Create new pds-deep-archive program and improve performance (#26)

* Resolutions for #13 and #21 - Resolve #21 with a new driver program `aipsip` that generates both the AIP and uses it to make the SIP as well, leaving all in the current working directory (along with two—count 'em, *two*—PDS labels for the price of one!). - Updates the Python `setuptools` metadata to generate the new `aipsip` (helps with #21). - Refactors logging and command-line argument setup (also for #21). - Unifies logging between `aipgen` and `sipgen` with the new `aipsip` so that there are `--debug` and `--quiet` options; without either you get a nominal amount of "hand-holding" of output. - Resolve #13 so that instead of billions of redundant XML parsing and XPath lookups we use a local `sqlite3` database and LRU caching. - Factor out XML parsing from `aipgen` and `sipgen` so we can apply caching. - Clear up logging messages so we can know what's calling what. - Create a temp DB in `sipgen` and populate it with mappings from lidvids to XML files for rapid lookups - But see also #25 for other uses of that DB. - Add standardized `--version` arguments for all three programs. With these changes, running `sipgen` on my Mac¹ can process a 272GiB `insight_cameras` export in 1:03. On `pdsimg-int1`, it handles the 1.5TiB`insight_cameras` dataset in under 4 hours. Footnotes: - ¹2.4 GHz 8-core Intel Core i9, SSD - ²2.3 GHz 8-core Intel Xeon Gold 6140, unknown drive * Improvements for usability and bug fixes for validate errors * After running validate, there were a few minor fixes that needed to be implemented. * Commented out / removed several CLI options for the time being until functionality is fully developed. * Updated file naming to take into the account bundle versioning separate from the AIP/SIP version * Updated docs per new pds-deep-archive script which combines aipgen and sipgen. Refs #21 Co-authored-by: Jordan Padams <jordan.h.padams@jpl.nasa.gov>
NASA-PDS · Apr 11, 2020 · 43d0f66 · 43d0f66
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diff --git a/README.rst b/README.rst
@@ -10,6 +10,8 @@ Archival Information System (OAIS_) standards.
 Features
 ========
 
+• Provides an exectuble Python script ``pds-deep-archive``. Run ``pds-deep-archive --help`` for
+  more details.
 • Provides an exectuble Python script ``aipgen``. Run ``aipgen --help`` for
   more details.
 • Provides an exectuble Python script ``sipgen``. Run ``sipgen --help`` for
@@ -42,6 +44,7 @@ well as ``libxsl2`` 1.1.28 or later.
     
 4. You should now be able to run the deep archive utilities::
 
+    (pds-deep-archive) bash> pds-deep-archive --help
     (pds-deep-archive) bash> aipgen --help
     (pds-deep-archive) bash> sipgen --help
 
@@ -63,102 +66,10 @@ To build the software for distribution:
 3. A tar.gz should now be available in the ``dist/`` directory for distribution.
 
