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Differential D8908

Add ListOriginContributors
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Authored by vlorentz on Dec 1 2022, 10:40 AM.

Details

Reviewers
anlambert
Group Reviewers
Reviewers
Maniphest Tasks
T4695: Provide a collaboration graph / dataset
Commits
rDGRPHf3235e318485: Add ListOriginContributors
Summary

This Java script (and related Luigi tasks) traverse the graph in
topological order, building up the set of all contributors to a
node and its ancestors, then dump the value of this set for every
origin node they encounter.

Depends on D8883.

Diff Detail

Event Timeline

vlorentz created this revision.Dec 1 2022, 10:40 AM
Herald added a reviewer: Reviewers. · View Herald TranscriptDec 1 2022, 10:40 AM
swh-public-ci added a comment.Dec 1 2022, 10:41 AM

Build has FAILED

Patch application report for D8908 (id=32109)

Could not rebase; Attempt merge onto ec7f568b13...

Updating ec7f568..603e24a
Fast-forward
 conftest.py                                        |   1 +
 .../graph/utils/ListOriginContributors.java        | 143 +++++++
 .../org/softwareheritage/graph/utils/TopoSort.java | 134 ++++++
 mypy.ini                                           |   3 +
 requirements-luigi.txt                             |   2 +
 requirements-swh-luigi.txt                         |   2 +-
 requirements-swh.txt                               |   1 +
 swh/graph/luigi.py                                 | 468 ++++++++++++++++++++-
 swh/graph/tests/test_origin_contributors.py        | 180 ++++++++
 swh/graph/tests/test_toposort.py                   |  59 +++
 10 files changed, 989 insertions(+), 4 deletions(-)
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/ListOriginContributors.java
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java
 create mode 100644 swh/graph/tests/test_origin_contributors.py
 create mode 100644 swh/graph/tests/test_toposort.py
Changes applied before test
commit 603e24a498964309f1c42ac47fd3b8f3caa83405
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Dec 1 10:39:09 2022 +0100

    Add ListOriginContributors
    
    This Java script (and related Luigi tasks) traverse the graph in
    topological order, building up the set of all contributors to a
    node and its ancestors, then dump the value of this set for every
    origin node they encounter.

commit 39fefbfc108087b4b7f86c39312d1f94f06cc16a
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:54:30 2022 +0100

    Add Luigi task TopoSort and add a simple test

commit 78b4d9016cfd5025811607c9f6069fea1b39eb23
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Mon Nov 28 16:02:56 2022 +0100

    Improve comments

commit 0a651262c32ff3bca6951323a2ab9fe5e5204f97
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 16:15:04 2022 +0100

    Add a sample of two ancestor with each node
    
    This allows readers to efficiently get ancestors of nodes with low indegree
    (ie. most revisions), as it avoids a random access / API call.

commit 23f9256cd34f97bc3e6dd9eda51c07232f736e0f
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:54:14 2022 +0100

    revert multithreading, it's actually twice as slow as singlethread

commit a62fa7f4b7c468ee7ef731986c7d7fc33c7f4042
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:06:21 2022 +0100

    tentative multithread DFS

commit ab744a8ada1de4cb6a9d3d904406f9e40d74a3db
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 11:49:32 2022 +0100

    Implement a naive topological sort

commit 550235e4e7a04f10e5c9869e5717b16ca5a2edf8
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:01:45 2022 +0100

    luigi: Add tasks UploadGraphToS3 and DownloadGraphFromS3

Link to build: https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/297/
See console output for more information: https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/297/console

Harbormaster returned this revision to the author for changes because remote builds failed.Dec 1 2022, 10:41 AM
Harbormaster failed remote builds in B33062: Diff 32109!
vlorentz updated this revision to Diff 32111.Dec 1 2022, 11:07 AM

mypy: ignore pyzstd

swh-public-ci added a comment.Dec 1 2022, 11:14 AM

Build is green

Patch application report for D8908 (id=32111)

Could not rebase; Attempt merge onto ec7f568b13...

