rcsb.exdb 1.31__py3-none-any.whl

rcsb/exdb/wf/EntryInfoEtlWorkflow.py

@@ -0,0 +1,71 @@
+##
+# File: EntryInfoEtlWorkflow.py
+# Date: 22-Sep-2021  jdw
+#
+#  Workflow wrapper  --  Entry-level annotations extracted from ExDB
+#
+#  Updates:
+#   1-Jun-2023 aae Don't back up resources to GitHub during cache update workflows
+#
+##
+__docformat__ = "google en"
+__author__ = "John Westbrook"
+__email__ = "jwest@rcsb.rutgers.edu"
+__license__ = "Apache 2.0"
+
+import logging
+import os
+
+
+from rcsb.exdb.entry.EntryInfoProvider import EntryInfoProvider
+from rcsb.utils.config.ConfigUtil import ConfigUtil
+
+logger = logging.getLogger(__name__)
+
+
+class EntryInfoEtlWorkflow(object):
+    def __init__(self, **kwargs):
+        """Workflow wrapper  --  extract selected entry-level annotations from ExDb
+
+        Args:
+            configPath (str, optional): path to configuration file (default: exdb-config-example.yml)
+            configName (str, optional): configuration section name (default: site_info_configuration)
+            cachePath (str, optional):  path to cache directory (default: '.')
+            stashRemotePrefix (str, optional): file name prefix (channel) applied to remote stash file artifacts (default: None)
+        """
+        configPath = kwargs.get("configPath", "exdb-config-example.yml")
+        self.__configName = kwargs.get("configName", "site_info_configuration")
+        mockTopPath = kwargs.get("mockTopPath", None)
+        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=self.__configName, mockTopPath=mockTopPath)
+        #
+        self.__cachePath = kwargs.get("cachePath", ".")
+        self.__cachePath = os.path.abspath(self.__cachePath)
+        self.__stashRemotePrefix = kwargs.get("stashRemotePrefix", None)
+        #
+        self.__debugFlag = kwargs.get("debugFlag", False)
+        if self.__debugFlag:
+            logger.setLevel(logging.DEBUG)
+        #
+
+    def update(self, backup=True):
+        """Update extraction of selected entry-level annotations from ExDB.
+
+        Returns:
+            (bool): True for success or False otherwise
+
+        """
+        try:
+            ok = False
+            eiP = EntryInfoProvider(cachePath=self.__cachePath, useCache=True)
+            eiP.update(self.__cfgOb, fmt="json", indent=3)
+            #
+            if backup:
+                ok = eiP.backup(self.__cfgOb, self.__configName, self.__stashRemotePrefix, useGit=False, useStash=True)
+                logger.info("Backup entry-level annotations (%r)", ok)
+            else:
+                ok = True
+
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        #
+        return ok

rcsb/exdb/wf/GlycanEtlWorkflow.py

@@ -0,0 +1,76 @@
+##
+# File: GlycanEtlWorkflow.py
+# Date: 30-Jun-2021  jdw
+#
+#  Workflow wrapper  --  Glycan ETL utilities
+#
+#  Updates:
+#   1-Jun-2023 aae Don't back up resources to GitHub during cache update workflows
+#
+##
+__docformat__ = "google en"
+__author__ = "John Westbrook"
+__email__ = "jwest@rcsb.rutgers.edu"
+__license__ = "Apache 2.0"
+
+import logging
+import os
+
+
+from rcsb.exdb.branch.GlycanProvider import GlycanProvider
+from rcsb.utils.config.ConfigUtil import ConfigUtil
+
+logger = logging.getLogger(__name__)
+
+
+class GlycanEtlWorkflow(object):
+    def __init__(self, **kwargs):
+        """Workflow wrapper  --  Glycan mapping ETL utilities
+
+        Args:
+            configPath (str, optional): path to configuration file (default: exdb-config-example.yml)
+            configName (str, optional): configuration section name (default: site_info_configuration)
+            cachePath (str, optional):  path to cache directory (default: '.')
+            stashRemotePrefix (str, optional): file name prefix (channel) applied to remote stash file artifacts (default: None)
+        """
+        configPath = kwargs.get("configPath", "exdb-config-example.yml")
+        self.__configName = kwargs.get("configName", "site_info_configuration")
+        mockTopPath = kwargs.get("mockTopPath", None)
+        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=self.__configName, mockTopPath=mockTopPath)
+        #
+        self.__cachePath = kwargs.get("cachePath", ".")
+        self.__cachePath = os.path.abspath(self.__cachePath)
+        self.__stashRemotePrefix = kwargs.get("stashRemotePrefix", None)
+        #
+        self.__debugFlag = kwargs.get("debugFlag", False)
+        if self.__debugFlag:
+            logger.setLevel(logging.DEBUG)
+        #
+
+    def updateMatchedIndex(self, backup=True):
+        """Update Glycan correspondence index.
+
+        Returns:
+            (bool): True for success or False otherwise
+
+        """
+        try:
+            ok1 = ok2 = False
+            gP = GlycanProvider(cachePath=self.__cachePath, useCache=True)
+            ok = gP.restore(self.__cfgOb, self.__configName, self.__stashRemotePrefix, useStash=True, useGit=True)
+            logger.info("Restore glycan matched identifiers status (%r)", ok)
+
+            ok1 = gP.update(self.__cfgOb, fmt="json", indent=3)
+            riD = gP.getIdentifiers()
+            logger.info("Matched glycan identifiers (%d)", len(riD))
+            #
+            if backup:
+                ok2 = gP.backup(self.__cfgOb, self.__configName, self.__stashRemotePrefix, useGit=False, useStash=True)
+                logger.info("Backup matched glycan identifiers (%r)", ok2)
+            else:
+                ok2 = True
+
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        #
+        return ok1 and ok2