 
-Usage
-=====
-
-1. If not already activated, activate your virtualenv::
-
-    bash> $HOME/.virtualenvs/pds-deep-archive/bin/activate
-    (pds-deep-archive) bash>
-
-2. Then you can run aipgen. Here's a basic example using data in the test directory::
-
-    (pds-deep-archive) bash> aipgen test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
-    INFO 🏃‍♀️ Starting AIP generation for test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
-    INFO 🧾 Writing checksum manifest for /Users/kelly/Documents/Clients/JPL/PDS/Development/pds-deep-archive/test/data/ladee_test/ladee_mission_bundle to ladee_mission_bundle_checksum_manifest_v1.0.tab
-    INFO 🚢 Writing transfer manifest for /Users/kelly/Documents/Clients/JPL/PDS/Development/pds-deep-archive/test/data/ladee_test/ladee_mission_bundle to ladee_mission_bundle_transfer_manifest_v1.0.tab
-    INFO 🏷  Writing AIP label to ladee_mission_bundle_aip_v1.0.xml
-    INFO 🎉  Success! All done, files generated:
-    INFO • Checksum manifest: ladee_mission_bundle_checksum_manifest_v1.0.tab
-    INFO • Transfer manifest: ladee_mission_bundle_transfer_manifest_v1.0.tab
-    INFO • XML label: ladee_mission_bundle_aip_v1.0.xml
-    INFO 👋 Thanks for using this program! Bye!
-
-3. You can also run sipgen. Here is a basic usage example using data in the test directory::
-
-    (pds-deep-archive) bash> sipgen -c ladee_mission_bundle_checksum_manifest_v1.0.tab -s PDS_ATM -n -b https://atmos.nmsu.edu/PDS/data/PDS4/LADEE/ test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
-    ⚙︎ ``sipgen`` — Submission Information Package (SIP) Generator, version 0.0.0
-    🎉 Success! From test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml, generated these output files:
-    • Manifest: ladee_mission_bundle_sip_v1.0.tab
-    • Label: ladee_mission_bundle_sip_v1.0.xml
-
-   Note how the checksum manifest from ``aipgen`` was the input to ``-c`` in
-   ``sipgen``.
-
-Full usage from the ``--help`` flag to ``aipgen``::
-
-    usage: aipgen [-h] [-v] IN-BUNDLE.XML
-
-    Generate an Archive Information Package or AIP. An AIP consists of three
-    files: ➀ a "checksum manifest" which contains MD5 hashes of *all* files in a
-    product; ➁ a "transfer manifest" which lists the "lidvids" for files within
-    each XML label mentioned in a product; and ➂ an XML label for these two files.
-    You can use the checksum manifest file ➀ as input to ``sipgen`` in order to
-    create a Submission Information Package.
-
-    positional arguments:
-      IN-BUNDLE.XML  Root bundle XML file to read
-
-    optional arguments:
-      -h, --help     show this help message and exit
-      -v, --verbose  Verbose logging; defaults False
-
-And usage from the ``--help`` flag for ``sipgen``::
-
-    usage: sipgen [-h] [-a {MD5,SHA-1,SHA-256}] -s
-                  {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}
-                  [-u URL | -n] [-k] [-c AIP-CHECKSUM-MANIFEST.TAB]
-                  [-b BUNDLE_BASE_URL] [-v] [-i PDS4_INFORMATION_MODEL_VERSION]
-                  IN-BUNDLE.XML
-
-    Generate Submission Information Packages (SIPs) from bundles. This program
-    takes a bundle XML file as input and produces two output files: ① A Submission
-    Information Package (SIP) manifest file; and ② A PDS XML label of that file.
-    The files are created in the current working directory when this program is
-    run. The names of the files are based on the logical identifier found in the
-    bundle file, and any existing files are overwritten. The names of the
-    generated files are printed upon successful completion.
-
-    positional arguments:
-      IN-BUNDLE.XML         Bundle XML file to read
-
-    optional arguments:
-      -h, --help            show this help message and exit
-      -a {MD5,SHA-1,SHA-256}, --algorithm {MD5,SHA-1,SHA-256}
-                            File hash (checksum) algorithm; default MD5
-      -s {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}, --site {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}
-                            Provider site ID for the manifest's label; default
-                            None
-      -u URL, --url URL     URL to the registry service; default https://pds-dev-
-                            el7.jpl.nasa.gov/services/registry/pds
-      -n, --offline         Run offline, scanning bundle directory for matching
-                            files instead of querying registry service
-      -k, --insecure        Ignore SSL/TLS security issues; default False
-      -c AIP-CHECKSUM-MANIFEST.TAB, --aip AIP-CHECKSUM-MANIFEST.TAB
-                            Archive Information Product checksum manifest file
-      -b BUNDLE_BASE_URL, --bundle-base-url BUNDLE_BASE_URL
-                            Base URL prepended to URLs in the generated manifest
-                            for local files in "offline" mode
-      -v, --verbose         Verbose logging; defaults False
-      -i PDS4_INFORMATION_MODEL_VERSION, --pds4-information-model-version PDS4_INFORMATION_MODEL_VERSION
-                            Specify PDS4 Information Model version to generate
-                            SIP. Must be 1.13.0.0+; default 1.13.0.0
-
-
 Documentation
 =============
 
-Additional documentation is available in the ``docs`` directory and also TBD.
+Installation and Usage information can be found in the documentation online at https://nasa-pds-incubator.github.io/pds-deep-archive/ or the latest version is maintained under the ``docs`` directory.
 