Updating ec7f568..36f6230
Fast-forward
 conftest.py                                        |   1 +
 .../graph/utils/ListOriginContributors.java        | 143 +++++++
 .../org/softwareheritage/graph/utils/TopoSort.java | 134 ++++++
 mypy.ini                                           |   6 +
 requirements-luigi.txt                             |   2 +
 requirements-swh-luigi.txt                         |   2 +-
 requirements-swh.txt                               |   1 +
 swh/graph/luigi.py                                 | 468 ++++++++++++++++++++-
 swh/graph/tests/test_origin_contributors.py        | 180 ++++++++
 swh/graph/tests/test_toposort.py                   |  59 +++
 10 files changed, 992 insertions(+), 4 deletions(-)
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/ListOriginContributors.java
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java
 create mode 100644 swh/graph/tests/test_origin_contributors.py
 create mode 100644 swh/graph/tests/test_toposort.py
Changes applied before test
commit 36f62302756d56c3d61234e2d46d582fe5125853
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Dec 1 10:39:09 2022 +0100

    Add ListOriginContributors
    
    This Java script (and related Luigi tasks) traverse the graph in
    topological order, building up the set of all contributors to a
    node and its ancestors, then dump the value of this set for every
    origin node they encounter.

commit 39fefbfc108087b4b7f86c39312d1f94f06cc16a
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:54:30 2022 +0100

    Add Luigi task TopoSort and add a simple test

commit 78b4d9016cfd5025811607c9f6069fea1b39eb23
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Mon Nov 28 16:02:56 2022 +0100

    Improve comments

commit 0a651262c32ff3bca6951323a2ab9fe5e5204f97
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 16:15:04 2022 +0100

    Add a sample of two ancestor with each node
    
    This allows readers to efficiently get ancestors of nodes with low indegree
    (ie. most revisions), as it avoids a random access / API call.

commit 23f9256cd34f97bc3e6dd9eda51c07232f736e0f
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:54:14 2022 +0100

    revert multithreading, it's actually twice as slow as singlethread

commit a62fa7f4b7c468ee7ef731986c7d7fc33c7f4042
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:06:21 2022 +0100

    tentative multithread DFS

commit ab744a8ada1de4cb6a9d3d904406f9e40d74a3db
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 11:49:32 2022 +0100

    Implement a naive topological sort

commit 550235e4e7a04f10e5c9869e5717b16ca5a2edf8
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:01:45 2022 +0100

    luigi: Add tasks UploadGraphToS3 and DownloadGraphFromS3

See https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/298/ for more details.

Harbormaster completed remote builds in B33064: Diff 32111.Dec 1 2022, 11:14 AM
vlorentz requested review of this revision.Dec 1 2022, 11:14 AM
vlorentz updated this revision to Diff 32112.Dec 1 2022, 11:26 AM

fix copyright header

vlorentz added a child revision: D8910: Regenerate the test dataset to include a release with no author.Dec 1 2022, 11:31 AM
swh-public-ci added a comment.Dec 1 2022, 11:34 AM

Build is green

Patch application report for D8908 (id=32112)

Could not rebase; Attempt merge onto ec7f568b13...

Updating ec7f568..9972a08
Fast-forward
 conftest.py                                        |   1 +
 .../graph/utils/ListOriginContributors.java        | 141 +++++++
 .../org/softwareheritage/graph/utils/TopoSort.java | 134 ++++++
 mypy.ini                                           |   6 +
 requirements-luigi.txt                             |   2 +
 requirements-swh-luigi.txt                         |   2 +-
 requirements-swh.txt                               |   1 +
 swh/graph/luigi.py                                 | 468 ++++++++++++++++++++-
 swh/graph/tests/test_origin_contributors.py        | 180 ++++++++
 swh/graph/tests/test_toposort.py                   |  59 +++
 10 files changed, 990 insertions(+), 4 deletions(-)
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/ListOriginContributors.java
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java
 create mode 100644 swh/graph/tests/test_origin_contributors.py
 create mode 100644 swh/graph/tests/test_toposort.py
Changes applied before test
commit 9972a08685c3d6e45119494ee6404c66a6374f26
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Dec 1 10:39:09 2022 +0100

