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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
39 stars 8 forks source link

Design JSON Lines Representation for KG2 #321

Closed ecwood closed 1 year ago

ecwood commented 1 year ago

This might help with memory issues with KG2. This will not be ready in time for KG2.8.4 at all.

ecwood commented 1 year ago

Possibly split into nodes and edges JSON

ecwood commented 1 year ago

In order to do this, we first need to consider which files are using kg2_util's save_json function. According to GitHub, there are 32 files that do so:

ecwood commented 1 year ago

With 699c202, I successfully made a nodes and edges JSON Lines file for DrugBank (no errors).

ecwood commented 1 year ago

As of c083301, these files have been adapted to JSON Lines representation. Only DrugBank has been tested:

ecwood commented 1 year ago

This will also help with the Steve's request to slim down the number of Snakefiles, because we'd no longer need a separate file for doing a test build with SemMedDB (since it will be streaming, the long load time will no longer be an issue - we can just stop streaming after 10000 results) and we'd no longer need a separate item in the Snakefile for building a nodes only file (they will automatically be separated). I think this process also will be beneficial for giving a hard look to things that have been grandfathered into the build process (especially scripts like multi_ont_to_json_kg.py which doesn't even follow the same naming convention as the others).

ecwood commented 1 year ago

At the end of today, all of the conversion scripts have been updated to use JSON Lines. I have also started working on updating report_stats_on_json_kg.py to use JSON Lines, but it isn't completely ironed out yet. f28365e didn't fail, but it also didn't give any meaningful output.

ecwood commented 1 year ago

With 806c369, the report script is working on JSON Lines files.

Next up, we need to ensure that a nodes or edges only JSON Lines file can be saved (this needs to be done in kg2_util.py).

We also need to ensure that the files opened in report_stats_on_json_kg.py are actually closed after they are opened.

ecwood commented 1 year ago

We also need to ensure that the files opened in report_stats_on_json_kg.py are actually closed after they are opened.

With 3e3b676, this step is done.

ecwood commented 1 year ago
Conversion Script JSON Lines Working? JSON Lines Runtime Original Runtime (from #312)
chembl_mysql_to_kg_json.py 00:00:00

Start: <br>End: | 00:24:06

Start: Fri Jul 21 01:27:01 2023
End: Fri Jul 21 01:51:07 2023
dgidb_tsv_to_kg_json.py Yes 00:00:02

Start: 2023-07-20 22:39:47
End: 2023-07-20 22:39:49		 00:00:08

Start: Thu Jul 20 19:26:17 2023
End: Thu Jul 20 19:26:25 2023
disgenet_tsv_to_kg_json.py Yes 00:00:21

Start: 2023-07-20 22:42:14
End: 2023-07-20 22:42:35		 00:00:47

Start: Thu Jul 20 19:29:40 2023
End: Thu Jul 20 19:30:27 2023
drugbank_xml_to_kg_json.py Yes 00:05:14

Start: 2023-07-21 05:10:35
End: 2023-07-21 05:15:49		 00:08:30

Start: Thu Jul 20 19:25:47 2023
End: Thu Jul 20 19:34:17 2023
drugcentral_json_to_kg_json.py Yes 00:00:09

Start: 2023-07-21 05:17:10
End: 2023-07-21 05:17:19		 00:00:31

Start: Thu Jul 20 19:29:43 2023
End: Thu Jul 20 19:30:14 2023
ensembl_json_to_kg_json.py Yes 00:02:33

Start: 2023-07-20 22:44:41
End: 2023-07-20 22:47:14		 00:05:18

Start: Thu Jul 20 19:28:56 2023
End: Thu Jul 20 19:34:14 2023
go_gpa_to_kg_json.py Yes 00:00:14

Start: 2023-07-21 05:53:11
End: 2023-07-21 05:53:25		 00:00:35

Start: Thu Jul 20 19:25:38 2023
End: Thu Jul 20 19:26:13 2023
hmdb_xml_to_kg_json.py Yes 00:18:37

Start: 2023-07-21 05:45:13
End: 2023-07-21 06:03:50		 00:21:17

Start: Thu Jul 20 19:27:01 2023
End: Thu Jul 20 19:48:18 2023
intact_tsv_to_kg_json.py Yes 00:00:37

Start: 2023-07-21 05:51:29
End: 2023-07-21 05:52:06		 00:00:55

Start: Thu Jul 20 19:26:54 2023
End: Thu Jul 20 19:27:49 2023
jensenlab_tsv_to_kg_json.py 00:00:00

Start: <br>End: |00:16:20

Start: Thu Jul 20 21:36:21 2023
End: Thu Jul 20 21:52:41 2023
kegg_json_to_kg_json.py Yes, with the changes from df3e7ee 00:00:15

Start: 2023-07-21 06:00:24
End: 2023-07-21 06:00:39		 00:00:00

Start: <br>End:
mirbase_dat_to_kg_json.py Yes 00:00:02

Start: 2023-07-21 05:54:32
End: 2023-07-21 05:54:34		 00:00:06

Start: Thu Jul 20 19:26:11 2023
End: Thu Jul 20 19:26:17 2023
multi_ont_to_json_kg.py 00:00:00

Start: <br>End: | 07:39:18

Start: Fri Jul 21 05:37:16
End: Fri Jul 21 13:16:34
* Entire build-multi-ont-kg.sh
ncbigene_tsv_to_kg_json.py 00:00:00

Start: <br>End: | 00:00:29

Start: Thu Jul 20 19:25:35 2023
End: Thu Jul 20 19:26:04 2023
reactome_mysql_to_kg_json.py Yes 00:01:25

Start: 2023-07-21 05:25:45
End: 2023-07-21 05:27:10		 00:01:52

Start: Thu Jul 20 21:30:43 2023
End: Thu Jul 20 21:32:35 2023
repodb_csv_to_kg_json.py 00:00:00

Start: <br>End: | 00:00:23

Start: Thu Jul 20 19:25:35 2023
End: Thu Jul 20 19:25:58 2023
semmeddb_tuple_list_json_to_kg_json.py 00:34:49