 
 

diff --git a/docs/source/development/index.rst b/docs/source/development/index.rst
@@ -9,8 +9,8 @@ build it out::
     python3 bootstrap.py
     bin/buildout
 
-At this point, you'll have the ``aipgen`` and ``sipgen`` programs ready to run
-as ``bin/aipgen`` and ``bin/sipgen`` that's set up to use source Python code
+At this point, you'll have the ``pds-deep-archive``, ``aipgen``, ``sipgen`` programs ready to run
+as ``bin/pds-deep-archive``, ``bin/aipgen``, and ``bin/sipgen`` that's set up to use source Python code
 under ``src``. Changes you make to the code are reflected in ``bin/sipgen``
 immediately.
 

diff --git a/docs/source/usage/index.rst b/docs/source/usage/index.rst
@@ -1,81 +1,77 @@
 🏃‍♀️ Usage
 ===========
 
-This package provides two executables, ``aipgen`` that generats Archive
-Information Packages; and ``sipgen``, that generates Submission Information
-Package (SIP)—both from PDS bundles.
-
-Running ``aipgen --help`` or ``sipgen --help`` will give a summary of the
+This package provides one primary executable, ``pds-deep-archive`` that generates both
+and Archive Information Package (AIP) and a Submission Information Package (SIP). The 
+SIP is what is delivered by the PDS to the NASA Space Science Data Coordinated Archive (NSSDCA).
+For more information about the products produced, see the following references:
+* OAIS Information - http://www.oais.info/
+* AIP Information - https://www.iasa-web.org/tc04/archival-information-package-aip
+* SIP Information - https://www.iasa-web.org/tc04/submission-information-package-sip
+
+This package also comes with the two sub-components of ``pds-deep-archive`` that can be ran
+individually:
+* ``aipgen`` that generates Archive Information Packages from a PDS4 bundle
+* ``sipgen`` that generates Submission Information from a PDS4 bundle
+
+Running ``pds-deep-archive --help`` will give a summary of the
 command-line invocation, its required arguments, and any options that refine
 the behavior.  For example, to create an AIP from the LADEE 1101 bundle in
-``test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml`` run::
+``test/data/ladee_test/mission_bundle/LADEE_Bundle_1101.xml`` run::
 
-    aipgen test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
+    aipgen test/data/ladee_test/mission_bundle/LADEE_Bundle_1101.xml
 
 The program will print::
 
-    INFO 🏃‍♀️ Starting AIP generation for test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
-    INFO 🧾 Writing checksum manifest for /Users/kelly/Documents/Clients/JPL/PDS/Development/pds-deep-archive/test/data/ladee_test/ladee_mission_bundle to ladee_mission_bundle_checksum_manifest_v1.0.tab
-    INFO 🚢 Writing transfer manifest for /Users/kelly/Documents/Clients/JPL/PDS/Development/pds-deep-archive/test/data/ladee_test/ladee_mission_bundle to ladee_mission_bundle_transfer_manifest_v1.0.tab
-    INFO 🏷  Writing AIP label to ladee_mission_bundle_aip_v1.0.xml
-    INFO 🎉  Success! All done, files generated:
-    INFO • Checksum manifest: ladee_mission_bundle_checksum_manifest_v1.0.tab
-    INFO • Transfer manifest: ladee_mission_bundle_transfer_manifest_v1.0.tab
-    INFO • XML label: ladee_mission_bundle_aip_v1.0.xml
-    INFO 👋 Thanks for using this program! Bye!
-
-This creates three output files in the current directory as part of the AIP:
+    INFO 👟 PDS Deep Archive, version 0.0.0
+    INFO 🏃‍♀️ Starting AIP generation for test/data/ladee_test/mission_bundle/LADEE_Bundle_1101.xml
 