rcsb/exdb/wf/PubChemEtlWorkflow.py

@@ -0,0 +1,240 @@
+##
+# File: PubChemEtlWorkflow.py
+# Date: 28-Jul-2020  jdw
+#
+#  Workflow wrapper  --  PubChem ETL utilities
+#
+#  Updates:
+#  13-Mar-2023 aae Updates to use multiprocess count, disable git stash testing
+#   1-Jun-2023 aae Don't back up resources to GitHub during cache update workflows
+##
+__docformat__ = "google en"
+__author__ = "John Westbrook"
+__email__ = "jwest@rcsb.rutgers.edu"
+__license__ = "Apache 2.0"
+
+import logging
+import os
+import time
+
+
+from rcsb.exdb.chemref.PubChemEtlWrapper import PubChemEtlWrapper
+from rcsb.utils.config.ConfigUtil import ConfigUtil
+
+logger = logging.getLogger(__name__)
+
+
+class PubChemEtlWorkflow(object):
+    def __init__(self, **kwargs):
+        """Workflow wrapper  --  PubChem ETL utilities
+
+        Args:
+            configPath (str, optional): path to configuration file (default: exdb-config-example.yml)
+            configName (str, optional): configuration section name (default: site_info_configuration)
+            cachePath (str, optional):  path to cache directory (default: '.')
+            stashRemotePrefix (str, optional): file name prefix (channel) applied to remote stash file artifacts (default: None)
+        """
+        configPath = kwargs.get("configPath", "exdb-config-example.yml")
+        self.__configName = kwargs.get("configName", "site_info_configuration")
+        mockTopPath = kwargs.get("mockTopPath", None)
+        self.__cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=self.__configName, mockTopPath=mockTopPath)
+        #
+        self.__cachePath = kwargs.get("cachePath", ".")
+        self.__cachePath = os.path.abspath(self.__cachePath)
+        self.__stashRemotePrefix = kwargs.get("stashRemotePrefix", None)
+        #
+        self.__debugFlag = kwargs.get("debugFlag", False)
+        if self.__debugFlag:
+            logger.setLevel(logging.DEBUG)
+        #
+
+    def dump(self, **kwargs):
+        """Dump the current object store of PubChem correspondences and data.
+
+        Args:
+            useStash (bool):  should stash (Buildlocker) be updated? (default: True)
+            useGit (bool):  should stash (GitHub) be updated? (default: True)
+
+        Returns:
+            (bool): True for success or False otherwise
+
+        """
+        ok1 = ok2 = ok3 = ok4 = False
+        try:
+            useStash = kwargs.get("useStash", True)
+            useGit = kwargs.get("useGit", True)  # Revisit stashing in GitHub as file timestamp will always cause a commit
+            #  -- Update local chemical indices and  create PubChem mapping index ---
+            pcewP = PubChemEtlWrapper(self.__cfgOb, self.__cachePath, stashRemotePrefix=self.__stashRemotePrefix)
+            sTime = time.time()
+            logger.info("Dumping index data")
+            ok1 = pcewP.dump(contentType="index")
+            eTime = time.time()
+            logger.info("Dumping index data done in (%.4f seconds)", eTime - sTime)
+            if useGit or useStash:
+                sTime = time.time()
+                logger.info("Stashing index data")
+                ok2 = pcewP.toStash(contentType="index", useStash=useStash, useGit=useGit)
+                eTime = time.time()
+                logger.info("Stashing index data done in (%.4f seconds)", eTime - sTime)
+            else:
+                ok2 = True
+
+            sTime = time.time()
+            logger.info("Dumping reference data")
+            ok3 = pcewP.dump(contentType="data")
+            if useGit or useStash:
+                sTime = time.time()
+                logger.info("Stashing reference data")
+                ok4 = pcewP.toStash(contentType="data", useStash=useStash, useGit=useGit)
+                eTime = time.time()