Start: 2023-07-25 06:43:36
End: 2023-07-25 07:17:25
*No hang time at the end		 18:57:46

Start: 2023-07-21 17:56:10
End: 2023-07-22 12:53:56 *Estimate based on log file birth and modify (at least additional 5 hours in hang time)
smpdb_csv_to_kg_json.py 00:00:00

Start: <br>End: | 02:41:11

Start: Thu Jul 20 21:36:51 2023
End: Fri Jul 21 00:18:02 2023
unichem_tsv_to_edges_json.py Yes 00:00:02

Start: 2023-07-21 05:29:06
End: 2023-07-21 05:29:08		 00:00:14

Start: Thu Jul 20 21:36:07 2023
End: Thu Jul 20 21:36:21 2023
uniprotkb_dat_to_json.py No, see comment below Yes, with commit 06d39b2, it is working 00:02:42

Start: 2023-07-21 05:44:41
End: 2023-07-21 05:47:23		 00:02:51

Start: Thu Jul 20 21:55:42 2023
End: Thu Jul 20 21:58:33 2023
ecwood commented 1 year ago

I committed a string of updates so that each of the scripts saves the starting and ending date, to make checking JSON Lines times easier (I don't want to use Snakemake since I'm not doing a complete build).

Having done that, I noticed there are a lot of inconsistencies in how the date is saved between different files. It would likely be beneficial to standardize on one solution (perhaps kg2_util.date()). Expanding on that, there are a lot of similarities between all of these scripts in general, but the exact same functionality is often formatted in completely different ways. Long term, it would also be great to standardize code structure. That would make it easier to maintain.

ecwood commented 1 year ago

While testing UniProtKB's JSON Lines changes, I encountered this error:

Traceback (most recent call last):
  File "uniprotkb_dat_to_json.py", line 430, in <module>
    nodes_dict = make_nodes(uniprot_records, nodes_output)
  File "uniprotkb_dat_to_json.py", line 406, in make_nodes
    nodes_output.write(node_dict)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/jsonlines/jsonlines.py", line 518, in write
    line = self._dumps(obj)
  File "/usr/lib/python3.7/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python3.7/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/usr/lib/python3.7/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type set is not JSON serializable
ecwood commented 1 year ago

Left To Do On This Issue:

ecwood commented 1 year ago

There was an issue with the semmeddb_mysql_to_tuple_list_json.py update:

Starting semmeddb_mysql_to_tuple_list_json.py at 2023-07-24 19:20:25
Traceback (most recent call last):
  File "semmeddb_mysql_to_tuple_list_json.py", line 87, in <module>
    cursor.execute(sql_statement)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute
    result = self._query(query)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query
    conn.query(q)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query
    self._affected_rows = self._read_query_result(unbuffered=unbuffered)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result
    result.read()
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 1082, in read
    self._read_result_packet(first_packet)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 1152, in _read_result_packet
    self._read_rowdata_packet()
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 1186, in _read_rowdata_packet
    packet = self.connection._read_packet()
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet
    packet.check_error()
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error
    err.raise_mysql_exception(self._data)
  File "/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception
    raise errorclass(errno, errval)
pymysql.err.InternalError: (3, "Error writing file '/tmp/MYfd=47' (OS errno 28 - No space left on device)")
ecwood commented 1 year ago

With the new streaming method of saving the data from SemMedDB, semmeddb_mysql_to_tuple_list_json.py only takes 2 hours, 32 minutes, and 4 seconds. I was expecting a much more challenging hit to efficiency with the more complicated MySQL command. However, there are a lot of edges with an error like:

/home/ubuntu/kg2-venv/lib/python3.7/site-packages/pymysql/cursors.py:170: Warning: (1260, 'Row 1710 was cut by GROUP_CONCAT()')

that we need to address. Currently, we have to simply drop the edges because they come out of MySQL too messy to parse.

It used to take roughly 1 hour and 7 minutes, based on an estimate from an older extraction script. Thus, we are not increasing the time significantly if it reduces the length of semmeddb_tuple_list_json_to_kg_json.py, which currently takes around 19 hours plus at least 5 hours of hang time.

ecwood commented 1 year ago

Even after c4ea737, there were 1024 lines dropped because of the max concat length. I am not entirely sure how much bigger I am comfortable making it. Also, for documentation purposes, on an r5a.8xlarge instance, it seems to max out at 13.9% of the available memory (for semmeddb_mysql_to_tuple_list_json.py) which is pretty good.

Also, for documentation's purpose, note that semmeddb_mysql_out.jsonl is 25,825,819 lines long.

ecwood commented 1 year ago

The JSON Lines-based SemMedDB conversion script was much more efficient than the original. It took 34 minutes and 49 seconds, a huge improvement from over 18 hours (without hang time, 24 hours with hang time). There were 19341 edges marked as needing longer max group concat out of over 25800000 rows (less than 0.075%). While we should address the optimal length of max group concat, I don't think it is urgent right now due to the minor scale of the issue. Additionally, semmeddb_tuple_list_json_to_kg_json.py maxed out at using 0.1% of the available memory on the r5a.8xlarge instance.

ecwood commented 1 year ago

Unsurprisingly, the string of updates (culminating in 56341a8) that worked on updating the Snakemake build system to use our JSON Lines input/output structure failed. (This was a lot of changes and there was likely to be at least one error.) This doesn't mean all of those commits are bad though. This just means there are additional spots to address.

ecwood commented 1 year ago

With 654768d, the Snakemake build system (not including documentation) is up to date with the JSON Lines update.

ecwood commented 1 year ago

Also, note that the commits above (including 56341a8 and d76afc0) reduce the number of Snakefiles in the repository, which Steve indicated was a goal at the beginning of the summer.

ecwood commented 1 year ago

I am currently running an end-to-end test on an r5a.8xlarge instance and tracking the memory usage in ~/kg2-code/instance-data-2023-07-26-23-38-58.log.

