dmis-lab / bern Goto Github PK

---------------------------------------------------------------------------
JSONDecodeError                           Traceback (most recent call last)
<ipython-input-37-d5e92984db1a> in <module>
----> 1 output = query_raw(str_new)

<ipython-input-31-190dc9c1a306> in query_raw(text, url)
      1 def query_raw(text, url="https://bern.korea.ac.kr/plain"):
----> 2     return requests.post(url, data={'sample_text': text}).json()

~\Anaconda3\lib\site-packages\requests\models.py in json(self, **kwargs)
    895                     # used.
    896                     pass
--> 897         return complexjson.loads(self.text, **kwargs)
    898 
    899     @property

~\Anaconda3\lib\json\__init__.py in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    346             parse_int is None and parse_float is None and
    347             parse_constant is None and object_pairs_hook is None and not kw):
--> 348         return _default_decoder.decode(s)
    349     if cls is None:
    350         cls = JSONDecoder

~\Anaconda3\lib\json\decoder.py in decode(self, s, _w)
    335 
    336         """
--> 337         obj, end = self.raw_decode(s, idx=_w(s, 0).end())
    338         end = _w(s, end).end()
    339         if end != len(s):

~\Anaconda3\lib\json\decoder.py in raw_decode(self, s, idx)
    353             obj, end = self.scan_once(s, idx)
    354         except StopIteration as err:
--> 355             raise JSONDecodeError("Expecting value", s, err.value) from None
    356         return obj, end

JSONDecodeError: Expecting value: line 1 column 1 (char 0)

<Response [200]>
content:  b''
Traceback (most recent call last):
  File "test.py", line 7, in <module>
    result_dict = response.json()
  File "/home/alex/.local/lib/python3.6/site-packages/requests/models.py", line 898, in json
    return complexjson.loads(self.text, **kwargs)
  File "/usr/lib/python3/dist-packages/simplejson/__init__.py", line 518, in loads
    return _default_decoder.decode(s)
  File "/usr/lib/python3/dist-packages/simplejson/decoder.py", line 370, in decode
    obj, end = self.raw_decode(s)
  File "/usr/lib/python3/dist-packages/simplejson/decoder.py", line 400, in raw_decode
    return self.scan_once(s, idx=_w(s, idx).end())
simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

Exception happened during processing of request from ('172.17.0.1', 40600)
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 196, in do_GET
    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 474, in recognize
    example, self.FLAGS.max_seq_length, req_id, "test")
  File "/app/biobert_ner/run_ner.py", line 846, in convert_single_example
    self.write_tokens(ntokens, mode, req_id)
  File "/app/biobert_ner/run_ner.py", line 854, in write_tokens
    with open(path, 'a') as wf:
FileNotFoundError: [Errno 2] No such file or directory: 'biobert_ner/tmp/token_test_Thread-1.txt'

docker run -it --gpus all -p 80:8888 -v $PWD/externalData/GNormPlusJava/Dictionary/:/app/GNormPlusJava/Dictionary/ -v $PWD/externalData/tmVarJava/Database:/app/tmVarJava/Database -v $PWD/externalData/biobert_ner_models/:/app/bern/biobert_ner/ -v $PWD/externalData/data/:/app/normalization/data/ -v $PWD/externalData/resources/:/app/normalization/resources/ bern-docker
nohup: nohup: appending output to 'nohup.out'appending output to 'nohup.out'