+                logger.info("Stashing reference data done in (%.4f seconds)", eTime - sTime)
+            else:
+                ok4 = True
+            eTime = time.time()
+            logger.info("Dumping data done in (%.4f seconds)", eTime - sTime)
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        return ok1 and ok2 and ok3 and ok4
+
+    def stash(self):
+        """Stash the current cache files containing PubChem correspondences and data."""
+        ok1 = ok2 = False
+        try:
+            #  -- Update local chemical indices and  create PubChem mapping index ---
+            pcewP = PubChemEtlWrapper(self.__cfgOb, self.__cachePath, stashRemotePrefix=self.__stashRemotePrefix)
+            sTime = time.time()
+            ok1 = pcewP. toStash(contentType="index")
+            eTime = time.time()
+            logger.info("Stashing index data done in (%.4f seconds)", eTime - sTime)
+
+            sTime = time.time()
+            logger.info("Stashing reference data")
+            ok2 = pcewP.toStash(contentType="data")
+            eTime = time.time()
+            logger.info("Stashing data done in (%.4f seconds)", eTime - sTime)
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        return ok1 and ok2
+
+    def restore(self):
+        """Restore the current object store of PubChem correspondences and data from stashed data sets."""
+        ok1 = ok2 = False
+        numObjData = numObjIndex = 0
+        try:
+            #  -- Update local chemical indices and  create PubChem mapping index ---
+            pcewP = PubChemEtlWrapper(self.__cfgOb, self.__cachePath, stashRemotePrefix=self.__stashRemotePrefix)
+            sTime = time.time()
+            logger.info("Restoring stashed index data")
+            ok1 = pcewP.fromStash(contentType="index")
+            numObjIndex = pcewP.reloadDump(contentType="index")
+            eTime = time.time()
+            logger.info("Restoring index data done in (%.4f seconds)", eTime - sTime)
+
+            sTime = time.time()
+            logger.info("Restoring reference data")
+            ok2 = pcewP.fromStash(contentType="data")
+            numObjData = pcewP.reloadDump(contentType="data")
+            eTime = time.time()
+            logger.info("Restoring data done in (%.4f seconds)", eTime - sTime)
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        return ok1 and ok2 and numObjData > 1 and numObjIndex > 1
+
+    def updateMatchedIndex(self, **kwargs):
+        """Update chemical indices and correspondence matches.
+
+        Args:
+            ccUrlTarget (str, optional): target url for chemical component dictionary resource file (default: None=all public)
+            birdUrlTarget (str, optional): target url for bird dictionary resource file (cc format) (default: None=all public)
+            ccFileNamePrefix (str, optional): index file prefix (default: full)
+            rebuildChemIndices (bool, optional): rebuild indices from source (default: False)
+            exportPath (str, optional): path to export raw PubChem search results  (default: None)
+            numProcChemComp (int, optional):  number processors to include in multiprocessing mode (default: 8)
+            numProc (int, optional):  number processors to include in multiprocessing mode (default: 2)
+            useStash (bool, optional):  should stash (Buildlocker) be updated? (default: True)
+            useGit (bool, optional):  should stash (GitHub) be updated? (default: True)
+
+        Returns:
+            (bool): True for success or False otherwise
+
+        """
+        try:
+            ok1 = ok2 = ok3 = False
+            #  -- Update local chemical indices and  create PubChem mapping index ---
+            ccUrlTarget = kwargs.get("ccUrlTarget", None)