ecwood commented 1 year ago

The end-to-end test failed at multi ont:

ubuntu@ip-172-31-59-112:~/kg2-build$ cat build-multi-ont-kg.log 
+ set -o nounset -o pipefail -o errexit
+ [[ /home/ubuntu/kg2-build/umls_cuis.tsv == \-\-\h\e\l\p ]]
+ [[ /home/ubuntu/kg2-build/umls_cuis.tsv == \-\h ]]
+ echo '================= starting build-multi-ont-kg.sh ================='
================= starting build-multi-ont-kg.sh =================
+ date
Thu Jul 27 05:43:52 UTC 2023
++ dirname /home/ubuntu/kg2-code/build-multi-ont-kg.sh
+ config_dir=/home/ubuntu/kg2-code
+ source /home/ubuntu/kg2-code/master-config.shinc
++ '[' -z ']'
++ test_suffix=
++ BUILD_DIR=/home/ubuntu/kg2-build
++ VENV_DIR=/home/ubuntu/kg2-venv
++ CODE_DIR=/home/ubuntu/kg2-code
++ umls_dir=/home/ubuntu/kg2-build/umls
++ umls_dest_dir=/home/ubuntu/kg2-build/umls/META
++ s3_region=us-west-2
++ s3_bucket=rtx-kg2
++ s3_bucket_public=rtx-kg2-public
++ s3_bucket_versioned=rtx-kg2-versioned
++ s3_cp_cmd='aws s3 cp --no-progress --region us-west-2'
++ mysql_conf=/home/ubuntu/kg2-build/mysql-config.conf
++ curl_get='curl -s -L -f -k'
++ python_command='/home/ubuntu/kg2-venv/bin/python3 -u'
++ curies_to_categories_file=/home/ubuntu/kg2-code/curies-to-categories.yaml
++ curies_to_urls_file=/home/ubuntu/kg2-code/curies-to-urls-map.yaml
++ predicate_mapping_file=/home/ubuntu/kg2-code/predicate-remap.yaml
++ infores_mapping_file=/home/ubuntu/kg2-code/kg2-provided-by-curie-to-infores-curie.yaml
++ ont_load_inventory_file=/home/ubuntu/kg2-code/ont-load-inventory.yaml
++ umls2rdf_config_master=/home/ubuntu/kg2-code/umls2rdf-umls.conf
++ rtx_config_file=RTXConfiguration-config.json
++ biolink_model_version=3.5.2
+ build_flag=
+ biolink_base_url_no_version=https://raw.githubusercontent.com/biolink/biolink-model/
+ biolink_raw_base_url=https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/biolink-model.owl.ttl
+ biolink_raw_base_url_curies_urls_map=https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/
+ curies_urls_map_replace_string='\    biolink_download_source: https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/'
+ ont_load_inventory_replace_string='\  url: https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/biolink-model.owl.ttl'
+ sed -i '\@https://raw.githubusercontent.com/biolink/biolink-model/@c\  url: https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/biolink-model.owl.ttl' /home/ubuntu/kg2-code/ont-load-inventory.yaml
+ sed -i '\@https://raw.githubusercontent.com/biolink/biolink-model/@c\    biolink_download_source: https://raw.githubusercontent.com/biolink/biolink-model/v3.5.2/' /home/ubuntu/kg2-code/curies-to-urls-map.yaml
+ [[ '' == \t\e\s\t ]]
+ test_suffix=
+ test_arg=
+ umls_cuis_file=/home/ubuntu/kg2-build/umls_cuis.tsv
+ output_nodes_file=/home/ubuntu/kg2-build/kg2-ont-nodes.jsonl
+ output_edges_file=/home/ubuntu/kg2-build/kg2-ont-edges.jsonl
/home/ubuntu/kg2-code/build-multi-ont-kg.sh: line 50: output_file: unbound variable
+ output_file_base=
ecwood commented 1 year ago

In the end-to-end test, here is the log output for timing purposes:

ubuntu@ip-172-31-59-112:~/kg2-build$ cat build-kg2-snakemake-extraction-conversion-merge.log 
+ echo '================= starting build-kg2-snakemake.sh =================='
================= starting build-kg2-snakemake.sh ==================
+ date
Sat Jul 29 20:44:52 UTC 2023
+ snakemake_config_file=/home/ubuntu/kg2-code/snakemake-config.yaml
+ snakefile=/home/ubuntu/kg2-code/Snakefile
+ /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/generate_snakemake_config_file.py ./master-config.shinc /home/ubuntu/kg2-code/snakemake-config-var.yaml /home/ubuntu/kg2-code/snakemake-config.yaml
+ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/kg2-build
+ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/kg2-build
+ graphic=
+ [[ all == \g\r\a\p\h\i\c ]]
+ [[ -F == \g\r\a\p\h\i\c ]]
+ [[ '' == \g\r\a\p\h\i\c ]]
+ echo configfile: '"/home/ubuntu/kg2-code/snakemake-config.yaml"'
+ cat /home/ubuntu/kg2-code/Snakefile-finish
+ echo 'include: "Snakefile-pre-etl"'
+ echo 'include: "Snakefile-conversion"'
+ echo 'include: "Snakefile-post-etl"'
+ [[ all == \a\l\l ]]
+ echo 'include: "Snakefile-extraction"'
+ cd /home/ubuntu
+ /home/ubuntu/kg2-venv/bin/snakemake --snakefile /home/ubuntu/kg2-code/Snakefile -F -R Finish -j 16
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   ChEMBL
    1   ChEMBL_Conversion
    1   DGIdb
    1   DGIdb_Conversion
    1   DisGeNET
    1   DisGeNET_Conversion
    1   DrugBank
    1   DrugBank_Conversion
    1   DrugCentral
    1   DrugCentral_Conversion
    1   Ensembl
    1   Ensembl_Conversion
    1   Finish
    1   GO_Annotations
    1   GO_Annotations_Conversion
    1   HMDB
    1   HMDB_Conversion
    1   IntAct
    1   IntAct_Conversion
    1   JensenLab
    1   JensenLab_Conversion
    1   KEGG
    1   KEGG_Conversion
    1   Merge
    1   NCBIGene
    1   NCBIGene_Conversion
    1   Ontologies_and_TTL
    1   Reactome
    1   Reactome_Conversion
    1   RepoDB
    1   RepoDB_Conversion
    1   SMPDB
    1   SMPDB_Conversion
    1   SemMedDB
    1   SemMedDB_Conversion
    1   Simplify
    1   Simplify_Stats
    1   Slim
    1   Stats
    1   TSV
    1   UMLS
    1   UniChem
    1   UniChem_Conversion
    1   UniProtKB
    1   UniProtKB_Conversion
    1   ValidationTests
    1   miRBase
    1   miRBase_Conversion
    48

