Jenkins string replacement and parsing errors

[caufieldjh]

A few errors in the Jenkins build are happening:

• Line 97 is missing a double quote, causing:

  11:43:17  /var/lib/jenkins/workspace/_automate-pheno-comparisons_main/working@tmp/durable-d2334e36/script.sh: 1: Syntax error: Unterminated quoted string

• The history command isn't found, so the SHORTHIST var isn't set:

  11:43:16  + history
  11:43:16  /var/lib/jenkins/workspace/_automate-pheno-comparisons_main/working@tmp/durable-0df3bc69/script.sh: 1: + history: not found
  11:43:16  tail -6
  11:43:16  + head -5
  11:43:16  + cut -c 8-
  11:43:16  + SHORTHIST=

• The combination of build name prefix and build date isn't parsed as expected, so it just becomes the build date. This leads to command looking like this:

  11:42:20  + mv 20240528.tsv.tmp 20240528.tsv

  when the command is specified like this:

  mv "$HP_VS_HP_PREFIX_$BUILDSTARTDATE.tsv.tmp" "$HP_VS_HP_PREFIX_$BUILDSTARTDATE.tsv"

[caufieldjh]

Aha, for the history command, the issue is that this build is literally calling sh for each shell and that doesn't support history. The easy but less satisfying option is to pass the literal commands as strings. I'll do that for now in the interest of getting a working output log.

[caufieldjh]

I think this may be a sign that it's time to convert this all to a Python script and stop fighting with string parsing in Groovy.

[caufieldjh]

Missed a filename correction in this line:

16:09:04  + ./duckdb -c CREATE TABLE semsim AS SELECT * FROM read_csv('HP_vs_HP_semsimian_phenio_20240528.tsv', header=TRUE); CREATE TABLE labels AS SELECT * FROM read_csv('HPO_terms.tsv', header=FALSE); CREATE TABLE labeled1 AS SELECT * FROM semsim n JOIN labels r ON (subject_id = column0); CREATE TABLE labeled2 AS SELECT * FROM labeled1 n JOIN labels r ON (object_id = r.column0); ALTER TABLE labeled2 DROP subject_label; ALTER TABLE labeled2 DROP object_label; ALTER TABLE labeled2 RENAME column1 TO subject_label; ALTER TABLE labeled2 RENAME column1_1 TO object_label; ALTER TABLE labeled2 DROP column0; ALTER TABLE labeled2 DROP column0_1; COPY (SELECT subject_id, subject_label, subject_source, object_id, object_label, object_source, ancestor_id, ancestor_label, ancestor_source, object_information_content, subject_information_content, ancestor_information_content, jaccard_similarity, cosine_similarity, dice_similarity, phenodigm_score FROM labeled2) TO '20240528.tsv.tmp' WITH (HEADER true, DELIMITER ' ')