rcsb.utils.ec 0.27__py3-none-any.whl

rcsb/__init__.py

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+__path__ = __import__("pkgutil").extend_path(__path__, __name__)

rcsb/utils/__init__.py

@@ -0,0 +1 @@
+__path__ = __import__("pkgutil").extend_path(__path__, __name__)

rcsb/utils/ec/EnzymeDatabaseProvider.py

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+##
+# File:    EnzymeDatabaseProvider.py
+# Author:  J. Westbrook
+# Date:    24-Jan-2019
+# Version: 0.001
+#
+# Update:
+# 21-Jul-2021 jdw  Make this provider a subclass of StashableBase
+#  8-May-2024 dwp  Add additional data quality check to file download (in case data file is empty)
+#
+##
+"""
+Various utilities for extracting data Enzyme database export data files
+and returning lineage details.
+"""
+
+import collections
+import copy
+import logging
+import os
+
+from bs4 import BeautifulSoup
+
+from rcsb.utils.io.FileUtil import FileUtil
+from rcsb.utils.io.MarshalUtil import MarshalUtil
+from rcsb.utils.io.StashableBase import StashableBase
+
+logger = logging.getLogger(__name__)
+
+
+class EnzymeDatabaseProvider(StashableBase):
+    """Various utilities for extracting data Enzyme database export data files
+    and returning lineage details.
+    """
+
+    def __init__(self, **kwargs):
+        dirName = "ec"
+        if "cachePath" in kwargs:
+            cachePath = os.path.abspath(kwargs.get("cachePath", None))
+            enzymeDirPath = os.path.join(cachePath, dirName)
+        else:
+            enzymeDirPath = kwargs.get("enzymeDirPath", ".")
+            cachePath, dirName = os.path.split(os.path.abspath(enzymeDirPath))
+        super(EnzymeDatabaseProvider, self).__init__(cachePath, [dirName])
+        #
+        urlTarget = kwargs.get("urlTarget", "https://www.enzyme-database.org/downloads/enzyme-data.xml.gz")
+        urlTargetFallback = "https://github.com/rcsb/py-rcsb_exdb_assets/raw/master/fall_back/enzyme-data.xml.gz"
+
+        useCache = kwargs.get("useCache", True)
+        enzymeDataFileName = kwargs.get("enzymeDataFileName", "enzyme-data.json")
+
+        self.__debug = False
+        #
+        self.__mU = MarshalUtil(workPath=enzymeDirPath)
+        self.__enzD = self.__reload(urlTarget, urlTargetFallback, enzymeDirPath, enzymeDataFileName=enzymeDataFileName, useCache=useCache)
+
+    def testCache(self):
+        logger.info("Length class dict %d", len(self.__enzD["class"]) if "class" in self.__enzD else 0)
+        if "class" in self.__enzD and len(self.__enzD["class"]) > 7600:
+            return True
+        return False
+
+    def replaced(self, ecId):
+        nS = hS = None
+        try:
+            nS = self.__enzD["replaced"][ecId]["note"]
+        except Exception:
+            pass
+        try:
+            hS = self.__enzD["replaced"][ecId]["history"]
+        except Exception:
+            pass
+        return nS, hS
+
+    def exists(self, ecId):
+        try:
+            return ecId in self.__enzD["class"]
+        except Exception:
+            return False
+
+    def normalize(self, ecId):
+        """Normalize the input class identifier removing any ambiguity markers.
+
+        Args:
+            ecId (str): EC class identifier
+
+        Returns:
+            (str) : normalized EC identifier
+        """
+        retId = None
+        try:
+            oL = []
+            tvL = ecId.strip().split(".")
+            for tv in tvL:
+                if not tv.isdigit():
+                    break
+                oL.append(tv)
+            retId = ".".join(oL)
+        except Exception as e:
+            logger.exception("Failing normalizing %r with %s", ecId, str(e))
+        return retId
+
+    def getClass(self, ecId):
+        try:
+            return self.__enzD["class"][ecId]
+        except Exception:
+            pass
+        return None
+
+    def getLineage(self, ecId):
+        try:
+            return self.__enzD["lineage"][ecId]
+        except Exception:
+            pass
+        return None
+
+    def getTreeNodeList(self):
+        treeL = self.__exportTreeNodeList(self.__enzD)
+        return treeL
+
+    def __reload(self, urlTarget, urlTargetFallback, dirPath, enzymeDataFileName, useCache=True):
+        """Reload input XML database dump file and return data transformed lineage data objects.
+        '
+                Returns:
+                    dictionary[ec_id] = {'name_list': ... , 'id_list': ... 'depth_list': ... }
+        """
+        enzD = {}
+        #
+        mU = MarshalUtil()
+        fU = FileUtil()
+        ok, okFetch = False, False
+        fn = fU.getFileName(urlTarget)
+        xmlFilePath = os.path.join(dirPath, fn)
+        enzymeDataPath = os.path.join(dirPath, enzymeDataFileName)
+        self.__mU.mkdir(dirPath)
+        #
+        if not useCache:
+            for fp in [xmlFilePath, enzymeDataPath]:
+                try:
+                    os.remove(fp)
+                except Exception:
+                    pass
+        #
+        if useCache and fU.exists(enzymeDataPath):
+            enzD = self.__mU.doImport(enzymeDataPath, fmt="json")
+        elif not useCache:
+            if useCache and fU.exists(xmlFilePath):
+                logger.info("Using an existing resource file %s", xmlFilePath)
+                ok = True
+            else:
+                logger.info("Fetching url %s to resource file %s", urlTarget, xmlFilePath)
+                okFetch = fU.get(urlTarget, xmlFilePath)
+                ok = fU.size(xmlFilePath) > 10000 and okFetch
+                logger.info("Enzyme data fetch status is %r, data integrity status is %r", okFetch, ok)
+                if not ok:
+                    logger.info("Fetching fallback url %s to resource file %s", urlTargetFallback, xmlFilePath)
+                    okFetch = fU.get(urlTargetFallback, xmlFilePath)
+                    ok = fU.size(xmlFilePath) > 10000 and okFetch
+                    logger.info("Enzyme data fallback fetch status is %r, data integrity status is %r", okFetch, ok)
+            if ok:
+                xrt = mU.doImport(xmlFilePath, fmt="xml")
+                if self.__debug:
+                    self.__traverse(xrt, ns="")
+                rD = self.__extract(xrt)
+                enzD = self.__build(rD)
+                ok = self.__mU.doExport(enzymeDataPath, enzD, fmt="json", indent=3)
+        return enzD
+
+    def __build(self, rD):
+        """Build the list of ancestor classifiers for each leaf classifier.
+
+        Source enzyme database exported data has the following organization:
+
+         "class": [
+                    {
+                    "id": "1",
+                    "class": "1",
+                    "subclass": "1",
+                    "subsubclass": "0",
+                    "heading": "Acting on the CH-OH group of donors",
+                    "note": "This subclass contains dehydrogenases that act on primary alcohols,",
+                    "last_change": "2006-05-18 10:47:54"
+                    }, ...
+
+        "entry": [
+                    {
+                    "ec_num": "1.1.1.1",
+                    "accepted_name": "alcohol dehydrogenase",
+                    "reaction": "(1) a primary alcohol + NAD+ = an aldehyde + NADH + H+;;(2) a secondary alcohol + NAD+ = a ketone + NADH + H+",
+                    "other_names": "aldehyde reductase; ADH; alcohol dehydrogenase (NAD); aliphatic alcohol dehydrogenase; ethanol dehydrogenase; NAD-dependent alcohol dehydrogenase;",
+                    "sys_name": "alcohol:NAD+ oxidoreductase",
+                    "comments": "A zinc protein. Acts on primary or secondary alcohols or hemi-acetals with very broad specificity; however the enzyme oxidizes ..... ",
+                    "links": "BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, UM-BBD",
+                    "class": "1",
+                    "subclass": "1",
+                    "subsubclass": "1",
+                    "serial": "1",
+                    "status": null,
+                    "diagram": null,
+                    "cas_num": "9031-72-5",
+                    "glossary": null,
+                    "last_change": "2012-02-17 13:19:04",
+                    "id": "1"
+                    }, ...
+
+
+        Returns:
+            dictionary[ec_id] = {'name_list': ... , 'id_list': ... 'depth_list': ... }
+
+        """
+        replacedD = {}
+        linD = {}
+        cD = {}
+        classD = {}
+        #
+        # list_of_words = your_string.split()
+        # next_word = list_of_words[list_of_words.index(your_search_word) + 1]
+        #
+        if "hist" in rD:
+            for dD in rD["hist"]:
+                ecId = dD["ec_num"]
+                ts1 = dD["note"] if "note" in dD and dD["note"] else None
+                if ts1:
+                    replacedD[ecId] = {"note": ts1}
+                ts2 = dD["history"] if "history" in dD and dD["history"] else None
+                if ts2:
+                    replacedD[ecId] = {"history": ts2}
+
+                if ts1 and any(xS in ts1 for xS in [" Now ", " transferred "]) and ("EC " in ts1):
+                    logger.debug("%s note is %r", ecId, ts1)
+                if ts2 and any(xS in ts2 for xS in [" Now ", " transferred "]) and ("EC " in ts2):
+                    logger.debug("%s hist is %r", ecId, ts2)
+
+        #
+        if "class" in rD:
+            for dD in rD["class"]:
+                clTup = tuple([dD[at] for at in ["class", "subclass", "subsubclass"]])
+                val = self.__stripMarkup(dD["heading"])
+                cD[clTup] = val
+                classD[".".join(clTup)] = val
+
+            for ecId in classD:
+                cL = ecId.split(".")
+                #
+                tt = cL
+                sscParent = tuple(tt)
+                tt = cL[:-1]
+                tt.append("0")