-•  ``ladee_mission_bundle_checksum_manifest_v1.0.tab``, the checksum manifest
-•  ``ladee_mission_bundle_transfer_manifest_v1.0.tab``, the transfer manifest
-•  ``ladee_mission_bundle_aip_v1.0.xml``, the label for these two files
+    INFO 🎉  Success! AIP done, files generated:
+    INFO • Checksum manifest: ladee_mission_bundle_v1.0_checksum_manifest_v1.0.tab
+    INFO • Transfer manifest: ladee_mission_bundle_v1.0_transfer_manifest_v1.0.tab
+    INFO • XML label for them both: ladee_mission_bundle_v1.0_aip_v1.0.xml
 
-The checkum manifest may then be fed into ``sipgen`` to create the SIP::
+    INFO 🏃‍♀️ Starting SIP generation for test/data/ladee_test/mission_bundle/LADEE_Bundle_1101.xml
 
-    sipgen --aip ladee_mission_bundle_checksum_manifest_v1.0.tab ladee_mission_bundle_checksum_manifest_v1.0.tab --s PDS_ATM --offline --bundle-base-url https://atmos.nmsu.edu/PDS/data/PDS4/LADEE/ test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml
+    INFO 🎉 Success! From /Users/jpadams/Documents/proj/pds/pdsen/workspace/pds-deep-archive/test/data/ladee_test/mission_bundle/LADEE_Bundle_1101.xml, generated these output files:
+    INFO • SIP Manifest: ladee_mission_bundle_v1.0_sip_v1.0.tab
+    INFO • XML label for the SIP: ladee_mission_bundle_v1.0_sip_v1.0.xml
 
-This program will print::
+    INFO 👋 That's it! Thanks for making an AIP and SIP with us today. Bye!
 
-    ⚙︎ ``sipgen`` — Submission Information Package (SIP) Generator, version 0.0.0
-    🎉 Success! From test/data/ladee_test/ladee_mission_bundle/LADEE_Bundle_1101.xml, generated these output files:
-    • Manifest: ladee_mission_bundle_sip_v1.0.tab
-    • Label: ladee_mission_bundle_sip_v1.0.xml
+This creates 5 output files in the current directory as part of the AIP and SIP Generation:
 
-And two new files will appear in the current directory:
+•  ``ladee_mission_bundle_v1.0_checksum_manifest_v1.0.tab``, the checksum manifest
+•  ``ladee_mission_bundle_v1.0_transfer_manifest_v1.0.tab``, the transfer manifest
+•  ``ladee_mission_bundle_v1.0_aip_v1.0.xml``, the label for these two files
 
-•  ``ladee_mission_bundle_sip_v1.0.tab``, the created SIP manifest as a
+•  ``ladee_mission_bundle_v1.0_sip_v1.0.tab``, the created SIP manifest as a
    tab-separated values file.
-•  ``ladee_mission_bundle_sip_v1.0.xml``, an PDS label for the SIP file.
-
-For reference, the full "usage" message from ``aipgen`` is::
-
-    usage: aipgen [-h] [-v] IN-BUNDLE.XML
-
-    Generate an Archive Information Package or AIP. An AIP consists of three
-    files: ➀ a "checksum manifest" which contains MD5 hashes of *all* files in a
-    product; ➁ a "transfer manifest" which lists the "lidvids" for files within
-    each XML label mentioned in a product; and ➂ an XML label for these two files.
-    You can use the checksum manifest file ➀ as input to ``sipgen`` in order to
-    create a Submission Information Package.
-
-    positional arguments:
-      IN-BUNDLE.XML  Root bundle XML file to read
-
-    optional arguments:
-      -h, --help     show this help message and exit
-      -v, --verbose  Verbose logging; defaults False
-
-For reference, the full "usage" message from ``sipgen`` follows::
-
-    usage: sipgen [-h] [-a {MD5,SHA-1,SHA-256}] -s
-                  {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}
-                  [-u URL | -n] [-k] [-c AIP-CHECKSUM-MANIFEST.TAB]
-                  [-b BUNDLE_BASE_URL] [-v] [-i PDS4_INFORMATION_MODEL_VERSION]
-                  IN-BUNDLE.XML
+•  ``ladee_mission_bundle_v1.0_sip_v1.0.xml``, an PDS label for the SIP file.
+
+For reference, the full "usage" message from ``pds-deep-archive`` is::
+
+    $ pds-deep-archive --help
+    usage: pds-deep-archive [-h] [--version] -s
+                            {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}
+                            [-n] -b BUNDLE_BASE_URL [-d] [-q]
+                            IN-BUNDLE.XML
+
+    Generate an Archive Information Package (AIP) and a Submission Information
+    Package (SIP). This creates three files for the AIP in the current directory
+    (overwriting them if they already exist):
+    ➀ a "checksum manifest" which contains MD5 hashes of *all* files in a product
+    ➁ a "transfer manifest" which lists the "lidvids" for files within each XML
+      label mentioned in a product
+    ➂ an XML label for these two files.
+
+    It also creates two files for the SIP (also overwriting them if they exist):
+    ① A "SIP manifest" file; and an XML label of that file too. The names of
+      the generated files are based on the logical identifier found in the
+      bundle file, and any existing files are overwritten. The names of the
+      generated files are printed upon successful completion.
+    ② A PDS XML label of that file.
 