[Sat Jul 29 20:44:53 2023]
rule ValidationTests:
    output: /home/ubuntu/kg2-build/validation-placeholder.empty
    log: /home/ubuntu/kg2-build/run-validation-tests.log
    jobid: 28

[Sat Jul 29 20:45:28 2023]
Finished job 28.
1 of 48 steps (2%) done

[Sat Jul 29 20:45:28 2023]
rule Ensembl:
    input: /home/ubuntu/kg2-code/extract-ensembl.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/ensembl/ensembl_genes_homo_sapiens.json
    log: /home/ubuntu/kg2-build/extract-ensembl.log
    jobid: 32

[Sat Jul 29 20:45:28 2023]
rule JensenLab:
    input: /home/ubuntu/kg2-code/extract-jensenlab.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/jensenlab-placeholder.empty
    log: /home/ubuntu/kg2-build/extract-jensenlab.log
    jobid: 43

[Sat Jul 29 20:45:28 2023]
rule DrugCentral:
    input: /home/ubuntu/kg2-code/extract-drugcentral.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/drugcentral/drugcentral_psql_json.json
    log: /home/ubuntu/kg2-build/extract-drugcentral.log
    jobid: 44

[Sat Jul 29 20:45:28 2023]
rule NCBIGene:
    input: /home/ubuntu/kg2-code/extract-ncbigene.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/ncbigene/Homo_sapiens_gene_info.tsv
    log: /home/ubuntu/kg2-build/extract-ncbigene.log
    jobid: 34

[Sat Jul 29 20:45:28 2023]
rule ChEMBL:
    input: /home/ubuntu/kg2-code/extract-chembl.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/chembl-placeholder.empty
    log: /home/ubuntu/kg2-build/extract-chembl.log
    jobid: 31

[Sat Jul 29 20:45:28 2023]
rule IntAct:
    input: /home/ubuntu/kg2-code/extract-intact.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/intact.txt
    log: /home/ubuntu/kg2-build/extract-intact.log
    jobid: 45

[Sat Jul 29 20:45:28 2023]
rule UniChem:
    input: /home/ubuntu/kg2-code/extract-unichem.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/unichem/unichem-mappings.tsv
    log: /home/ubuntu/kg2-build/extract-unichem.log
    jobid: 33

[Sat Jul 29 20:45:28 2023]
rule SemMedDB:
    input: /home/ubuntu/kg2-code/extract-semmeddb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/semmeddb-tuplelist.jsonl, /home/ubuntu/kg2-build/semmed-exclude-list.yaml, /home/ubuntu/kg2-build/semmeddb-version.txt
    log: /home/ubuntu/kg2-build/extract-semmeddb.log
    jobid: 30

[Sat Jul 29 20:45:28 2023]
rule DisGeNET:
    input: /home/ubuntu/kg2-code/extract-disgenet.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/all_gene_disease_pmid_associations.tsv
    log: /home/ubuntu/kg2-build/extract-disgenet.log
    jobid: 46

[Sat Jul 29 20:45:28 2023]
rule GO_Annotations:
    input: /home/ubuntu/kg2-code/extract-go-annotations.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/goa_human.gpa
    log: /home/ubuntu/kg2-build/extract-go-annotations.log
    jobid: 40

[Sat Jul 29 20:45:29 2023]
rule UMLS:
    input: /home/ubuntu/kg2-code/extract-umls.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/umls_cuis.tsv
    log: /home/ubuntu/kg2-build/extract-umls.log
    jobid: 27

[Sat Jul 29 20:45:29 2023]
rule SMPDB:
    input: /home/ubuntu/kg2-code/extract-smpdb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/smpdb/pathbank_pathways.csv
    log: /home/ubuntu/kg2-build/extract-smpdb.log
    jobid: 38

[Sat Jul 29 20:45:29 2023]
rule UniProtKB:
    input: /home/ubuntu/kg2-code/extract-uniprotkb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/uniprotkb/uniprot_sprot.dat
    log: /home/ubuntu/kg2-build/extract-uniprotkb.log
    jobid: 29

[Sat Jul 29 20:45:29 2023]
rule Reactome:
    input: /home/ubuntu/kg2-code/extract-reactome.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/reactome-placeholder.empty
    log: /home/ubuntu/kg2-build/extract-reactome.log
    jobid: 41

[Sat Jul 29 20:45:29 2023]
rule DGIdb:
    input: /home/ubuntu/kg2-code/extract-dgidb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/dgidb/interactions.tsv
    log: /home/ubuntu/kg2-build/extract-dgidb.log
    jobid: 35

[Sat Jul 29 20:45:29 2023]
rule miRBase:
    input: /home/ubuntu/kg2-code/extract-mirbase.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/miRNA.dat
    log: /home/ubuntu/kg2-build/extract-mirbase.log
    jobid: 42

[Sat Jul 29 20:45:29 2023]
Finished job 35.
2 of 48 steps (4%) done

[Sat Jul 29 20:45:29 2023]
rule DGIdb_Conversion:
    input: /home/ubuntu/kg2-code/dgidb_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/dgidb/interactions.tsv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-dgidb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-dgidb-edges.jsonl
    log: /home/ubuntu/kg2-build/dgidb_tsv_to_kg_jsonl.log
    jobid: 14

[Sat Jul 29 20:45:31 2023]
Finished job 34.
3 of 48 steps (6%) done

[Sat Jul 29 20:45:31 2023]
rule NCBIGene_Conversion:
    input: /home/ubuntu/kg2-code/ncbigene_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/ncbigene/Homo_sapiens_gene_info.tsv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-ncbigene-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ncbigene-edges.jsonl
    log: /home/ubuntu/kg2-build/ncbigene_tsv_to_kg_jsonl.log
    jobid: 13