+                scParent = tuple(tt)
+                tt = cL[:-2]
+                tt.extend(["0", "0"])
+                cParent = tuple(tt)
+                #
+                try:
+                    idL = [".".join(cL[:-2]), ".".join(cL[:-1]), ".".join(cL)]
+                    classVal = cD[cParent] if cParent in cD else ""
+                    subClassVal = cD[scParent] if scParent in cD else ""
+                    subsubClassVal = cD[sscParent] if sscParent in cD else ""
+                    nmL = [classVal, subClassVal, subsubClassVal]
+                    depthL = [1, 2, 3]
+                    #
+                    logger.debug("%s idL %r", ecId, idL)
+                    logger.debug("%s nmL %r", ecId, nmL)
+                    fL = [t for t in cL if t != "0"]
+                    fLen = len(fL)
+                    for jj in range(1, fLen + 1):
+                        tId = ".".join(cL[:jj])
+                        if tId not in linD:
+                            linD[tId] = [(depthL[ii], idL[ii], nmL[ii]) for ii in range(jj)]
+                            logger.debug("%s %r", tId, linD[tId])
+                except Exception as e:
+                    logger.exception("Failing with %s", str(e))
+
+        for k in sorted(classD):
+            logger.debug("%10s %s", k, classD[k])
+        #
+        if "entry" in rD:
+            for dD in rD["entry"]:
+                if "serial" not in dD:
+                    logger.error("Missing serial field in %r", dD)
+                    continue
+                cL = list([dD[at] for at in ["class", "subclass", "subsubclass", "serial"]])
+                #
+                tt = cL[:-1]
+                sscParent = tuple(tt)
+                tt = cL[:-2]
+                tt.append("0")
+                scParent = tuple(tt)
+                tt = cL[:-3]
+                tt.extend(["0", "0"])
+                cParent = tuple(tt)
+                #
+                try:
+                    idL = [".".join(cL[:-3]), ".".join(cL[:-2]), ".".join(cL[:-1]), ".".join(cL)]
+                    classVal = cD[cParent] if cParent in cD else ""
+                    subClassVal = cD[scParent] if scParent in cD else ""
+                    subsubClassVal = cD[sscParent] if sscParent in cD else ""
+                    serialValue = dD["accepted_name"] if "accepted_name" in dD else ""
+                    if serialValue is None or not serialValue:
+                        serialValue = ""
+                        logger.debug("Missing accepted name data for %s", ".".join(cL))
+                    else:
+                        serialValue = self.__stripMarkup(serialValue)
+                        classD[".".join(cL)] = serialValue
+
+                    nmL = [classVal, subClassVal, subsubClassVal, serialValue]
+                    depthL = [1, 2, 3, 4]
+                    # linD['.'.join(cL)] = {'name_list': nmL, 'id_list': idL, 'depth_list': depthL}
+                    for jj in range(1, 5):
+                        ecId = ".".join(cL[:jj])
+                        if ecId not in linD:
+                            linD[ecId] = [(depthL[ii], idL[ii], nmL[ii]) for ii in range(jj)]
+
+                except Exception as e:
+                    logger.error("cL %r cParent %r scParent %r sscParent %r val %r", cL, cParent, scParent, sscParent, val)
+                    logger.error("d is %r", dD)
+                    logger.error("Failing with %s", str(e))
+        #
+        # strip 0 placeholders
+        #
+        rD = {}
+        for ky in classD:
+            ff = [t for t in ky.split(".") if t != "0"]
+            rD[".".join(ff)] = classD[ky]
+
+        #
+        enzD = {"class": rD, "lineage": linD, "replaced": replacedD}
+        return enzD
+
+    def __exportTreeNodeList(self, enzD):
+        """ """
+        # create parent dictionary
+        #
+        pL = []
+        pD = {}
+        for ecId in enzD["class"]:
+            ff = ecId.split(".")
+            if len(ff) == 1:
+                pEcId = None
+                pL.append(ecId)
+            else:
+                pEcId = ".".join(ff[:-1])
+            logger.debug("ecId %s parent %s", ecId, pEcId)
+            pD[ecId] = pEcId
+        #
+        logger.info("enzD %d pD %d", len(enzD["class"]), len(pD))
+        cD = {}
+        for cEcId, pEcId in pD.items():
+            cD.setdefault(pEcId, []).append(cEcId)
+        #
+        logger.info("cD %d", len(cD))
+        #
+        idL = []
+        for rootId in sorted(pL):
+            visited = set([rootId])
+            queue = collections.deque(visited)
+            while queue:
+                ecId = queue.popleft()
+                idL.append(ecId)
+                if ecId not in cD:
+                    logger.debug("No children for ecId %s", ecId)
+                    continue
+                for childId in cD[ecId]:
+                    if childId not in visited:
+                        queue.append(childId)
+                        visited.add(childId)
+        #
+        dL = []
+        for ecId in idL:
+            displayName = enzD["class"][ecId]
+            pEcId = pD[ecId]
+
+            lL = [t[1] for t in enzD["lineage"][ecId]]
+
+            #
+            if pEcId is None:
+                dD = {"id": ecId, "name": displayName, "depth": 0}
+            else:
+                dD = {"id": ecId, "name": displayName, "parents": [pEcId], "depth": len(lL) - 1}
+            dL.append(dD)
+
+        return dL
+
+    def __extract(self, xrt):
+        """Extract data from the input document and return a dictionary
+            of objects containing rows of dictionaries with attribute naming.
+
+        Args:
+            xrt: ElementTree root element
+
+        Returns:
+            Extracted data (dict): dictionary organized by category with
+                                   XML native data names.
+        """
+        rD = {}
+        for el in xrt.getroot():
+            logger.debug("-- Element tag %r name %r", el.tag, el.attrib["name"])
+            # rD.setdefault(el.tag, []).append(q)
+            #
+            for ch in el:
+                logger.debug("-- --> child element tag %r attrib %r", ch.tag, ch.attrib["name"])
+                #
+                if ch.tag == "table_data" and ch.attrib["name"] in ["class", "entry", "hist"]:
+                    dL = self.__getTableData(ch)
+                    rD[ch.attrib["name"]] = dL
+
+                # for gch in ch:
+                #    logger.debug("-- -- --> grand child element tag %r attrib count %r" % (gch.tag, len(gch.attrib)))
+                #    for ggch in gch:
+                #        logger.debug("-- -- --> grand child element tag %r attrib %r" % (ggch.tag, ggch.attrib['name']))
+                # add parent cardinal attributes
+        return rD
+        #
+
+    def __getTableData(self, el):
+        """Parse table data sections:
+
+        Example --
+
+          'table_data' {'name': 'cite'}
+             'row' {}
+             'field' {'name': 'cite_key'}
+             'field' {'name': 'ec_num'}
+             'field' {'name': 'ref_num'}
+             'field' {'name': 'acc_no'}
+             'field' {'name': 'last_change'}
+             'row' {}
+             'field' {'name': 'cite_key'}
+             'field' {'name': 'ec_num'}
+             'field' {'name': 'ref_num'}
+             'field' {'name': 'acc_no'}
+             'field' {'name': 'last_change'}
+        """
+        dL = []
+        if el.tag != "table_data":
+            return dL
+        for ch in el:
+            if ch.tag == "row":
+                dD = {}
+                for gch in ch:
+                    if gch.tag == "field":
+                        nm = gch.attrib["name"]
+                        val = gch.text
+                        dD[nm] = val
+                        logger.debug(" Field %s val %r", nm, val)
+                #
+                dL.append(copy.copy(dD))
+        return dL
+
+    def __stripMarkup(self, text):
+        try:
+            tS = text.replace("—", "-").replace("—", "-").replace("—", "-")
+            bs = BeautifulSoup(tS, features="lxml")
+            return bs.get_text()
+        except Exception as e:
+            logger.exception("Failing for %r with %s", text, str(e))
+        return ""
+
+    # -
+    def __traverse(self, xrt, ns):
+        """Internal routine to traverse the dom covering/logging all elements and attributes.
+
+        Args:
+            xrt (object): ElementTree root element
+            ns (str): XML namespace
+
+        """
+
+        for el in xrt.getroot():
+            pEl = el.tag.replace(ns, "")
+            logger.info("-- %r %r", pEl, el.attrib)
+            for ch in el:
+                chEl = ch.tag.replace(ns, "")
+                logger.info("-- -->  %r %r", chEl, ch.attrib)
+                if ch.text is not None and ch.text:
+                    logger.info("-- -->  %s", ch.text)
+                for gch in ch:
+                    gchEl = gch.tag.replace(ns, "")
+                    logger.info("-- -- -->  %r %r", gchEl, gch.attrib)
+                    if gch.text is not None and gch.text:
+                        logger.info("-- -- -->  %s", gch.text)
+                    for ggch in gch:
+                        ggchEl = ggch.tag.replace(ns, "")
+                        logger.info("-- -- -- -->  %r %r", ggchEl, ggch.attrib)
+                        if ggch.text is not None and ggch.text:
+                            logger.info("-- -- -- -->  %s", ggch.text)
+                        for gggch in ggch:
+                            gggchEl = gggch.tag.replace(ns, "")
+                            logger.info("-- -- -- -- -->  %r %r", gggchEl, gggch.attrib)
+                            if gggch.text is not None and gggch.text:
+                                logger.info("-- -- -- -- -->  %s", gggch.text)