    Add ListOriginContributors
    
    This Java script (and related Luigi tasks) traverse the graph in
    topological order, building up the set of all contributors to a
    node and its ancestors, then dump the value of this set for every
    origin node they encounter.

commit 39fefbfc108087b4b7f86c39312d1f94f06cc16a
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:54:30 2022 +0100

    Add Luigi task TopoSort and add a simple test

commit 78b4d9016cfd5025811607c9f6069fea1b39eb23
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Mon Nov 28 16:02:56 2022 +0100

    Improve comments

commit 0a651262c32ff3bca6951323a2ab9fe5e5204f97
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 16:15:04 2022 +0100

    Add a sample of two ancestor with each node
    
    This allows readers to efficiently get ancestors of nodes with low indegree
    (ie. most revisions), as it avoids a random access / API call.

commit 23f9256cd34f97bc3e6dd9eda51c07232f736e0f
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:54:14 2022 +0100

    revert multithreading, it's actually twice as slow as singlethread

commit a62fa7f4b7c468ee7ef731986c7d7fc33c7f4042
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:06:21 2022 +0100

    tentative multithread DFS

commit ab744a8ada1de4cb6a9d3d904406f9e40d74a3db
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 11:49:32 2022 +0100

    Implement a naive topological sort

commit 550235e4e7a04f10e5c9869e5717b16ca5a2edf8
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:01:45 2022 +0100

    luigi: Add tasks UploadGraphToS3 and DownloadGraphFromS3

See https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/299/ for more details.

Harbormaster completed remote builds in B33065: Diff 32112.Dec 1 2022, 11:34 AM
vlorentz added a task: T4695: Provide a collaboration graph / dataset.Dec 1 2022, 4:15 PM
anlambert accepted this revision.Dec 6 2022, 4:04 PM
anlambert added a subscriber: anlambert.

LGTM, added a couple of nitpicks as inline comments.

requirements-swh.txt
3

put it in requirements-test.txt then

swh/graph/luigi.py
456–458
with open(tmp_output_path, "wb") as tmp_output:
    subprocess.run(
        ["bash", "-c", script.strip()], stdout=tmp_output, env=env, check=True
    )

I find it more readable this way but maybe there is a reason you cannot use it.

548–553

More readable by wrapping lines imho.

_run_script(
    f"""
    psql '{self.storage_dsn}' -c "\
        COPY (select encode(digest(fullname, 'sha256'), 'base64') as sha256_base64,\
                      encode(fullname, 'base64') as base64,\
                      encode(fullname, 'escape') as escaped from person)\
        TO STDOUT CSV HEADER\
    " | zstdmt -19
    """,
    self.deanonymization_table_path,
)
563

s/cas/was/

This revision is now accepted and ready to land.Dec 6 2022, 4:04 PM
vlorentz marked 2 inline comments as done.Dec 7 2022, 9:45 AM
vlorentz added inline comments.
requirements-swh.txt
3

It would need to be in requirements-swh-test.txt so it's installed from the local clone, but our tooling doesn't currently support that.

swh/graph/luigi.py
456–458

You're right, it works and has same throughput and CPU usage.

vlorentz updated this revision to Diff 32159.Dec 7 2022, 10:08 AM

rebase

vlorentz mentioned this in D8930: origin_contributors: Fix typo and improve readability.Dec 7 2022, 10:09 AM
vlorentz added a comment.Dec 7 2022, 10:09 AM

fixed by D8930

swh-public-ci added a comment.Dec 7 2022, 10:21 AM

Build was aborted

Patch application report for D8908 (id=32159)

Could not rebase; Attempt merge onto 0a8ae5de6f...

