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FileNotFoundError#4
@avacaondata

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@avacaondata
avacaondata
opened on Sep 24, 2020

Hi, I'm running into the following problem when calling POST method:
FileNotFoundError: [Errno 2] No such file or directory: 'biobert_ner/tmp/token_test_Thread-10.txt'

The complete log:

root 6 0.0 0.0 110388 8024 ? Sl 08:59 0:00 java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895
root 7 0.0 0.0 108156 7984 ? Sl 08:59 0:00 java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896
root 9 0.0 0.0 25408 6244 ? R 08:59 0:00 python3 normalizers/chemical_normalizer.py
root 10 0.0 0.0 25408 6324 ? R 08:59 0:00 python3 normalizers/species_normalizer.py
root 11 0.0 0.0 25568 6500 ? R 08:59 0:00 python3 normalizers/mutation_normalizer.py
root 12 0.0 0.0 110388 7880 ? Sl 08:59 0:00 java -Xmx16G -jar resources/normalizers/disease/disease_normalizer_19.jar
root 13 0.0 0.0 37420 2252 ? R 08:59 0:00 java -Xmx20G -jar gnormplus-normalization_19.jar
Starting tmVar 2.0 Service at 172.17.0.5:18896
Starting GNormPlus Service at 172.17.0.5:18895
Reading POS tagger model from lib/taggers/english-left3words-distsim.tagger ... done [0.8 sec].
Loading tmVar : Processing Time:0.923sec
Ready
[24/Sep/2020 08:59:57.590374] Starting..
2020-09-24 08:59:57.603323: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2020-09-24 08:59:57.609473: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2394500000 Hz
2020-09-24 08:59:57.611389: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x4229f80 executing computations on platform Host. Devices:
2020-09-24 08:59:57.611417: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): ,
A GPU is NOT available

WARNING: The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:

WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder..model_fn at 0x7f1fe8cc77b8>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_train_distribute': None, '_save_checkpoints_steps': 1000, '_protocol': None, '_eval_distribute': None, '_model_dir': './biobert_ner/pretrainedBERT/gene', '_task_id': 0, '_tpu_config': TPUConfig(iterations_per_loop=1000, num_shards=8, num_cores_per_replica=None, per_host_input_for_training=3, tpu_job_name=None, initial_infeed_sleep_secs=None, input_partition_dims=None), '_keep_checkpoint_every_n_hours': 10000, '_evaluation_master': '', '_tf_random_seed': None, '_num_worker_replicas': 1, '_global_id_in_cluster': 0, '_master': '', '_service': None, '_log_step_count_steps': None, '_save_checkpoints_secs': None, '_is_chief': True, '_device_fn': None, '_session_config': gpu_options {
allow_growth: true
}
, '_cluster': None, '_save_summary_steps': 100, '_task_type': 'worker', '_keep_checkpoint_max': 5, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7f1fe3ad3748>, '_experimental_distribute': None, '_num_ps_replicas': 0}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder..model_fn at 0x7f1f343652f0>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_train_distribute': None, '_save_checkpoints_steps': 1000, '_protocol': None, '_eval_distribute': None, '_model_dir': './biobert_ner/pretrainedBERT/disease', '_task_id': 0, '_tpu_config': TPUConfig(iterations_per_loop=1000, num_shards=8, num_cores_per_replica=None, per_host_input_for_training=3, tpu_job_name=None, initial_infeed_sleep_secs=None, input_partition_dims=None), '_keep_checkpoint_every_n_hours': 10000, '_evaluation_master': '', '_tf_random_seed': None, '_num_worker_replicas': 1, '_global_id_in_cluster': 0, '_master': '', '_service': None, '_log_step_count_steps': None, '_save_checkpoints_secs': None, '_is_chief': True, '_device_fn': None, '_session_config': gpu_options {
allow_growth: true
}
, '_cluster': None, '_save_summary_steps': 100, '_task_type': 'worker', '_keep_checkpoint_max': 5, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7f1f342f9710>, '_experimental_distribute': None, '_num_ps_replicas': 0}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder..model_fn at 0x7f1f342fe400>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_train_distribute': None, '_save_checkpoints_steps': 1000, '_protocol': None, '_eval_distribute': None, '_model_dir': './biobert_ner/pretrainedBERT/drug', '_task_id': 0, '_tpu_config': TPUConfig(iterations_per_loop=1000, num_shards=8, num_cores_per_replica=None, per_host_input_for_training=3, tpu_job_name=None, initial_infeed_sleep_secs=None, input_partition_dims=None), '_keep_checkpoint_every_n_hours': 10000, '_evaluation_master': '', '_tf_random_seed': None, '_num_worker_replicas': 1, '_global_id_in_cluster': 0, '_master': '', '_service': None, '_log_step_count_steps': None, '_save_checkpoints_secs': None, '_is_chief': True, '_device_fn': None, '_session_config': gpu_options {
allow_growth: true
}
, '_cluster': None, '_save_summary_steps': 100, '_task_type': 'worker', '_keep_checkpoint_max': 5, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7f1f342f9828>, '_experimental_distribute': None, '_num_ps_replicas': 0}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder..model_fn at 0x7f1f342fe510>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_train_distribute': None, '_save_checkpoints_steps': 1000, '_protocol': None, '_eval_distribute': None, '_model_dir': './biobert_ner/pretrainedBERT/species', '_task_id': 0, '_tpu_config': TPUConfig(iterations_per_loop=1000, num_shards=8, num_cores_per_replica=None, per_host_input_for_training=3, tpu_job_name=None, initial_infeed_sleep_secs=None, input_partition_dims=None), '_keep_checkpoint_every_n_hours': 10000, '_evaluation_master': '', '_tf_random_seed': None, '_num_worker_replicas': 1, '_global_id_in_cluster': 0, '_master': '', '_service': None, '_log_step_count_steps': None, '_save_checkpoints_secs': None, '_is_chief': True, '_device_fn': None, '_session_config': gpu_options {
allow_growth: true
}
, '_cluster': None, '_save_summary_steps': 100, '_task_type': 'worker', '_keep_checkpoint_max': 5, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7f1f342f9940>, '_experimental_distribute': None, '_num_ps_replicas': 0}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
BioBERT init_t 0.770 sec.
[24/Sep/2020 08:59:58.381913] Starting server at http://0.0.0.0:8888
gid2oid loaded 59849
goid2goid loaded 3468
gene meta #ids 42916, #ext_ids 42916
disease meta #ids 12122, #ext_ids 15040
chem meta #ids 179063, #ext_ids 179463
code2mirs size 9447
mirbase_id2mirna_id size 14945
mirna_id2accession size 6308

of pathway regex 514

Loading Gene Dictionary : Processing Time:10.555sec
Ready
172.17.0.1 - - [24/Sep/2020 09:02:30] "GET /?pmid=30429607&format=json HTTP/1.1" 200 -
[24/Sep/2020 09:02:30.707598] [Thread-1] text_hash: 8204711c440ab265ed3cf83f794413f16eca6fc7e841330e1ec59f56
[24/Sep/2020 09:02:31.209803] [Thread-1] tmTool: PubMed & GNormPlus & tmVar 0.502 sec
WARNING:tensorflow:From /usr/local/lib/python3.5/dist-packages/tensorflow/python/ops/resource_variable_ops.py:435: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
WARNING:tensorflow:From /usr/local/lib/python3.5/dist-packages/tensorflow/python/data/ops/dataset_ops.py:429: py_func (from tensorflow.python.ops.script_ops) is deprecated and will be removed in a future version.
Instructions for updating:
tf.py_func is deprecated in TF V2. Instead, use
tf.py_function, which takes a python function which manipulates tf eager
tensors instead of numpy arrays. It's easy to convert a tf eager tensor to
an ndarray (just call tensor.numpy()) but having access to eager tensors
means tf.py_functions can use accelerators such as GPUs as well as
being differentiable using a gradient tape.