[Sat Jul 29 20:45:33 2023]
Finished job 40.
4 of 48 steps (8%) done

[Sat Jul 29 20:45:33 2023]
rule GO_Annotations_Conversion:
    input: /home/ubuntu/kg2-code/go_gpa_to_kg_jsonl.py, /home/ubuntu/kg2-build/goa_human.gpa, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-go-annotations-nodes.jsonl, /home/ubuntu/kg2-build/kg2-go-annotations-edges.jsonl
    log: /home/ubuntu/kg2-build/go_gpa_to_kg_jsonl.log
    jobid: 19

[Sat Jul 29 20:45:35 2023]
Finished job 46.
5 of 48 steps (10%) done

[Sat Jul 29 20:45:35 2023]
rule DisGeNET_Conversion:
    input: /home/ubuntu/kg2-code/disgenet_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/all_gene_disease_pmid_associations.tsv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-disgenet-nodes.jsonl, /home/ubuntu/kg2-build/kg2-disgenet-edges.jsonl
    log: /home/ubuntu/kg2-build/disgenet_tsv_to_kg_jsonl.log
    jobid: 25

[Sat Jul 29 20:45:36 2023]
Finished job 14.
6 of 48 steps (12%) done

[Sat Jul 29 20:45:36 2023]
rule DrugBank:
    input: /home/ubuntu/kg2-code/extract-drugbank.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/drugbank.xml
    log: /home/ubuntu/kg2-build/extract-drugbank.log
    jobid: 37

[Sat Jul 29 20:45:42 2023]
Finished job 42.
7 of 48 steps (15%) done

[Sat Jul 29 20:45:42 2023]
rule miRBase_Conversion:
    input: /home/ubuntu/kg2-code/mirbase_dat_to_kg_jsonl.py, /home/ubuntu/kg2-build/miRNA.dat, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-mirbase-nodes.jsonl, /home/ubuntu/kg2-build/kg2-mirbase-edges.jsonl
    log: /home/ubuntu/kg2-build/mirbase_dat_to_kg_jsonl.log
    jobid: 21

[Sat Jul 29 20:45:48 2023]
Finished job 21.
8 of 48 steps (17%) done

[Sat Jul 29 20:45:48 2023]
rule HMDB:
    input: /home/ubuntu/kg2-code/extract-hmdb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/hmdb_metabolites.xml
    log: /home/ubuntu/kg2-build/extract-hmdb.log
    jobid: 39

[Sat Jul 29 20:45:49 2023]
Finished job 13.
9 of 48 steps (19%) done

[Sat Jul 29 20:45:49 2023]
rule KEGG:
    input: /home/ubuntu/kg2-code/extract-kegg.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kegg.jsonl
    log: /home/ubuntu/kg2-build/extract-kegg.log
    jobid: 47

[Sat Jul 29 20:45:50 2023]
Finished job 37.
10 of 48 steps (21%) done

[Sat Jul 29 20:45:50 2023]
rule DrugBank_Conversion:
    input: /home/ubuntu/kg2-code/drugbank_xml_to_kg_jsonl.py, /home/ubuntu/kg2-build/drugbank.xml, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-drugbank-nodes.jsonl, /home/ubuntu/kg2-build/kg2-drugbank-edges.jsonl
    log: /home/ubuntu/kg2-build/drugbank_xml_to_kg_jsonl.log
    jobid: 16

[Sat Jul 29 20:45:56 2023]
Finished job 19.
11 of 48 steps (23%) done

[Sat Jul 29 20:45:56 2023]
rule RepoDB:
    input: /home/ubuntu/kg2-code/extract-repodb.sh, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/repodb/repodb.csv
    log: /home/ubuntu/kg2-build/extract-repodb.log
    jobid: 36

[Sat Jul 29 20:45:57 2023]
Finished job 36.
12 of 48 steps (25%) done

[Sat Jul 29 20:45:57 2023]
rule RepoDB_Conversion:
    input: /home/ubuntu/kg2-code/repodb_csv_to_kg_jsonl.py, /home/ubuntu/kg2-build/repodb/repodb.csv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-repodb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-repodb-edges.jsonl
    log: /home/ubuntu/kg2-build/repodb_csv_to_kg_jsonl.log
    jobid: 15

[Sat Jul 29 20:46:08 2023]
Finished job 25.
13 of 48 steps (27%) done
[Sat Jul 29 20:46:25 2023]
Finished job 15.
14 of 48 steps (29%) done
[Sat Jul 29 20:46:51 2023]
Finished job 45.
15 of 48 steps (31%) done

[Sat Jul 29 20:46:51 2023]
rule IntAct_Conversion:
    input: /home/ubuntu/kg2-code/intact_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/intact.txt, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-intact-nodes.jsonl, /home/ubuntu/kg2-build/kg2-intact-edges.jsonl
    log: /home/ubuntu/kg2-build/intact_tsv_to_kg_jsonl.log
    jobid: 24

[Sat Jul 29 20:47:35 2023]
Finished job 24.
16 of 48 steps (33%) done
[Sat Jul 29 20:48:52 2023]
Finished job 32.
17 of 48 steps (35%) done

[Sat Jul 29 20:48:52 2023]
rule Ensembl_Conversion:
    input: /home/ubuntu/kg2-code/ensembl_json_to_kg_jsonl.py, /home/ubuntu/kg2-build/ensembl/ensembl_genes_homo_sapiens.json, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-ensembl-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ensembl-edges.jsonl
    log: /home/ubuntu/kg2-build/ensembl_json_to_kg_jsonl.log
    jobid: 11

[Sat Jul 29 20:49:37 2023]
Finished job 44.
18 of 48 steps (38%) done

[Sat Jul 29 20:49:37 2023]
rule DrugCentral_Conversion:
    input: /home/ubuntu/kg2-code/drugcentral_json_to_kg_jsonl.py, /home/ubuntu/kg2-build/drugcentral/drugcentral_psql_json.json, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-drugcentral-nodes.jsonl, /home/ubuntu/kg2-build/kg2-drugcentral-edges.jsonl
    log: /home/ubuntu/kg2-build/drugcentral_json_to_kg_jsonl.log
    jobid: 23

