Moving tools out of submodules (sorry!)

3 files changed, 0 insertions, 116 deletions

diff --git a/workflows/tools/normalize/README.md b/workflows/tools/normalize/README.md
deleted file mode 100644
index b780a68..0000000
--- a/workflows/tools/normalize/README.md
+++ /dev/null
@@ -1,14 +0,0 @@
-# Normalization steps
-
-This library contains generic logic to normalize (string) data and
-transforms strings to URIs.  It should be applicable to data from
-any source (GenBank, ENA etc).
-
-Important: missing data should be missing or None! Do not fill
-in data by 'guessing'.
-
-When data is malformed a warning should be logged and added to the
-warning list. Functions should be small enough to return only 1
-warning!
-
-Pjotr Prins (c) 2021
diff --git a/workflows/tools/normalize/__init__.py b/workflows/tools/normalize/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/workflows/tools/normalize/__init__.py
+++ /dev/null
diff --git a/workflows/tools/normalize/mapping.py b/workflows/tools/normalize/mapping.py
deleted file mode 100644
index 3ed09c2..0000000
--- a/workflows/tools/normalize/mapping.py
+++ /dev/null
@@ -1,102 +0,0 @@
-# Normalization steps
-#
-# This library contains generic logic to normalize (string) data and
-# transforms strings to URIs.  It should be applicable to data from
-# any source (GenBank, ENA etc).
-#
-#   Important: missing data should be missing or None! Do not fill
-#   in data by 'guessing'.
-#
-#   When data is malformed a warning should be logged and added to the
-#   warning list. Functions should be small enough to return only 1
-#   warning!
-#
-#   Pjotr Prins (c) 2021
-
-import re
-import types
-
-def host_species(host,mapping):
-    Homo_sapiens = "http://purl.obolibrary.org/obo/NCBITaxon_9606"
-
-    SPECIES_TERMS = { # since Python 3.7 dict is ordered! Note that re is allowed
-        "human": Homo_sapiens,
-        "sapiens": Homo_sapiens,
-        "Mustela lutreola": "http://purl.obolibrary.org/obo/NCBITaxon_9666",
-        "Manis javanica": "http://purl.obolibrary.org/obo/NCBITaxon_9974",
-        "Felis catus": "http://purl.obolibrary.org/obo/NCBITaxon_9685",
-        "Panthera tigris": "http://purl.obolibrary.org/obo/NCBITaxon_419130",
-        "Canis lupus": "http://purl.obolibrary.org/obo/NCBITaxon_9615",
-        # Mink:
-        "vison": "http://purl.obolibrary.org/obo/NCBITaxon_452646"
-        }
-
-    warning = None
-    host = types.SimpleNamespace(**host)
-    if not 'obolibrary' in host.host_species:
-        key = host.host_species
-        host.host_species = None
-        if key in mapping:
-            host.host_species = mapping[key]
-        else:
-            for term in SPECIES_TERMS:
-                p = re.compile(".*?"+term,re.IGNORECASE)
-                m = p.match(key)
-                if m: host.host_species = SPECIES_TERMS[term]
-        if not host.host_species:
-            warning = f"No URI mapping for host_species <{key}>"
-        if host.host_species == Unknown or host.host_species == None:
-            del(host.host_species)
-    return host.__dict__,warning
-
-Unknown = "Not found" # So as not to create a warning
-
-def specimen_source(sample,mapping):
-    Oronasopharynx = "http://purl.obolibrary.org/obo/NCIT_C155835"
-    Oropharyngeal = "http://purl.obolibrary.org/obo/NCIT_C155835"
-    Nasopharyngeal = "http://purl.obolibrary.org/obo/NCIT_C155831"
-    Bronchoalveolar_Lavage_Fluid = "http://purl.obolibrary.org/obo/NCIT_C13195"
-    Saliva = "http://purl.obolibrary.org/obo/NCIT_C13275"
-    Nasal_Swab = Nasopharyngeal # "http://purl.obolibrary.org/obo/NCIT_C132119"
-    Frozen_Food = "https://www.wikidata.org/wiki/Q751728"
-    Bronchoalveolar_Lavage = "http://purl.obolibrary.org/obo/NCIT_C13195",
-    Biospecimen = "http://purl.obolibrary.org/obo/NCIT_C70699"
-    SPECIMEN_TERMS = { # since Python 3.7 dict is ordered! Note that re is allowed
-        "Oronasopharynx": Oronasopharynx,
-        "orophar": Oropharyngeal,
-        "pharyngeal": Nasopharyngeal,
-        "\snares": Nasal_Swab,
-        "saliva": Saliva,
-        "swab": Nasal_Swab,
-        "broncho": Bronchoalveolar_Lavage,
-        "seafood": Frozen_Food,
-        "packaging": Frozen_Food,
-        "specimen": Biospecimen,
-        "patient": Biospecimen,
-        "uknown": Unknown,
-        "unknown": Unknown
-        }
-    warning = None
-    sample = types.SimpleNamespace(**sample)
-    try:
-        if sample.specimen_source:
-            keys = sample.specimen_source
-            sample.specimen_source = []
-            for key in keys:
-                if 'obolibrary' in key:
-                    sample.specimen_source.append(key)
-                    continue
-                if key in mapping:
-                    sample.specimen_source.append(mapping[key])
-                else:
-                    for term in SPECIMEN_TERMS:
-                        p = re.compile(".*?"+term,re.IGNORECASE)
-                        m = p.match(key)
-                        if m: sample.specimen_source = [SPECIMEN_TERMS[term]]
-                if len(sample.specimen_source)==0:
-                    warning = f"No URI mapping for specimen_source <{key}>"
-        if sample.specimen_source == Unknown or sample.specimen_source == None:
-            del(sample.specimen_source)
-    except AttributeError:
-        pass
-    return sample.__dict__,warning