root          6  0.0  0.0  37412  3432 pts/0    R+   03:14   0:00 java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895
root          7  0.0  0.0  37412  3524 pts/0    R+   03:14   0:00 java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896
root          9  0.0  0.0  24628  4472 pts/0    R+   03:14   0:00 python3 normalizers/chemical_normalizer.py
root         10  0.0  0.0  24628  4712 pts/0    R+   03:14   0:00 python3 normalizers/species_normalizer.py
root         11  0.0  0.0  24628  4400 pts/0    R+   03:14   0:00 python3 normalizers/mutation_normalizer.py
root         12  0.0  0.0  37412  3440 pts/0    R+   03:14   0:00 java -Xmx16G -jar resources/normalizers/disease/disease_normalizer_19.jar
root         13  0.0  0.0  37412  2376 pts/0    R+   03:14   0:00 java -Xmx20G -jar gnormplus-normalization_19.jar
[23/Apr/2020 03:14:17.105468] Starting..
2020-04-23 03:14:17.118139: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2020-04-23 03:14:17.265485: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:998] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2020-04-23 03:14:17.268081: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x3d8ae20 executing computations on platform CUDA. Devices:
2020-04-23 03:14:17.268144: I tensorflow/compiler/xla/service/service.cc:158]   StreamExecutor device (0): GeForce GTX 1080 Ti, Compute Capability 6.1
2020-04-23 03:14:17.288584: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3393280000 Hz
2020-04-23 03:14:17.290987: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x3f2c490 executing computations on platform Host. Devices:
2020-04-23 03:14:17.291048: I tensorflow/compiler/xla/service/service.cc:158]   StreamExecutor device (0): <undefined>, <undefined>
2020-04-23 03:14:17.291345: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1433] Found device 0 with properties: 
name: GeForce GTX 1080 Ti major: 6 minor: 1 memoryClockRate(GHz): 1.6705
pciBusID: 0000:43:00.0
totalMemory: 10.91GiB freeMemory: 7.44GiB
2020-04-23 03:14:17.291440: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1512] Adding visible gpu devices: 0
2020-04-23 03:14:17.292519: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] Device interconnect StreamExecutor with strength 1 edge matrix:
2020-04-23 03:14:17.292554: I tensorflow/core/common_runtime/gpu/gpu_device.cc:990]      0 
2020-04-23 03:14:17.292616: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1003] 0:   N 
2020-04-23 03:14:17.292743: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1115] Created TensorFlow device (/device:GPU:0 with 7239 MB memory) -> physical GPU (device: 0, name: GeForce GTX 1080 Ti, pci bus id: 0000:43:00.0, compute capability: 6.1)
A GPU is available

WARNING: The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:
  * https://github.com/tensorflow/community/blob/master/rfcs/20180907-contrib-sunset.md
  * https://github.com/tensorflow/addons
If you depend on functionality not listed there, please file an issue.

WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder.<locals>.model_fn at 0x7fb16ec46840>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_eval_distribute': None, '_num_worker_replicas': 1, '_keep_checkpoint_max': 5, '_model_dir': './biobert_ner/pretrainedBERT/gene', '_master': '', '_log_step_count_steps': None, '_cluster': None, '_train_distribute': None, '_num_ps_replicas': 0, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fb16e05b9e8>, '_experimental_distribute': None, '_is_chief': True, '_protocol': None, '_evaluation_master': '', '_task_type': 'worker', '_global_id_in_cluster': 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), '_device_fn': None, '_tf_random_seed': None, '_save_checkpoints_secs': None, '_task_id': 0, '_keep_checkpoint_every_n_hours': 10000, '_service': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_save_checkpoints_steps': 1000, '_save_summary_steps': 100}
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.<locals>.model_fn at 0x7fb04042a378>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_eval_distribute': None, '_num_worker_replicas': 1, '_keep_checkpoint_max': 5, '_model_dir': './biobert_ner/pretrainedBERT/disease', '_master': '', '_log_step_count_steps': None, '_cluster': None, '_train_distribute': None, '_num_ps_replicas': 0, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fb04043b9b0>, '_experimental_distribute': None, '_is_chief': True, '_protocol': None, '_evaluation_master': '', '_task_type': 'worker', '_global_id_in_cluster': 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), '_device_fn': None, '_tf_random_seed': None, '_save_checkpoints_secs': None, '_task_id': 0, '_keep_checkpoint_every_n_hours': 10000, '_service': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_save_checkpoints_steps': 1000, '_save_summary_steps': 100}
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.<locals>.model_fn at 0x7fb0403c0488>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_eval_distribute': None, '_num_worker_replicas': 1, '_keep_checkpoint_max': 5, '_model_dir': './biobert_ner/pretrainedBERT/drug', '_master': '', '_log_step_count_steps': None, '_cluster': None, '_train_distribute': None, '_num_ps_replicas': 0, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fb04043bac8>, '_experimental_distribute': None, '_is_chief': True, '_protocol': None, '_evaluation_master': '', '_task_type': 'worker', '_global_id_in_cluster': 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), '_device_fn': None, '_tf_random_seed': None, '_save_checkpoints_secs': None, '_task_id': 0, '_keep_checkpoint_every_n_hours': 10000, '_service': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_save_checkpoints_steps': 1000, '_save_summary_steps': 100}
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.<locals>.model_fn at 0x7fb0403c0598>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_eval_distribute': None, '_num_worker_replicas': 1, '_keep_checkpoint_max': 5, '_model_dir': './biobert_ner/pretrainedBERT/species', '_master': '', '_log_step_count_steps': None, '_cluster': None, '_train_distribute': None, '_num_ps_replicas': 0, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fb04043bbe0>, '_experimental_distribute': None, '_is_chief': True, '_protocol': None, '_evaluation_master': '', '_task_type': 'worker', '_global_id_in_cluster': 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), '_device_fn': None, '_tf_random_seed': None, '_save_checkpoints_secs': None, '_task_id': 0, '_keep_checkpoint_every_n_hours': 10000, '_service': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_save_checkpoints_steps': 1000, '_save_summary_steps': 100}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
BioBERT init_t 0.592 sec.
[23/Apr/2020 03:14:17.886905] 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

INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
BioBERT init_t 1.040 sec.
[19/Apr/2020 22:26:03.602298] 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

import requests
import json
body_data = {"param": json.dumps({"text": "CLAPO syndrome: identification of somatic activating PIK3CA mutations and the syndrome."})}
response = requests.post('http://<YOUR_SERVER_ADDRESS>:8888', data=body_data)
result_dict = response.json()

print(result_dict)

~/bern » python3 -u server.py --port 8888 --gnormplus_home ~/bern/GNormPlusJava --gnormplus_port 18895 --tmvar2_home ~/bern/tmVarJava --tmvar2_port 18896
2022-09-05 16:32:04.232546: I tensorflow/core/util/util.cc:169] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2022-09-05 16:32:04.237711: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-09-05 16:32:04.237742: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Traceback (most recent call last):
  File "server.py", line 8, in <module>
    from biobert_ner.run_ner import BioBERT, FLAGS
  File "/data/wenyuhao/bern/biobert_ner/run_ner.py", line 24, in <module>
    flags = tf.flags
AttributeError: module 'tensorflow' has no attribute 'flags'

tensorboard==2.9.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow-estimator==2.9.0
tensorflow-gpu==2.9.1
tensorflow-io-gcs-filesystem==0.26.0

~/bern » pip install tensorflow-gpu==1.13 
ERROR: Could not find a version that satisfies the requirement tensorflow-gpu==1.13 (from versions: 2.2.0, 2.2.1, 2.2.2, 2.2.3, 2.3.0, 2.3.1, 2.3.2, 2.3.3, 2.3.4, 2.4.0, 2.4.1, 2.4.2, 2.4.3, 2.4.4, 2.5.0, 2.5.1, 2.5.2, 2.5.3, 2.6.0, 2.6.1, 2.6.2, 2.6.3, 2.6.4, 2.6.5, 2.7.0rc0, 2.7.0rc1, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.8.0rc0, 2.8.0rc1, 2.8.0, 2.8.1, 2.8.2, 2.8.3, 2.9.0rc0, 2.9.0rc1, 2.9.0rc2, 2.9.0, 2.9.1, 2.9.2, 2.10.0rc0, 2.10.0rc1, 2.10.0rc2, 2.10.0rc3)
ERROR: No matching distribution found for tensorflow-gpu==1.13