[Sat Jul 29 20:49:54 2023]
Finished job 23.
19 of 48 steps (40%) done
[Sat Jul 29 20:50:34 2023]
Finished job 39.
20 of 48 steps (42%) done

[Sat Jul 29 20:50:34 2023]
rule HMDB_Conversion:
    input: /home/ubuntu/kg2-code/hmdb_xml_to_kg_jsonl.py, /home/ubuntu/kg2-build/hmdb_metabolites.xml, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-hmdb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-hmdb-edges.jsonl
    log: /home/ubuntu/kg2-build/hmdb_xml_to_kg_jsonl.log
    jobid: 18

[Sat Jul 29 20:52:04 2023]
Finished job 11.
21 of 48 steps (44%) done
[Sat Jul 29 20:52:37 2023]
Finished job 16.
22 of 48 steps (46%) done
[Sat Jul 29 20:53:30 2023]
Finished job 41.
23 of 48 steps (48%) done

[Sat Jul 29 20:53:30 2023]
rule Reactome_Conversion:
    input: /home/ubuntu/kg2-code/reactome_mysql_to_kg_jsonl.py, /home/ubuntu/kg2-build/reactome-placeholder.empty, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-reactome-nodes.jsonl, /home/ubuntu/kg2-build/kg2-reactome-edges.jsonl
    log: /home/ubuntu/kg2-build/reactome_mysql_to_kg_jsonl.log
    jobid: 20

[Sat Jul 29 20:55:14 2023]
Finished job 20.
24 of 48 steps (50%) done
[Sat Jul 29 20:55:20 2023]
Finished job 43.
25 of 48 steps (52%) done

[Sat Jul 29 20:55:20 2023]
rule JensenLab_Conversion:
    input: /home/ubuntu/kg2-code/jensenlab_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/validation-placeholder.empty, /home/ubuntu/kg2-build/jensenlab-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-jensenlab-nodes.jsonl, /home/ubuntu/kg2-build/kg2-jensenlab-edges.jsonl
    log: /home/ubuntu/kg2-build/jensenlab_tsv_to_kg_jsonl.log
    jobid: 22

[Sat Jul 29 21:01:11 2023]
Finished job 33.
26 of 48 steps (54%) done

[Sat Jul 29 21:01:11 2023]
rule UniChem_Conversion:
    input: /home/ubuntu/kg2-code/unichem_tsv_to_kg_jsonl.py, /home/ubuntu/kg2-build/unichem/unichem-mappings.tsv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-unichem-nodes.jsonl, /home/ubuntu/kg2-build/kg2-unichem-edges.jsonl
    log: /home/ubuntu/kg2-build/unichem_tsv_to_kg_jsonl.log
    jobid: 12

[Sat Jul 29 21:01:20 2023]
Finished job 12.
27 of 48 steps (56%) done
[Sat Jul 29 21:03:28 2023]
Finished job 38.
28 of 48 steps (58%) done

[Sat Jul 29 21:03:28 2023]
rule SMPDB_Conversion:
    input: /home/ubuntu/kg2-code/smpdb_csv_to_kg_jsonl.py, /home/ubuntu/kg2-build/smpdb/pathbank_pathways.csv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-smpdb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-smpdb-edges.jsonl
    log: /home/ubuntu/kg2-build/smpdb_csv_to_kg_jsonl.log
    jobid: 17

[Sat Jul 29 21:14:17 2023]
Finished job 18.
29 of 48 steps (60%) done
[Sat Jul 29 21:16:33 2023]
Finished job 22.
30 of 48 steps (62%) done
[Sat Jul 29 21:26:37 2023]
Finished job 29.
31 of 48 steps (65%) done

[Sat Jul 29 21:26:37 2023]
rule UniProtKB_Conversion:
    input: /home/ubuntu/kg2-code/uniprotkb_dat_to_kg_jsonl.py, /home/ubuntu/kg2-build/uniprotkb/uniprot_sprot.dat, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-uniprotkb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-uniprotkb-edges.jsonl
    log: /home/ubuntu/kg2-build/uniprotkb_dat_to_kg_jsonl.log
    jobid: 8

[Sat Jul 29 21:29:42 2023]
Finished job 8.
32 of 48 steps (67%) done
[Sat Jul 29 23:42:56 2023]
Finished job 17.
33 of 48 steps (69%) done
[Sun Jul 30 01:01:01 2023]
Finished job 31.
34 of 48 steps (71%) done

[Sun Jul 30 01:01:01 2023]
rule ChEMBL_Conversion:
    input: /home/ubuntu/kg2-code/chembl_mysql_to_kg_jsonl.py, /home/ubuntu/kg2-build/chembl-placeholder.empty, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-chembl-nodes.jsonl, /home/ubuntu/kg2-build/kg2-chembl-edges.jsonl
    log: /home/ubuntu/kg2-build/chembl_mysql_to_kg_jsonl.log
    jobid: 10

[Sun Jul 30 01:27:16 2023]
Finished job 47.
35 of 48 steps (73%) done

[Sun Jul 30 01:27:16 2023]
rule KEGG_Conversion:
    input: /home/ubuntu/kg2-code/kegg_jsonl_to_kg_jsonl.py, /home/ubuntu/kg2-build/kegg.jsonl, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-kegg-nodes.jsonl, /home/ubuntu/kg2-build/kg2-kegg-edges.jsonl
    log: /home/ubuntu/kg2-build/kegg_jsonl_to_kg_jsonl.log
    jobid: 26

[Sun Jul 30 01:27:39 2023]
Finished job 26.
36 of 48 steps (75%) done
[Sun Jul 30 01:29:56 2023]
Finished job 10.
37 of 48 steps (77%) done
[Sun Jul 30 02:26:56 2023]
Finished job 27.
38 of 48 steps (79%) done