INFO:tensorflow:Calling model_fn.
INFO:tensorflow:Running infer on CPU
INFO:tensorflow:Calling model_fn.
INFO:tensorflow:Running infer on CPU
INFO:tensorflow:Calling model_fn.
INFO:tensorflow:Calling model_fn.
INFO:tensorflow:Running infer on CPU
INFO:tensorflow:Running infer on CPU
WARNING:tensorflow:From /app/biobert_ner/modeling.py:680: dense (from tensorflow.python.layers.core) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.dense instead.
INFO:tensorflow:Done calling model_fn.
INFO:tensorflow:Done calling model_fn.
INFO:tensorflow:Done calling model_fn.
INFO:tensorflow:Done calling model_fn.
INFO:tensorflow:Graph was finalized.
WARNING:tensorflow:From /usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
INFO:tensorflow:Graph was finalized.
INFO:tensorflow:Restoring parameters from ./biobert_ner/pretrainedBERT/disease/model.ckpt-45000
INFO:tensorflow:Restoring parameters from ./biobert_ner/pretrainedBERT/species/model.ckpt-90000
INFO:tensorflow:Graph was finalized.
INFO:tensorflow:Restoring parameters from ./biobert_ner/pretrainedBERT/drug/model.ckpt-28020
INFO:tensorflow:Graph was finalized.
INFO:tensorflow:Restoring parameters from ./biobert_ner/pretrainedBERT/gene/model.ckpt-6678
INFO:tensorflow:Running local_init_op.
INFO:tensorflow:Running local_init_op.
INFO:tensorflow:Running local_init_op.
INFO:tensorflow:Done running local_init_op.
INFO:tensorflow:Done running local_init_op.
INFO:tensorflow:Running local_init_op.
INFO:tensorflow:Done running local_init_op.
INFO:tensorflow:Done running local_init_op.
[24/Sep/2020 09:03:12.836412] [Thread-1] NER 41.626 sec, #entities: 49, #articles: 1
Not found!!! /app/normalization/resources/outputs/gene/8204711c440ab265ed3cf83f794413f16eca6fc7e841330e1ec59f56_Thread-1.oid
[24/Sep/2020 09:03:12.958752] [Thread-1] [gene] 0.119 sec, CUI-less: 100.0% (17/17)
[24/Sep/2020 09:03:12.966791] [Thread-1] [disease] 0.127 sec, CUI-less: 5.9% (1/17)
[24/Sep/2020 09:03:15.112145] [Thread-1] [species] 2.272 sec, CUI-less: 0.0% (0/2)
[24/Sep/2020 09:03:27.921173] [Thread-1] [drug] 15.081 sec, CUI-less: 0.0% (0/13)
[24/Sep/2020 09:03:27.921462] [Thread-1] Normalization models 15.085 sec (1 article(s), 4 entity type(s))
[24/Sep/2020 09:03:27.923206] [Thread-1] Done. Total 57.216 sec

172.17.0.1 - - [24/Sep/2020 09:09:35] "POST / HTTP/1.1" 200 -
[24/Sep/2020 09:09:35.811988] [Thread-10] text_hash: 3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7
/3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7.PubTator - (PubTator format) : Processing Time:0.91sec
[24/Sep/2020 09:09:36.728412] [Thread-10] GNormPlus 0.916 sec
input/3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7.PubTator - (PubTator format) : Processing Time:0.666sec
[24/Sep/2020 09:09:37.400996] [Thread-10] tmVar 2.0 0.672 sec

Exception happened during processing of request from ('172.17.0.1', 33872)
Traceback (most recent call last):
File "/usr/lib/python3.5/socketserver.py", line 625, in process_request_thread
self.finish_request(request, client_address)
File "/usr/lib/python3.5/socketserver.py", line 354, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python3.5/socketserver.py", line 681, in init
self.handle()
File "/usr/lib/python3.5/http/server.py", line 422, in handle
self.handle_one_request()
File "/usr/lib/python3.5/http/server.py", line 410, in handle_one_request
method()
File "server.py", line 317, in do_POST
text, cur_thread_name, is_raw_text=True, reuse=False)
File "server.py", line 452, in tag_entities
self.biobert_recognize(dict_list, is_raw_text, cur_thread_name)
File "server.py", line 490, in biobert_recognize
thread_id=cur_thread_name)
File "/app/biobert_ner/utils.py", line 15, in with_profiling
ret = fn(*args, **kwargs)
File "/app/biobert_ner/run_ner.py", line 488, in recognize
with open(token_path, 'r') as reader:
FileNotFoundError: [Errno 2] No such file or directory: 'biobert_ner/tmp/token_test_Thread-10.txt'

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