Track changes against upstream reference version

README.rst

@@ -1,3 +1,5 @@
+**Obsolete**: see https://github.com/oirlab/liger_iris_crds
+
 ====
 CRDS
 ====

crds/core/constants.py

@@ -1,5 +1,5 @@
 # List of all the observatory package names
-ALL_OBSERVATORIES = ["hst", "jwst", "tobs"]
+ALL_OBSERVATORIES = ["hst", "jwst", "tobs", "tmt"]
 
 # keywords used to identify instrument from headers
 INSTRUMENT_KEYWORDS = ["INSTRUME", "META.INSTRUMENT.NAME",

crds/core/heavy_client.py

@@ -292,7 +292,7 @@ def warn_bad_reference(observatory, reftype, reference):
 
 def check_observatory(observatory):
     """Make sure `observatory` is valid."""
-    assert observatory in ["hst", "jwst", "tobs"]
+    assert observatory in ["hst", "jwst", "tobs", "tmt"]
 
 def check_parameters(header):
     """Make sure dict-like `header` is a mapping from strings to simple types.

crds/tmt/__init__.py

@@ -0,0 +1,25 @@
+import os.path
+
+from crds.certify import reftypes
+
+HERE  = os.path.abspath(os.path.dirname(__file__) or ".")
+
+TYPES = reftypes.from_package_file("tmt", __file__)
+
+OBSERVATORY = TYPES.observatory
+INSTRUMENTS = TYPES.instruments
+EXTENSIONS = TYPES.extensions
+TEXT_DESCR = TYPES.text_descr
+FILEKINDS = TYPES.filekinds
+
+INSTRUMENT_FIXERS = {
+}
+
+TYPE_FIXERS = {
+}
+
+PROVENANCE_KEYWORDS = ("META.DESCRIPTION", "META.PEDIGREE", "META.USEAFTER","META.HISTORY", "META.AUTHOR", "META.MODEL_TYPE")
+# PROVENANCE_KEYWORDS = ("DESCRIP", "PEDIGREE", "USEAFTER","HISTORY", "AUTHOR")
+USEAFTER_KEYWORDS = ("META.OBSERVATION.DATE", "META.OBSERVATION.TIME") # Dataset keywords matching in UseAfter selectors
+
+DEFAULT_SELECTORS = ("Match", "UseAfter")   # Normal selector hierarchy in rmap