[Sun Jul 30 02:26:56 2023]
rule Ontologies_and_TTL:
    input: /home/ubuntu/kg2-code/build-multi-ont-kg.sh, /home/ubuntu/kg2-build/umls_cuis.tsv, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-ont-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ont-edges.jsonl
    log: /home/ubuntu/kg2-build/build-multi-ont-kg.log
    jobid: 7

[Sun Jul 30 08:04:12 2023]
Finished job 30.
39 of 48 steps (81%) done

[Sun Jul 30 08:04:12 2023]
rule SemMedDB_Conversion:
    input: /home/ubuntu/kg2-code/semmeddb_tuplelist_json_to_kg_jsonl.py, /home/ubuntu/kg2-build/semmeddb-tuplelist.jsonl, /home/ubuntu/kg2-build/umls_cuis.tsv, /home/ubuntu/kg2-build/semmed-exclude-list.yaml, /home/ubuntu/kg2-build/semmeddb-version.txt, /home/ubuntu/kg2-build/validation-placeholder.empty
    output: /home/ubuntu/kg2-build/kg2-semmeddb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-semmeddb-edges.jsonl
    log: /home/ubuntu/kg2-build/semmeddb_tuplelist_json_to_kg_jsonl.log
    jobid: 9

[Sun Jul 30 08:40:00 2023]
Finished job 9.
40 of 48 steps (83%) done
[Sun Jul 30 09:15:15 2023]
Finished job 7.
41 of 48 steps (85%) done

[Sun Jul 30 09:15:15 2023]
rule Merge:
    input: /home/ubuntu/kg2-code/merge_graphs.py, /home/ubuntu/kg2-build/kg2-ont-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ont-edges.jsonl, /home/ubuntu/kg2-build/kg2-uniprotkb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-uniprotkb-edges.jsonl, /home/ubuntu/kg2-build/kg2-semmeddb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-semmeddb-edges.jsonl, /home/ubuntu/kg2-build/kg2-chembl-nodes.jsonl, /home/ubuntu/kg2-build/kg2-chembl-edges.jsonl, /home/ubuntu/kg2-build/kg2-ensembl-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ensembl-edges.jsonl, /home/ubuntu/kg2-build/kg2-unichem-nodes.jsonl, /home/ubuntu/kg2-build/kg2-unichem-edges.jsonl, /home/ubuntu/kg2-build/kg2-ncbigene-nodes.jsonl, /home/ubuntu/kg2-build/kg2-ncbigene-edges.jsonl, /home/ubuntu/kg2-build/kg2-dgidb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-dgidb-edges.jsonl, /home/ubuntu/kg2-build/kg2-repodb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-repodb-edges.jsonl, /home/ubuntu/kg2-build/kg2-drugbank-nodes.jsonl, /home/ubuntu/kg2-build/kg2-drugbank-edges.jsonl, /home/ubuntu/kg2-build/kg2-smpdb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-smpdb-edges.jsonl, /home/ubuntu/kg2-build/kg2-hmdb-nodes.jsonl, /home/ubuntu/kg2-build/kg2-hmdb-edges.jsonl, /home/ubuntu/kg2-build/kg2-go-annotations-nodes.jsonl, /home/ubuntu/kg2-build/kg2-go-annotations-edges.jsonl, /home/ubuntu/kg2-build/kg2-reactome-nodes.jsonl, /home/ubuntu/kg2-build/kg2-reactome-edges.jsonl, /home/ubuntu/kg2-build/kg2-mirbase-nodes.jsonl, /home/ubuntu/kg2-build/kg2-mirbase-edges.jsonl, /home/ubuntu/kg2-build/kg2-jensenlab-nodes.jsonl, /home/ubuntu/kg2-build/kg2-jensenlab-edges.jsonl, /home/ubuntu/kg2-build/kg2-drugcentral-nodes.jsonl, /home/ubuntu/kg2-build/kg2-drugcentral-edges.jsonl, /home/ubuntu/kg2-build/kg2-intact-nodes.jsonl, /home/ubuntu/kg2-build/kg2-intact-edges.jsonl, /home/ubuntu/kg2-build/kg2-disgenet-nodes.jsonl, /home/ubuntu/kg2-build/kg2-disgenet-edges.jsonl, /home/ubuntu/kg2-build/kg2-kegg-nodes.jsonl, /home/ubuntu/kg2-build/kg2-kegg-edges.jsonl
    output: /home/ubuntu/kg2-build/kg2-merged-nodes.jsonl, /home/ubuntu/kg2-build/kg2-merged-edges.jsonl, /home/ubuntu/kg2-build/kg2-orphan-edges.jsonl
    log: /home/ubuntu/kg2-build/merge_graphs.log
    jobid: 1

[Sun Jul 30 17:50:00 2023]
Finished job 1.
42 of 48 steps (88%) done

Note: it failed at Simplify, so I did not include that here.

ecwood commented 1 year ago

In TSV, we encountered this error:

ubuntu@ip-172-31-59-112:~/kg2-build$ cat kg_json_to_tsv.log 
/home/ubuntu/kg2-venv/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.0.  Please remove rdflib-jsonld from your project's dependencies.
  DeprecationWarning,
Start time: 2023-07-30 20:11:51
usage: kg_json_to_tsv.py [-h]
                         inputNodesFile inputEdgesFile
                         kg2ProvidedByCurieToInforesCurieFile
                         outputFileLocation
kg_json_to_tsv.py: error: the following arguments are required: outputFileLocation
ecwood commented 1 year ago

The end-to-end test has completed, though I did have to restart (for a partial build, not complete restart) at Simplify and TSV. Here is the memory usage and disk space usage throughout this build. It peaks at 26% of the available memory on the r5a.8xlarge.