+            birdUrlTarget = kwargs.get("birdUrlTarget", None)
+            ccFileNamePrefix = kwargs.get("ccFileNamePrefix", "cc-full")
+            numProcChemComp = kwargs.get("numProcChemComp", 8)
+            numProc = kwargs.get("numProc", 4)
+            rebuildChemIndices = kwargs.get("rebuildChemIndices", True)
+            exportPath = kwargs.get("exportPath", None)
+            useStash = kwargs.get("useStash", True)
+            useGit = kwargs.get("useGit", False)
+            #
+            pcewP = PubChemEtlWrapper(self.__cfgOb, self.__cachePath, stashRemotePrefix=self.__stashRemotePrefix)
+            ok1 = pcewP.updateIndex(
+                ccUrlTarget=ccUrlTarget,
+                birdUrlTarget=birdUrlTarget,
+                ccFileNamePrefix=ccFileNamePrefix,
+                exportPath=exportPath,
+                rebuildChemIndices=rebuildChemIndices,
+                numProcChemComp=numProcChemComp,
+                numProc=numProc,
+            )
+            logger.info("updateIndex completed with status %r", ok1)
+            ok2 = pcewP.dump(contentType="index")
+            logger.info("dump completed with status %r", ok2)
+            if useGit or useStash:
+                ok3 = pcewP.toStash(contentType="index", useStash=useStash, useGit=useGit)
+                logger.info("toStash completed with status %r", ok3)
+            else:
+                ok3 = True
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        #
+        return ok1 and ok2 and ok3
+
+    def updateMatchedData(self, **kwargs):
+        """Update PubChem annotation data for matched correspondences.  Generate and stash
+        related identifiers for corresponding components and BIRD chemical definitions.
+
+        Args:
+            numProc(int):  number processors to include in multiprocessing mode (default: 2)
+            useStash(bool):  should stash (Buildlocker) be updated? (default: True)
+            useGit(bool):  should stash (GitHub) be updated? (default: True)
+
+        Returns:
+            (bool): True for success or False otherwise
+        """
+        try:
+            ok1 = ok2 = ok3 = ok4 = ok5 = ok6 = False
+            #  --
+            numProc = kwargs.get("numProc", 4)
+            useStash = kwargs.get("useStash", True)
+            useGit = kwargs.get("useGit", False)
+            #
+            pcewP = PubChemEtlWrapper(self.__cfgOb, self.__cachePath, stashRemotePrefix=self.__stashRemotePrefix)
+            ok1 = pcewP.updateMatchedData(numProc=numProc)
+            logger.info("PubChemEtlWrapper.updateMatchedData completed with status %r", ok1)
+            ok2 = pcewP.dump(contentType="data")
+            logger.info("PubChemEtlWrapper.dump 'data' completed with status %r", ok2)
+            if useGit or useStash:
+                ok3 = pcewP.toStash(contentType="data", useStash=useStash, useGit=useGit)
+                logger.info("PubChemEtlWrapper.toStash 'data' completed with status %r", ok3)
+            else:
+                ok3 = True
+            #
+            ok4 = pcewP.updateIdentifiers()
+            logger.info("PubChemEtlWrapper.updateIdentifiers completed with status %r", ok4)
+            ok5 = pcewP.dump(contentType="identifiers")
+            logger.info("PubChemEtlWrapper.dump 'identifiers' completed with status %r", ok5)
+            if useGit or useStash:
+                ok6 = pcewP.toStash(contentType="identifiers", useStash=useStash, useGit=useGit)
+                logger.info("PubChemEtlWrapper.toStash 'identifiers' completed with status %r", ok6)
+            else:
+                ok6 = True
+            #
+        except Exception as e:
+            logger.exception("Failing with %s", str(e))
+        #
+        return ok1 and ok2 and ok3 and ok4 and ok5 and ok6