nohup: ignoring input
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:523: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:524: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:527: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/ubuntu/.local/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:532: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
[05/Nov/2019 16:35:28.802904] Starting..
2019-11-05 16:35:28.835150: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
A GPU is NOT available
WARNING:tensorflow:Estimator's model_fn (<function model_fn_builder.<locals>.model_fn at 0x7fbd33f8c8c8>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_model_dir': './biobert_ner/pretrainedBERT/gene', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': 1000, '_save_checkpoints_secs': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_keep_checkpoint_max': 5, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': None, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_service': None, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fbd2a69f358>, '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1, '_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), '_cluster': None}
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.<locals>.model_fn at 0x7fbd2a92d6a8>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_model_dir': './biobert_ner/pretrainedBERT/disease', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': 1000, '_save_checkpoints_secs': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_keep_checkpoint_max': 5, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': None, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_service': None, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fbd2a69f4e0>, '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1, '_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), '_cluster': None}
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.<locals>.model_fn at 0x7fbd2a69c7b8>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_model_dir': './biobert_ner/pretrainedBERT/drug', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': 1000, '_save_checkpoints_secs': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_keep_checkpoint_max': 5, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': None, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_service': None, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fbd2a69f668>, '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1, '_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), '_cluster': None}
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.<locals>.model_fn at 0x7fbd2a69c8c8>) includes params argument, but params are not passed to Estimator.
INFO:tensorflow:Using config: {'_model_dir': './biobert_ner/pretrainedBERT/species', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': 1000, '_save_checkpoints_secs': None, '_session_config': gpu_options {
  allow_growth: true
}
, '_keep_checkpoint_max': 5, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': None, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_service': None, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x7fbd2a69f7f0>, '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1, '_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), '_cluster': None}
INFO:tensorflow:_TPUContext: eval_on_tpu True
WARNING:tensorflow:eval_on_tpu ignored because use_tpu is False.
BioBERT init_t 3.838 sec.
[05/Nov/2019 16:35:32.679049] Starting server at http://0.0.0.0:8888
gid2oid loaded 59849
gene meta #ids 42916, #ext_ids 42916
disease meta #ids 12122, #ext_ids 15040
chem meta #ids 178395, #ext_ids 178795

import requests
import json
body_data = {"param": json.dumps({"text": "CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype. PURPOSE: CLAPO syndrome is a rare vascular disorder characterized by capillary malformation of the lower lip, lymphatic malformation predominant on the face and neck, asymmetry, and partial/generalized overgrowth. Here we tested the hypothesis that, although the genetic cause is not known, the tissue distribution of the clinical manifestations in CLAPO seems to follow a pattern of somatic mosaicism. METHODS: We clinically evaluated a cohort of 13 patients with CLAPO and screened 20 DNA blood/tissue samples from 9 patients using high-throughput, deep sequencing. RESULTS: We identified five activating mutations in the PIK3CA gene in affected tissues from 6 of the 9 patients studied; one of the variants (NM_006218.2:c.248T>C; p.Phe83Ser) has not been previously described in developmental disorders. CONCLUSION: We describe for the first time the presence of somatic activating PIK3CA mutations in patients with CLAPO. We also report an update of the phenotype and natural history of the syndrome."})}
response = requests.post('http://127.0.01:8888', data=body_data)
result_dict = response.json()
print(result_dict)

127.0.0.1 - - [05/Nov/2019 16:41:05] "POST / HTTP/1.1" 200 -
[05/Nov/2019 16:41:05.504282] [Thread-1] text_hash: 3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7
[05/Nov/2019 16:41:06.330533] [Thread-1] GNormPlus 0.826 sec
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 51812)
Traceback (most recent call last):
  File "/usr/lib/python3.6/shutil.py", line 550, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/home/ubuntu/bern/GNormPlusJava/output/3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7.PubTator' -> '/home/ubuntu/bern/tmVarJava/input/3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7.PubTator'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.6/socketserver.py", line 654, in process_request_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python3.6/socketserver.py", line 364, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python3.6/socketserver.py", line 724, in __init__
    self.handle()
  File "/usr/lib/python3.6/http/server.py", line 418, in handle
    self.handle_one_request()
  File "/usr/lib/python3.6/http/server.py", line 406, 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 420, in tag_entities
    shutil.move(output_gnormplus, input_tmvar2)
  File "/usr/lib/python3.6/shutil.py", line 564, in move
    copy_function(src, real_dst)
  File "/usr/lib/python3.6/shutil.py", line 263, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3.6/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/home/ubuntu/bern/GNormPlusJava/output/3da0b63ecd8efcc2a76bbe02df6fc42b9003c94c0662a9223396c2f7.PubTator'