-    Generate Submission Information Packages (SIPs) from bundles. This program
-    takes a bundle XML file as input and produces two output files: ① A Submission
-    Information Package (SIP) manifest file; and ② A PDS XML label of that file.
     The files are created in the current working directory when this program is
     run. The names of the files are based on the logical identifier found in the
     bundle file, and any existing files are overwritten. The names of the
@@ -86,22 +82,19 @@ For reference, the full "usage" message from ``sipgen`` follows::
 
     optional arguments:
       -h, --help            show this help message and exit
-      -a {MD5,SHA-1,SHA-256}, --algorithm {MD5,SHA-1,SHA-256}
-                            File hash (checksum) algorithm; default MD5
+      --version             show program's version number and exit
       -s {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}, --site {PDS_ATM,PDS_ENG,PDS_GEO,PDS_IMG,PDS_JPL,PDS_NAI,PDS_PPI,PDS_PSI,PDS_RNG,PDS_SBN}
-                            Provider site ID for the manifest's label; default
-                            None
-      -u URL, --url URL     URL to the registry service; default https://pds-dev-
-                            el7.jpl.nasa.gov/services/registry/pds
+                            Provider site ID for the manifest's label
       -n, --offline         Run offline, scanning bundle directory for matching
-                            files instead of querying registry service
-      -k, --insecure        Ignore SSL/TLS security issues; default False
-      -c AIP-CHECKSUM-MANIFEST.TAB, --aip AIP-CHECKSUM-MANIFEST.TAB
-                            Archive Information Product checksum manifest file
+                            files instead of querying registry service. NOTE: By
+                            default, set to True until online mode is available.
       -b BUNDLE_BASE_URL, --bundle-base-url BUNDLE_BASE_URL
-                            Base URL prepended to URLs in the generated manifest
-                            for local files in "offline" mode
-      -v, --verbose         Verbose logging; defaults False
-      -i PDS4_INFORMATION_MODEL_VERSION, --pds4-information-model-version PDS4_INFORMATION_MODEL_VERSION
-                            Specify PDS4 Information Model version to generate
-                            SIP. Must be 1.13.0.0+; default 1.13.0.0
+                            Base URL for Node data archive. This URL will be
+                            prepended to the bundle directory to form URLs to the
+                            products. For example, if we are generating a SIP for
+                            mission_bundle/LADEE_Bundle_1101.xml, and bundle-base-
+                            url is https://atmos.nmsu.edu/PDS/data/PDS4/LADEE/,
+                            the URL in the SIP will be https://atmos.nmsu.edu/PDS/
+                            data/PDS4/LADEE/mission_bundle/LADEE_Bundle_1101.xml.
+      -d, --debug           Log debugging messages for developers
+      -q, --quiet           Don't log informational messages
diff --git a/setup.py b/setup.py
@@ -64,7 +64,8 @@
     entry_points={
         'console_scripts': [
             'sipgen=pds.aipgen.sip:main',
-            'aipgen=pds.aipgen.aip:main'
+            'aipgen=pds.aipgen.aip:main',
+            'pds-deep-archive=pds.aipgen.main:main'
         ]
     },
     namespace_packages=['pds'],