ubuntu@ip-172-31-59-112:~/kg2-code$ cat ~/kg2-code/instance-data-2023-07-29-20-44-20.log 
================= starting primative-instance-data-tracker.sh =================
Time: 2023-07-29-20-44-20; Memory: 0%; Disk: 40.3% of 991.28GB
Time: 2023-07-29-20-45-21; Memory: 0%; Disk: 40.3% of 991.28GB
Time: 2023-07-29-20-46-22; Memory: 2%; Disk: 34.7% of 991.28GB
Time: 2023-07-29-20-47-23; Memory: 3%; Disk: 37.6% of 991.28GB
Time: 2023-07-29-20-48-24; Memory: 4%; Disk: 39.3% of 991.28GB
Time: 2023-07-29-20-49-25; Memory: 8%; Disk: 40.0% of 991.28GB
Time: 2023-07-29-20-50-26; Memory: 14%; Disk: 41.0% of 991.28GB
Time: 2023-07-29-20-51-27; Memory: 17%; Disk: 42.0% of 991.28GB
Time: 2023-07-29-20-52-28; Memory: 11%; Disk: 40.0% of 991.28GB
Time: 2023-07-29-20-53-29; Memory: 10%; Disk: 40.4% of 991.28GB
Time: 2023-07-29-20-54-30; Memory: 11%; Disk: 40.7% of 991.28GB
Time: 2023-07-29-20-55-31; Memory: 12%; Disk: 41.3% of 991.28GB
Time: 2023-07-29-20-56-32; Memory: 16%; Disk: 42.2% of 991.28GB
Time: 2023-07-29-20-57-32; Memory: 21%; Disk: 43.1% of 991.28GB
Time: 2023-07-29-20-58-33; Memory: 21%; Disk: 31.8% of 991.28GB
Time: 2023-07-29-20-59-34; Memory: 21%; Disk: 31.4% of 991.28GB
Time: 2023-07-29-21-00-35; Memory: 22%; Disk: 25.9% of 991.28GB
Time: 2023-07-29-21-01-36; Memory: 22%; Disk: 25.2% of 991.28GB
Time: 2023-07-29-21-02-37; Memory: 23%; Disk: 24.4% of 991.28GB
Time: 2023-07-29-21-03-38; Memory: 23%; Disk: 21.6% of 991.28GB
Time: 2023-07-29-21-04-39; Memory: 24%; Disk: 21.6% of 991.28GB
Time: 2023-07-29-21-05-40; Memory: 24%; Disk: 21.7% of 991.28GB
Time: 2023-07-29-21-06-41; Memory: 25%; Disk: 21.8% of 991.28GB
Time: 2023-07-29-21-07-42; Memory: 25%; Disk: 21.9% of 991.28GB
Time: 2023-07-29-21-08-43; Memory: 26%; Disk: 21.9% of 991.28GB
Time: 2023-07-29-21-09-43; Memory: 26%; Disk: 22.0% of 991.28GB
Time: 2023-07-29-21-10-44; Memory: 26%; Disk: 22.1% of 991.28GB
Time: 2023-07-29-21-11-45; Memory: 19%; Disk: 22.2% of 991.28GB
Time: 2023-07-29-21-12-46; Memory: 20%; Disk: 22.4% of 991.28GB
Time: 2023-07-29-21-13-47; Memory: 20%; Disk: 22.5% of 991.28GB
Time: 2023-07-29-21-14-48; Memory: 11%; Disk: 22.6% of 991.28GB
Time: 2023-07-29-21-15-49; Memory: 11%; Disk: 22.6% of 991.28GB
Time: 2023-07-29-21-16-50; Memory: 3%; Disk: 22.7% of 991.28GB
Time: 2023-07-29-21-17-51; Memory: 3%; Disk: 22.8% of 991.28GB
Time: 2023-07-29-21-18-52; Memory: 3%; Disk: 22.8% of 991.28GB
Time: 2023-07-29-21-19-52; Memory: 3%; Disk: 22.9% of 991.28GB
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ecwood commented 1 year ago

I have put the time comparison document here, to make it easier to find and access: https://github.com/RTXteam/RTX-KG2/blob/jsonlines/JSONLines_Time_Comparison.md

ecwood commented 1 year ago

There are inconsistencies in the diff log (https://github.com/RTXteam/RTX-KG2/blob/jsonlines/JSONLines_Time_Comparison.md#diff-log-for-report-files, 6165071) that seem to pop up in UMLS nodes, which can have multiple sources in their provided_by field.

ecwood commented 1 year ago

While running a build (in order to test out #339) on an r5a.4xlarge instance using the merged code, I ran into this issue:

http://purl.obolibrary.org/obo/cl.owl
Reading ontology file: cl.owl; size: 53949.34 KiB
/usr/bin/java -Xms2G -Xmx124G -DentityExpansionLimit=4086000 -Djava.awt.headless=true -classpath /home/ubuntu/kg2-build/owltools owltools.cli.CommandLineInterface cl.owl -o -f json /tmp/kg2-j7dhz18n.json
Reading ontology JSON file: cl.json; size: 30993.82 KiB
file: cl.owl; last modified: 2023-08-04 04:52:54 GMT
http://purl.obolibrary.org/obo/foodon.owl
Reading ontology file: foodon.pickle; size: 40463.44 KiB
file: foodon.owl; last modified: 2023-08-04 04:53:38 GMT
http://data.bioontology.org/ontologies/ORDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
Traceback (most recent call last):
  File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 1400, in <module>
    save_pickle)
  File "/home/ubuntu/kg2-code/multi_ont_to_kg_jsonl.py", line 145, in make_kg2
    ont_source_info_dict['file'])
  File "/home/ubuntu/RTX-KG2/kg2_util.py", line 682, in download_file_if_not_exist_locally
    with urllib.request.urlopen(url, context=ctx) as u, open(temp_file_name, 'wb') as f:
  File "/usr/lib/python3.7/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/lib/python3.7/urllib/request.py", line 531, in open
    response = meth(req, response)
  File "/usr/lib/python3.7/urllib/request.py", line 641, in http_response
    'http', request, response, code, msg, hdrs)
  File "/usr/lib/python3.7/urllib/request.py", line 569, in error
    return self._call_chain(*args)
  File "/usr/lib/python3.7/urllib/request.py", line 503, in _call_chain
    result = func(*args)
  File "/usr/lib/python3.7/urllib/request.py", line 649, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 422: Unprocessable Entity
ecwood commented 1 year ago

This was completed as of KG2.8.5pre.