Merge branch 'master' of https://github.com/chen42/atpub

8 files changed, 11 insertions, 44 deletions

diff --git a/requirements.md b/requirements.md
index a791b8c..80574c7 100644
--- a/requirements.md
+++ b/requirements.md
@@ -8,14 +8,10 @@
     * Click==7.0
     * itsdangerous==1.1.0
     * Jinja2==2.10.3
-      * MarkupSafe
+      * MarkupSafe==1.0
     * Werkzeug==1.0.0
   * SQLAlchemy==1.3.12
 
-* nltk==3.4.5
-  * six==1.14.0
-
-
 * Keras==2.3.1
   * h5py==2.10.0
     * numpy==1.18.1
@@ -34,8 +30,10 @@
     * numpy==1.18.1
   * six==1.14.0
 
+* nltk==3.4.5
+  * six==1.14.0
 
-* tensorflow==2.1.0
+* tensorflow==1.14.0
   * absl-py==0.9.0
     * six==1.14.0
   * astor==0.8.1
@@ -53,41 +51,13 @@
     * numpy==1.18.1
     * six==1.14.0
   * numpy==1.18.1
-  * opt-einsum==3.2.0
-    * numpy==1.18.1
   * protobuf==3.11.3
     * setuptools==45.2.0
     * six==1.14.0
-  * scipy==1.4.1
-    * numpy==1.18.1
   * six==1.14.0
-  * tensorboard==2.1.1
+  * tensorboard==1.14.0
     * absl-py==0.9.0
       * six==1.14.0
-    * google-auth==1.13.1
-      * cachetools==4.1.0
-      * pyasn1-modules==0.2.8
-        * pyasn1==0.4.8
-      * rsa==4.0
-        * pyasn1==0.4.8
-      * setuptools==45.2.0
-      * six==1.14.0
-    * google-auth-oauthlib==0.4.1
-      * google-auth==1.13.1
-        * cachetools==4.1.0
-        * pyasn1-modules==0.2.8
-          * pyasn1==0.4.8
-        * rsa==4.0
-          * pyasn1==0.4.8
-        * setuptools==45.2.0
-        * six==1.14.0
-      * requests-oauthlib==1.3.0
-        * oauthlib==3.1.0
-        * requests==2.22.0
-          * certifi==2019.11.28
-          * chardet==3.0.4
-          * idna==2.8
-          * urllib3==1.25.8
     * grpcio==1.27.2
       * six==1.14.0
     * Markdown==3.2.1
@@ -96,18 +66,14 @@
     * protobuf==3.11.3
       * setuptools==45.2.0
       * six==1.14.0
-    * requests==2.22.0
-      * certifi==2019.11.28
-      * chardet==3.0.4
-      * idna==2.8
-      * urllib3==1.25.8
     * setuptools==45.2.0
     * six==1.14.0
     * Werkzeug==1.0.0
     * wheel==0.34.2
-  * tensorflow-estimator==2.1.0
+  * tensorflow-estimator==1.14.0
   * termcolor==1.1.0
   * wheel==0.34.2
   * wrapt==1.11.2
 
 * python==3.6.9
+
diff --git a/server.py b/server.py
index c61ca5a..1ac44f7 100755
--- a/server.py
+++ b/server.py
@@ -629,12 +629,13 @@ def sentences():
                 if(pmid+cat0 not in pmid_list):
                     pmid_list.append(pmid+cat0)
                 if(cat0=='stress'):
-                    out_pred = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"                    
                     out4 = predict_sent(text)
                     if(out4 == 'pos'):
-                        out_pos += out_pred
+                        out_pred_pos = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"                    
+                        out_pos += out_pred_pos
                     else:
-                        out_neg += out_pred
+                        out_pred_neg = "<li>"+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"                    
+                        out_neg += out_pred_neg
     out1="<h3>"+gene0 + " and " + cat0  + "</h3>\n"
     if len(pmid_list)>1:
         out2 = str(num_abstract) + ' sentences in ' + str(len(pmid_list)) + ' studies' + "<br><br>"
diff --git a/process_gwas.py b/utility/process_gwas.py
index eba59c0..eba59c0 100644
--- a/process_gwas.py
+++ b/utility/process_gwas.py
diff --git a/topGene_step0_extract_gene_alias_from_gene_info.sh b/utility/topGene_step0_extract_gene_alias_from_gene_info.sh
index 4d3118b..4d3118b 100755
--- a/topGene_step0_extract_gene_alias_from_gene_info.sh
+++ b/utility/topGene_step0_extract_gene_alias_from_gene_info.sh
diff --git a/topGene_step1_cnt_abstracts.py b/utility/topGene_step1_cnt_abstracts.py
index 420c9cf..420c9cf 100755
--- a/topGene_step1_cnt_abstracts.py
+++ b/utility/topGene_step1_cnt_abstracts.py
diff --git a/topGene_step2_cnt_sentences.py b/utility/topGene_step2_cnt_sentences.py
index b05aa7a..b05aa7a 100755
--- a/topGene_step2_cnt_sentences.py
+++ b/utility/topGene_step2_cnt_sentences.py
diff --git a/topGene_step3_generate_html.py b/utility/topGene_step3_generate_html.py
index 036325b..036325b 100755
--- a/topGene_step3_generate_html.py
+++ b/utility/topGene_step3_generate_html.py
diff --git a/topGene_step4_get_pmids_for_all_top_genes.py b/utility/topGene_step4_get_pmids_for_all_top_genes.py
index adf527c..adf527c 100755
--- a/topGene_step4_get_pmids_for_all_top_genes.py
+++ b/utility/topGene_step4_get_pmids_for_all_top_genes.py