| #!/bin/bash |
| |
| set -x |
| export PYTHONPATH=/root/patientphex/retrain_t1/code |
| export NLTK_DATA=/root/patientphex/retrain_t1/third_party/PhenoTagger-Plus/nltk_data |
| PY=/opt/anaconda3/envs/pt_env310/bin/python |
| C=/root/patientphex/retrain_t1/code |
| PB=/root/patientphex/retrain_t1/third_party/PhenoBERT |
| O=/root/patientphex/pb_runtime |
| R=$C/artifacts/b_retrain |
| B=/root/patientphex/PatientPheX-V1-B/PatientPheX-V1-B.jsonl |
|
|
| |
| for i in $(seq 1 240); do |
| pgrep -f dl_pb_mirror.sh > /dev/null || break |
| sleep 30 |
| done |
| pgrep -f dl_pb_mirror.sh > /dev/null && { echo PB_DL_STILL_RUNNING; exit 1; } |
|
|
| |
| for i in $(seq 1 120); do |
| grep -q STANZA_TAR_DONE /root/patientphex/dl_stanza4.out 2>/dev/null && break |
| sleep 30 |
| done |
| grep -q STANZA_TAR_DONE /root/patientphex/dl_stanza4.out || { echo STANZA_NOT_READY; exit 1; } |
| ls /root/stanza_resources/en/ | head -4 |
|
|
| ls -la $PB/phenobert/models/ $PB/phenobert/embeddings/ | head -50 |
| [ -f $PB/phenobert/models/HPOModel_H/model_layer1.pkl ] || { echo PB_LAYER1_MISSING; exit 2; } |
| [ -f $PB/phenobert/models/bert_model_max_triple.pkl ] || { echo PB_BERTPKL_MISSING; exit 2; } |
| [ -f $PB/phenobert/embeddings/fasttext_pubmed.bin ] || { echo PB_FASTTEXT_MISSING; exit 2; } |
| du -sb $PB/phenobert/embeddings/fasttext_pubmed.bin |
| echo PB_WEIGHTS_READY |
|
|
| |
| mkdir -p $O/smoke_in $O/smoke_out |
| head -c 100000 $O/corpus/$(ls $O/corpus | head -1) > /dev/null |
| cp $(ls -d $O/corpus/* | head -1) $O/smoke_in/ |
| CUDA_VISIBLE_DEVICES=4 $PY $C/scripts/run_phenobert_official_compat.py \ |
| --phenobert $PB --input-dir $O/smoke_in --output-dir $O/smoke_out \ |
| --threads 16 || { echo PB_SMOKE_FAIL; exit 3; } |
| ls $O/smoke_out/ |
| cat $O/smoke_out/*.json 2>/dev/null | head -c 600 |
| echo PB_SMOKE_DONE |
|
|
| |
| mkdir -p $O/out |
| CUDA_VISIBLE_DEVICES=4 $PY $C/scripts/run_phenobert_official_compat.py \ |
| --phenobert $PB --input-dir $O/corpus --output-dir $O/out \ |
| --threads 32 || { echo PB_FULL_FAIL; exit 4; } |
| ls $O/out | wc -l |
| echo PB_FULL_DONE |
|
|
| |
| $PY $C/scripts/prepare_phenobert_official.py convert \ |
| --input $B \ |
| --annotations $O/out \ |
| --ontology /root/patientphex/PatientPheX-V1-A/hp.obo \ |
| --raw-output $R/B-phenobert-raw.jsonl \ |
| --compatible-output $R/B-phenobert-official-hpo2026.jsonl \ |
| --report $R/B-phenobert-conversion-report.json || { echo PB_CONVERT_FAIL; exit 5; } |
| /root/patientphex/judge_venv/bin/python /root/patientphex/count_ents.py $R/B-phenobert-official-hpo2026.jsonl 8110 |
| echo PB_CHAIN_DONE |
|
|