rcsb_exdb-1.31.dist-info/METADATA

@@ -0,0 +1,103 @@
+Metadata-Version: 2.4
+Name: rcsb.exdb
+Version: 1.31
+Summary: RCSB Python ExDB data extraction and loading workflows
+Project-URL: Homepage, https://github.com/rcsb/py-rcsb_exdb
+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 :: 3.12
+Requires-Python: >=3.9
+Requires-Dist: jsonschema>=2.6.0
+Requires-Dist: numpy
+Requires-Dist: openeye-toolkits>=2024.1.1
+Requires-Dist: rcsb-db>=1.808
+Requires-Dist: rcsb-utils-chem>=0.84
+Requires-Dist: rcsb-utils-chemref>=0.91
+Requires-Dist: rcsb-utils-config>=0.40
+Requires-Dist: rcsb-utils-dictionary>=1.27
+Requires-Dist: rcsb-utils-ec>=0.25
+Requires-Dist: rcsb-utils-go>=0.18
+Requires-Dist: rcsb-utils-io>=1.48
+Requires-Dist: rcsb-utils-seq>=0.82
+Requires-Dist: rcsb-utils-struct>=0.47
+Requires-Dist: rcsb-utils-targets>=0.82
+Requires-Dist: rcsb-utils-taxonomy>=0.43
+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: rcsb-utils-citation>=0.25; extra == 'tests'
+Requires-Dist: tox; extra == 'tests'
+Description-Content-Type: text/markdown
+
+# py-rcsb_exdb
+
+[![Build Status](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_apis/build/status/rcsb.py-rcsb_exdb?branchName=master)](https://dev.azure.com/rcsb/RCSB%20PDB%20Python%20Projects/_build/latest?definitionId=18&branchName=master)
+
+RCSB exchange database extraction and loading workflow tools
+
+## Introduction
+
+This module contains a collection of utility classes for extracting data from
+the RCSB exchange database and subsequently reloading processed or integrated data.
+
+### Installation
+
+Download the library source software from the project repository:
+
+```bash
+
+git clone --recurse-submodules https://github.com/rcsb/py-rcsb_exdb.git
+
+```
+
+Optionally, run test suite (Python versions 2.7 and 3.7) 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).  To run tests
+from the source tree, the package must be installed in editable mode (i.e. -e):
+
+```bash
+pip install -e . --extra-index-url https://pypi.anaconda.org/OpenEye/simple
+
+# or using uv
+
+uv pip install -e .
+```
+
+#### Installing in Ubuntu Linux (tested in 18.04)
+
+You will need a few packages, before `pip install .` can work:
+
+```bash
+
+sudo apt install flex bison
+
+```
+
+### Installing on macOS
+
+To use and develop this package on macOS requires a number of packages that are not
+distributed as part of the base macOS operating system.
+The following steps provide one approach to creating the development environment for this
+package.  First, install the Apple [XCode](https://developer.apple.com/xcode/) package and associate command-line tools.
+This will provide essential compilers and supporting tools.  The [HomeBrew](https://brew.sh/) package
+manager provides further access to a variety of common open source services and tools.
+Follow the instructions provided by at the [HomeBrew](https://brew.sh/) site to
+install this system.   Once HomeBrew is installed, you can further install the
+[MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
+are required to support the ExDB tools.  HomeBrew also provides a variety of options for
+managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).

rcsb_exdb-1.31.dist-info/RECORD

@@ -0,0 +1,98 @@
+rcsb/__init__.py,sha256=ED6jHcYiuYpr_0vjGz0zx2lrrmJT9sDJCzIljoDfmlM,65
+rcsb/exdb/__init__.py,sha256=ED6jHcYiuYpr_0vjGz0zx2lrrmJT9sDJCzIljoDfmlM,65
+rcsb/exdb/branch/BranchedEntityExtractor.py,sha256=et-rQWTMbvzFcOW3PPKeGLdvOzyCxwQo1p_y3LJqjJo,2645
+rcsb/exdb/branch/GlycanProvider.py,sha256=D5jhSGKc6pembx-eQX2zQcEULffQ1yrkgVOzPDclhP8,4000
+rcsb/exdb/branch/GlycanUtils.py,sha256=lovKiRrYwmVxk4VItrrUj0D6wQ_BIOojiM5dgNdY0g4,4507
+rcsb/exdb/branch/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rcsb/exdb/chemref/ChemRefEtlWorker.py,sha256=pGVsCJt6gzIWAGRRUULiyvaFul5LHx5UfFBUbv6B6lI,5439
+rcsb/exdb/chemref/ChemRefExtractor.py,sha256=D-m8oga4PtntTTkpxc9k8gwMbn16vkGKq0BrDicUZaM,2580
+rcsb/exdb/chemref/ChemRefMappingProvider.py,sha256=UMrJtQHTThMBFhV1ZzDAwz6-ZXU4VPn2vemNzAPDPW0,5290
+rcsb/exdb/chemref/PubChemDataCacheProvider.py,sha256=g1O9FoDbqsLqET_D-oFxqiOf50bIpBSnSwjg4OJMqNc,15479
+rcsb/exdb/chemref/PubChemEtlWrapper.py,sha256=uvGsNH_vTdJg11n2iftR5mq5UVKuM2GbgtotsR5kYSQ,11699
+rcsb/exdb/chemref/PubChemIndexCacheProvider.py,sha256=5SRTA437XVuCawJDT4JT3hV9zDkNk0peOpRJNKFlkMA,29299
+rcsb/exdb/chemref/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rcsb/exdb/citation/CitationAdapter.py,sha256=rgzzv2BChlv38kO-QO67KHucvAXT-HaQbYz5coYHke4,3501
+rcsb/exdb/citation/CitationExtractor.py,sha256=tPJv9UJlUjNVwHnOdfZoOUlkFWMQHqUEYNpbHnCNTHM,7574
+rcsb/exdb/citation/CitationUtils.py,sha256=4W1_-HgblZ4fk_rC5mzWinwZqDujV8K-QZxOL6e0ldk,1487
+rcsb/exdb/citation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rcsb/exdb/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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