rcsb_utils_ec-0.27.dist-info/METADATA

@@ -0,0 +1,62 @@
+Metadata-Version: 2.4
+Name: rcsb.utils.ec
+Version: 0.27
+Summary: RCSB Python utility classes for processing EC classification data
+Project-URL: Homepage, https://github.com/rcsb/py-rcsb_utils_ec
+Author-email: John Westbrook <john.westbrook@rcsb.org>
+Maintainer-email: Dennis Piehl <dennis.piehl@rcsb.org>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Requires-Dist: beautifulsoup4
+Requires-Dist: lxml
+Requires-Dist: rcsb-utils-io>=1.50
+Provides-Extra: tests
+Requires-Dist: black>=21.5b1; extra == 'tests'
+Requires-Dist: check-manifest; extra == 'tests'
+Requires-Dist: coverage; extra == 'tests'
+Requires-Dist: flake8; extra == 'tests'
+Requires-Dist: pylint; extra == 'tests'
+Requires-Dist: tox; extra == 'tests'
+Description-Content-Type: text/markdown
+
+# RCSB Python Enzyme Classification Data Utilities
+
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb_utils_ec?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=3&branchName=master)
+
+## Introduction
+
+Python utility classes for accessing Enzyme Commission classification data
+
+### Installation
+
+Download the library source software from the project repository:
+
+```bash
+
+git clone --recurse-submodules https://github.com/rcsb/py-rcsb_utils_ec.git
+
+```
+
+Optionally, run test suite (Python versions 3.9+) using
+[tox](http://tox.readthedocs.io/en/latest/example/platform.html):
+
+```bash
+tox
+```
+
+Installation is via the program [pip](https://pypi.python.org/pypi/pip).
+
+```bash
+pip install rcsb.utils.ec
+
+or for the local repository:
+
+pip install .
+```

rcsb_utils_ec-0.27.dist-info/RECORD

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+rcsb/__init__.py,sha256=ED6jHcYiuYpr_0vjGz0zx2lrrmJT9sDJCzIljoDfmlM,65
+rcsb/utils/__init__.py,sha256=ED6jHcYiuYpr_0vjGz0zx2lrrmJT9sDJCzIljoDfmlM,65
+rcsb/utils/ec/EnzymeDatabaseProvider.py,sha256=ltEjjzlkqHSvq_5rBBvn1gVzkMFBJvzJ4IDLBmdNQ8w,18908
+rcsb/utils/ec/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rcsb_utils_ec-0.27.dist-info/METADATA,sha256=WyRmPEGpva49H3Gs6RM1F6MviiskqneL-La8BcUV2gY,1926
+rcsb_utils_ec-0.27.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rcsb_utils_ec-0.27.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+rcsb_utils_ec-0.27.dist-info/RECORD,,

rcsb_utils_ec-0.27.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

rcsb_utils_ec-0.27.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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