import mods for reorg

lifemapper · Nov 18, 2021 · 1334ed9 · 1334ed9
1 parent 30e51cb
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diff --git a/docs/debugging.md b/docs/debugging.md
@@ -15,9 +15,15 @@
 * Set up python virtual environment for the project
 * Connect IDE to venv python interpreter
 * Run flask at command prompt
+* Assuming that the project directory is 
 
 ```zsh
+export PROJDIR=~/git/lmtrex
+cd $PROJDIR/lmtrex/flask_app/broker/
+
+export PYTHONPATH=$PROJECT_DIR
 export FLASK_ENV=development
+export FLASK_APP=routes
 flask run
 ```
 

diff --git a/lmtrex/flask_app/broker/resolve.py b/lmtrex/flask_app/broker/resolve.py
@@ -1,7 +1,7 @@
 from http import HTTPStatus
 from werkzeug.exceptions import (BadRequest, InternalServerError)
 
-from lmtrex.common.lmconstants import (APIService, ServiceProvider)
+from lmtrex.common.lmconstants import (APIService)
 from lmtrex.common.s2n_type import (S2nKey, S2nOutput, S2nSchema, print_s2n_output)
 from lmtrex.flask_app.broker.base import _S2nService
 from lmtrex.tools.provider.specify_resolver import SpecifyResolverAPI

diff --git a/lmtrex/tools/misc/dwca.py b/lmtrex/tools/misc/dwca.py
@@ -6,9 +6,9 @@
 from lmtrex.common.lmconstants import (
     SPECIFY_ARK_PREFIX, DWCA, ENCODING, TEST_SPECIFY7_SERVER, TST_VALUES,
     SPECIFY7_RECORD_ENDPOINT, SPECIFY7_SERVER_KEY, SPCOCO_FIELDS)
-from lmtrex.fileop.logtools import (LMLog, log_info, log_warn, log_error)
-from lmtrex.fileop.csvtools import (get_csv_dict_reader, get_csv_dict_writer)
-from lmtrex.fileop.ready_file import ready_filename, delete_file
+from lmtrex.tools.fileop.logtools import (LMLog, log_info, log_warn, log_error)
+from lmtrex.tools.fileop.csvtools import (get_csv_dict_reader, get_csv_dict_writer)
+from lmtrex.tools.fileop.ready_file import ready_filename, delete_file
 from lmtrex.tools.provider.api import APIQuery
 import lmtrex.tools.misc.solr as SpSolr
 from lmtrex.tools.s2n.utils import is_valid_uuid

diff --git a/lmtrex/tools/misc/lm_xml.py b/lmtrex/tools/misc/lm_xml.py
@@ -2,7 +2,7 @@
 
 Note: Mainly wraps elementTree functionality to fit Lifemapper needs
 """
-from lmtrex.tools.attribute_object import LmAttList, LmAttObj
+from lmtrex.tools.misc.attribute_object import LmAttList, LmAttObj
 
 from types import (BuiltinFunctionType, BuiltinMethodType, FunctionType,
                    LambdaType, MethodType)

diff --git a/lmtrex/tools/provider/api.py b/lmtrex/tools/provider/api.py
@@ -6,8 +6,8 @@
 
 from lmtrex.common.lmconstants import (URL_ESCAPES, ENCODING)
 from lmtrex.common.s2n_type import S2nKey, S2nOutput
-from lmtrex.fileop.logtools import (log_warn)
-from lmtrex.tools.lm_xml import fromstring, deserialize
+from lmtrex.tools.fileop.logtools import (log_warn)
+from lmtrex.tools.misc.lm_xml import fromstring, deserialize
 from lmtrex.tools.s2n.utils import add_errinfo, combine_errinfo, get_traceback
 
 import lmtrex.tools.s2n.utils as lmutil

diff --git a/lmtrex/tools/provider/gbif.py b/lmtrex/tools/provider/gbif.py
@@ -8,7 +8,7 @@
 from lmtrex.common.lmconstants import (
     APIService, GBIF, ServiceProvider, URL_ESCAPES, ENCODING)
 from lmtrex.common.s2n_type import S2nEndpoint, S2nKey, S2nOutput, S2nSchema
-from lmtrex.fileop.logtools import (log_info, log_error)
+from lmtrex.tools.fileop.logtools import (log_info, log_error)
 
 
 from lmtrex.tools.provider.api import APIQuery

diff --git a/lmtrex/tools/provider/idigbio.py b/lmtrex/tools/provider/idigbio.py
@@ -6,8 +6,8 @@
 from lmtrex.common.lmconstants import (
     GBIF_MISSING_KEY, Idigbio, ServiceProvider, ENCODING, DATA_DUMP_DELIMITER)
 from lmtrex.common.s2n_type import S2nEndpoint, S2nKey, S2nSchema
-from lmtrex.fileop.logtools import (log_info)
-from lmtrex.fileop.ready_file import ready_filename
+from lmtrex.tools.fileop.logtools import (log_info)
+from lmtrex.tools.fileop.ready_file import ready_filename
 
 from lmtrex.tools.provider.api import APIQuery
 from lmtrex.tools.s2n.utils import add_errinfo

diff --git a/lmtrex/tools/provider/itis.py b/lmtrex/tools/provider/itis.py
@@ -5,7 +5,7 @@
 from lmtrex.common.lmconstants import (
     ITIS, ServiceProvider, URL_ESCAPES, TST_VALUES)
 from lmtrex.common.s2n_type import S2nEndpoint, S2nOutput, S2nSchema
-from lmtrex.fileop.logtools import log_info
+from lmtrex.tools.fileop.logtools import log_info
 from lmtrex.tools.provider.api import APIQuery
 from lmtrex.tools.s2n.utils import get_traceback, add_errinfo
 

diff --git a/lmtrex/tools/provider/mopho.py b/lmtrex/tools/provider/mopho.py
@@ -2,7 +2,7 @@
 
 from lmtrex.common.lmconstants import (MorphoSource, ServiceProvider, TST_VALUES)
 from lmtrex.common.s2n_type import S2nEndpoint, S2nKey, S2nSchema
-from lmtrex.fileop.logtools import (log_info)
+from lmtrex.tools.fileop.logtools import (log_info)
 from lmtrex.tools.provider.api import APIQuery
 from lmtrex.tools.s2n.utils import add_errinfo, get_traceback
 

diff --git a/tests/test_specify_resolver/test_dwca.py b/tests/test_specify_resolver/test_dwca.py
@@ -2,7 +2,7 @@
 import shutil
 import time
 
-from lmtrex.tools.dwca import (
+from lmtrex.tools.misc.dwca import (
     assemble_download_filename, DwCArchive, get_dwca_urls, download_dwca)
 from lmtrex.tools.s2n.utils import is_valid_uuid
 from lmtrex.common.lmconstants import (DWCA, TST_VALUES)