ".json"), ("key: value\nnum: 2", {
             "key": "value",
             "num": 2
-            }, ".yaml"), ("plain meta txt", "plain meta txt", ".txt")]
+            }, ".yaml"), ("plain meta txt", {
+                "table": "plain meta txt"
+                }, ".txt")]
     )
 def test_parse_apo_meta(content, expected, suffix):
     string_io = io.StringIO(content)