Updating 0a8ae5d..f3235e3
Fast-forward
 conftest.py                                        |   1 +
 .../graph/utils/ListOriginContributors.java        | 141 +++++++
 .../org/softwareheritage/graph/utils/TopoSort.java | 134 ++++++
 mypy.ini                                           |   6 +
 requirements-luigi.txt                             |   2 +
 requirements-swh-luigi.txt                         |   2 +-
 requirements-swh.txt                               |   1 +
 swh/graph/luigi.py                                 | 468 ++++++++++++++++++++-
 swh/graph/tests/test_origin_contributors.py        | 180 ++++++++
 swh/graph/tests/test_toposort.py                   |  59 +++
 10 files changed, 990 insertions(+), 4 deletions(-)
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/ListOriginContributors.java
 create mode 100644 java/src/main/java/org/softwareheritage/graph/utils/TopoSort.java
 create mode 100644 swh/graph/tests/test_origin_contributors.py
 create mode 100644 swh/graph/tests/test_toposort.py
Changes applied before test
commit f3235e3184850b074b2a332686911688aafcdd84
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Dec 1 10:39:09 2022 +0100

    Add ListOriginContributors
    
    This Java script (and related Luigi tasks) traverse the graph in
    topological order, building up the set of all contributors to a
    node and its ancestors, then dump the value of this set for every
    origin node they encounter.

commit ab2703efcb9ad93a3d959596ed7edef27d908164
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:54:30 2022 +0100

    Add Luigi task TopoSort and add a simple test

commit 58f44785816bde0f6cdbf86e3ff6f1fbf385a487
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Mon Nov 28 16:02:56 2022 +0100

    Improve comments

commit 922894410b6e14f5a9eeec445d4a0b503df77a9e
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 16:15:04 2022 +0100

    Add a sample of two ancestor with each node
    
    This allows readers to efficiently get ancestors of nodes with low indegree
    (ie. most revisions), as it avoids a random access / API call.

commit 7bee5d47a6eb49ac594f2d019222c176373a5248
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:54:14 2022 +0100

    revert multithreading, it's actually twice as slow as singlethread

commit 30dad16a2365021bedf72df78d0753e125765016
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 12:06:21 2022 +0100

    tentative multithread DFS

commit ed6636c26be869a7309581d0ec664488b4d69e9f
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Thu Nov 24 11:49:32 2022 +0100

    Implement a naive topological sort

commit b8dc411ccd304597df96d7dd36158fb86e5239fd
Author: Valentin Lorentz <vlorentz@softwareheritage.org>
Date:   Tue Nov 29 17:01:45 2022 +0100

    luigi: Add tasks UploadGraphToS3 and DownloadGraphFromS3

Link to build: https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/312/
See console output for more information: https://jenkins.softwareheritage.org/job/DGRPH/job/tests-on-diff/312/console

Harbormaster failed remote builds in B33113: Diff 32159!Dec 7 2022, 10:21 AM
This revision was landed with ongoing or failed builds.Dec 7 2022, 10:40 AM
Closed by commit rDGRPHf3235e318485: Add ListOriginContributors (authored by vlorentz). · Explain Why
This revision was automatically updated to reflect the committed changes.
vlorentz added a commit: rDGRPHf3235e318485: Add ListOriginContributors.

Revision Contents
Changeset List

PathSizeCoverage (All)Coverage (Touched)
1 line--
java/
src/
main/
java/
org/
softwareheritage/
graph/
utils/
143 lines--
3 lines--
1 line--
1 line--
swh/
graph/
205 lines63%
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tests/
180 lines100%
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11 lines100%
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Diff 32111

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conftest.py

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java/src/main/java/org/softwareheritage/graph/utils/ListOriginContributors.java

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mypy.ini

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requirements-luigi.txt

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requirements-swh.txt

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swh/graph/luigi.py

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swh/graph/tests/test_origin_contributors.py

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swh/graph/tests/test_toposort.py

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