crds/tmt/gen_system_crdscfg.py

@@ -0,0 +1,201 @@
+"""This module is used to generate the SYSTEM CRDSCFG reference file.  The code
+is directly edited and the module itself is run to emit a new reference as in:
+
+$ python -m crds.jwst.gen_system_crdscfg  updated_inputs.yaml  >new_reference.yaml
+
+Suggested approach for obtaining updated inputs is downloading the most current
+SYSTEM CRDSCFG reference file and updating MANUAL sections.
+
+Current calibration code must be available in order to automatically
+regenerates since CRDS will inspect the installed .cfg files to determine Step
+configurations and required reference types.
+"""
+import sys
+import re
+import fnmatch
+import os.path
+
+# ----------------------------------------------------------------------------------------------
+
+import yaml
+
+# ----------------------------------------------------------------------------------------------
+
+from jwst import __version__ as jwst_version
+from jwst.stpipe import pipeline
+from jwst import pipeline as pipepkg
+
+# ----------------------------------------------------------------------------------------------
+
+import crds
+from crds.core import log, exceptions, utils, timestamp, pysh
+from crds.core.log import srepr
+
+# ----------------------------------------------------------------------------------------------
+VERSION_RE_STR = r"(\d+\.\d+.\d+).*"
+
+CAL_VER = re.match(r"^" + VERSION_RE_STR, jwst_version).group(1)
+
+GENERATION_DATE = timestamp.now("T").split(".")[0]
+
+REFERENCE_DIVIDER = "# vvvvvvvv GENERATED vvvvvvvv"
+
+# --------------------------------------------------------------------------------------
+
+class CrdsCfgGenerator:
+    """Used to re-generate SYSTEM CRDSCFG reference files based on modified
+    versions of previous reference files.
+    """
+    def __init__(self, input_yaml):
+        self.input_yaml = input_yaml
+        self.loaded_cfg = self.get_body()
+        self.levels = self.loaded_cfg.levels
+        self.exp_types = self.loaded_cfg.exp_types
+        self.pipeline_cfgs_to_steps = {}
+        self.steps_to_reftypes = {}
+        self.generate_pipeline_info()
+        self.exptypes_to_cfgs = { exp_type : self.exptype_to_pipelines(exp_type)
+                                  for exp_type in self.exp_types }
+        self.exptypes_to_reftypes = { exp_type : self.exptype_to_reftypes(exp_type)
+                                      for exp_type in self.exp_types }
+
+    def get_body(self):
+        """Load the input_yaml as a CRDS Struct and return it."""
+        return utils.Struct(yaml.safe_load(self.input_yaml))
+
+    def get_updated_yaml(self):
+        """Modify the input_yaml to replace the cal code version and generation date,
+        useful for updating an existing reference and running it through this generator.
+        """
+        input_body = []
+        for line in self.input_yaml.splitlines():
+            line2 = line.strip()
+            if line2.startswith("calibration_software_version:"):
+                input_body += ["    calibration_software_version: " + CAL_VER]
+            elif line2.startswith("generation_date:"):
+                input_body += ["    generation_date: " + GENERATION_DATE]
+            elif line2.startswith("crds_version:"):
+                input_body += ["    crds_version: " + crds.__version__]
+            else:
+                input_body += [line]
+        return "\n".join(input_body).split(REFERENCE_DIVIDER)[0] + "\n" + REFERENCE_DIVIDER + "\n"
+
+    def generate_pipeline_info(self):
+        """Based on the input YAML and JWST cal code,  generate the mappings:
+        pipeline_cfgs_to_steps
+        steps_to_reftypes
+        """
+        pysh.sh("rm -rf configs")
+        pysh.sh("collect_pipeline_cfgs configs")
+        self.pipeline_cfgs_to_steps["skip_2b.cfg"] = []
+        for pipeline_cfg in self.loaded_cfg.pipeline_cfgs:
+            log.info("Processing", repr(pipeline_cfg))
+            cfgdir = "configs" # os.path.dirname(pipepkg.__file__) or ""
+            cfgpath = os.path.join(cfgdir, pipeline_cfg)
+            p = pipeline.Pipeline.from_config_file(cfgpath)
+            steps_to_reftypes = {}
+            for name, stepcfg in p.steps.items():
+                if stepcfg.get("skip", True):
+                    log.info("Considering", repr(name), "skip")
+                else:
+                    log.info("Considering", repr(name), "keep")
+                    step = p.step_defs[name]  # class
+                    steps_to_reftypes[name] = step.reference_file_types
+            self.pipeline_cfgs_to_steps[pipeline_cfg] = sorted(list(steps_to_reftypes.keys()))
+            self.steps_to_reftypes.update(steps_to_reftypes)
+
+    def generate_output_yaml(self):
+        """Generate the SYSTEM CRDSCFG reference YAML."""
+        output_yaml = self.get_updated_yaml()
+        output_yaml += yaml.dump({"pipeline_cfgs_to_steps" : self.pipeline_cfgs_to_steps}) + "\n"
+        output_yaml += yaml.dump({"steps_to_reftypes" : self.steps_to_reftypes}) + "\n"
+        output_yaml += yaml.dump({"exptypes_to_pipelines" : self.exptypes_to_cfgs}) + "\n"
+        output_yaml += yaml.dump({"exptypes_to_reftypes" : self.exptypes_to_reftypes}) + "\n"
+        return output_yaml
+
+    def __str__(self):
+        return self.generate_output_yaml()
+
+    def exptype_to_pipelines(self, exp_type):
+        """For a given EXP_TYPE string, return a list of reftypes needed to process that
+        EXP_TYPE through the data levels appropriate for that EXP_TYPE.
+
+        Return [reftypes... ]
+        """
+        pipelines = []
+        for level in self.levels:
+            pipelines.extend(self.get_level_pipeline(level, exp_type))
+        return pipelines
+
+    def exptype_to_reftypes(self, exp_type):
+        """Return all reftypes associated with processing all steps of all pipelines for `exp_type`."""
+        # with log.error_on_exception("Failed exptype_to_reftypes for", srepr(exp_type)):
+        reftypes = []
+        for pipeline in self.exptype_to_pipelines(exp_type):
+            reftypes.extend(self.get_pipeline_types(pipeline, exp_type))
+        reftypes = sorted(list(set(reftypes)))
+        return reftypes
+
+    def get_level_pipeline(self, level, exp_type):
+        """Interpret the level_pipeline_exptypes data structure relative to
+        processing `level` and `exp_type` to determine a pipeline .cfg file.
+
+        Return [ pipeline .cfg ]  or  []
+        """
+        pipeline_exptypes = self.loaded_cfg.level_pipeline_exptypes[level]
+        for mapping in pipeline_exptypes:
+            for pipeline, exptypes in mapping.items():
+                for exptype_pattern in exptypes:
+                    if glob_match(exptype_pattern, exp_type):
+                        return [pipeline]
+        log.error("Unhandled EXP_TYPE", srepr(exp_type), "for", srepr(level))
+        return []
+
+        # raise exceptions.CrdsPipelineCfgDeterminationError("Unhandled EXP_TYPE", srepr(exp_type))
+
+    def get_pipeline_types(self, pipeline, exp_type):
+        """Based on a pipeline .cfg filename and an EXP_TYPE,  look up
+        the Steps corresponding to the .cfg and extrapolate those to the
+        reftypes used by those Steps.   If there are exceptions to the
+        reftypes assigned for a particular Step that depend on EXP_TYPE,
+        return the revised types for that Step instead.
+
+        Return [reftypes, ...]
+        """
+        steps = self.pipeline_cfgs_to_steps[pipeline]
+        reftypes = []
+        for step in steps:
+            if step not in self.loaded_cfg.steps_to_reftypes_exceptions:
+                reftypes.extend(self.steps_to_reftypes[step])
+            else:
+                for case in self.loaded_cfg.steps_to_reftypes_exceptions[step]:
+                    item = list(case.values())[0]
+                    more_reftypes = item["reftypes"][:]
+                    exptypes = item["exp_types"][:]
+                    found = False
+                    for exptype_pattern in exptypes:
+                        if glob_match(exptype_pattern, exp_type):
+                            log.verbose("Adding exceptional types", more_reftypes,
+                                        "for step", srepr(step), "case", srepr(exptype_pattern),
+                                        "based on exp_type", srepr(exp_type))
+                            found = True
+                            reftypes.extend(more_reftypes)
+                            break
+                    if found:
+                        break
+                else:
+                    raise exceptions.CrdsPipelineTypeDeterminationError("Unhandled EXP_TYPE for exceptional Step", srepr(step))
+        return reftypes
+
+# --------------------------------------------------------------------------------------
+
+def glob_match(expr, value):
+    """Convert the given glob `expr` to a regex and match it to `value`."""
+    re_str = fnmatch.translate(expr)
+    return re.match(re_str, value)
+
+# --------------------------------------------------------------------------------------
+
+if __name__ == "__main__":
+    with open(sys.argv[1]) as infile:
+        print(CrdsCfgGenerator(infile.read()))

crds/tmt/iris.py

@@ -0,0 +1 @@
+